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Mozzarelli AM, Simanshu DK, Castel P. Functional and structural insights into RAS effector proteins. Mol Cell 2024; 84:2807-2821. [PMID: 39025071 PMCID: PMC11316660 DOI: 10.1016/j.molcel.2024.06.027] [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: 03/08/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
RAS proteins are conserved guanosine triphosphate (GTP) hydrolases (GTPases) that act as molecular binary switches and play vital roles in numerous cellular processes. Upon GTP binding, RAS GTPases adopt an active conformation and interact with specific proteins termed RAS effectors that contain a conserved ubiquitin-like domain, thereby facilitating downstream signaling. Over 50 effector proteins have been identified in the human proteome, and many have been studied as potential mediators of RAS-dependent signaling pathways. Biochemical and structural analyses have provided mechanistic insights into these effectors, and studies using model organisms have complemented our understanding of their role in physiology and disease. Yet, many critical aspects regarding the dynamics and biological function of RAS-effector complexes remain to be elucidated. In this review, we discuss the mechanisms and functions of known RAS effector proteins, provide structural perspectives on RAS-effector interactions, evaluate their significance in RAS-mediated signaling, and explore their potential as therapeutic targets.
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Affiliation(s)
- Alessandro M Mozzarelli
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter NYU Cancer Center, NYU Langone Health, New York, NY, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Laura and Isaac Perlmutter NYU Cancer Center, NYU Langone Health, New York, NY, USA.
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2
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Klomp JE, Diehl JN, Klomp JA, Edwards AC, Yang R, Morales AJ, Taylor KE, Drizyte-Miller K, Bryant KL, Schaefer A, Johnson JL, Huntsman EM, Yaron TM, Pierobon M, Baldelli E, Prevatte AW, Barker NK, Herring LE, Petricoin EF, Graves LM, Cantley LC, Cox AD, Der CJ, Stalnecker CA. Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer. Science 2024; 384:eadk0850. [PMID: 38843329 PMCID: PMC11301400 DOI: 10.1126/science.adk0850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 04/17/2024] [Indexed: 06/16/2024]
Abstract
To delineate the mechanisms by which the ERK1 and ERK2 mitogen-activated protein kinases support mutant KRAS-driven cancer growth, we determined the ERK-dependent phosphoproteome in KRAS-mutant pancreatic cancer. We determined that ERK1 and ERK2 share near-identical signaling and transforming outputs and that the KRAS-regulated phosphoproteome is driven nearly completely by ERK. We identified 4666 ERK-dependent phosphosites on 2123 proteins, of which 79 and 66%, respectively, were not previously associated with ERK, substantially expanding the depth and breadth of ERK-dependent phosphorylation events and revealing a considerably more complex function for ERK in cancer. We established that ERK controls a highly dynamic and complex phosphoproteome that converges on cyclin-dependent kinase regulation and RAS homolog guanosine triphosphatase function (RHO GTPase). Our findings establish the most comprehensive molecular portrait and mechanisms by which ERK drives KRAS-dependent pancreatic cancer growth.
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Affiliation(s)
- Jennifer E. Klomp
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey A. Klomp
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - A. Cole Edwards
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Runying Yang
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexis J. Morales
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Khalilah E. Taylor
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristina Drizyte-Miller
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kirsten L. Bryant
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jared L. Johnson
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emily M. Huntsman
- Meyer Cancer Center, Weill Cornell Medicine; New York, NY 10065, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tomer M. Yaron
- Meyer Cancer Center, Weill Cornell Medicine; New York, NY 10065, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Elisa Baldelli
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
| | - Alex W. Prevatte
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie K. Barker
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura E. Herring
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Lee M. Graves
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lewis C. Cantley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Adrienne D. Cox
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Channing J. Der
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Clint A. Stalnecker
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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3
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Liu NF, Enomoto M, Marshall CB, Ikura M. Reconstitution and characterization of BRAF in complex with 14-3-3 and KRAS4B on nanodiscs. Protein Sci 2024; 33:e5016. [PMID: 38747381 PMCID: PMC11094772 DOI: 10.1002/pro.5016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/17/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
RAF kinases are key components of the RAS-MAPK signaling pathway, which drives cell growth and is frequently overactivated in cancer. Upstream signaling activates the small GTPase RAS, which recruits RAF to the cell membrane, driving a transition of the latter from an auto-inhibited monomeric conformation to an active dimer. Despite recent progress, mechanistic details underlying RAF activation remain unclear, particularly the role of RAS and the membrane in mediating this conformational rearrangement of RAF together with 14-3-3 to permit RAF kinase domain dimerization. Here, we reconstituted an active complex of dimeric BRAF, a 14-3-3 dimer and two KRAS4B on a nanodisc bilayer and verified that its assembly is GTP-dependent. Biolayer interferometry (BLI) was used to compare the binding affinities of monomeric versus dimeric full-length BRAF:14-3-3 complexes for KRAS4B-conjugated nanodiscs (RAS-ND) and to investigate the effects of membrane lipid composition and spatial density of KRAS4B on binding. 1,2-Dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) and higher KRAS4B density enhanced the interaction of BRAF:14-3-3 with RAS-ND to different degrees depending on BRAF oligomeric state. We utilized our reconstituted system to dissect the effects of KRAS4B and the membrane on the kinase activity of monomeric and dimeric BRAF:14-3-3 complexes, finding that KRAS4B or nanodiscs alone were insufficient to stimulate activity, whereas RAS-ND increased activity of both states of BRAF. The reconstituted assembly of full-length BRAF with 14-3-3 and KRAS on a cell-free, defined lipid bilayer offers a more holistic biophysical perspective to probe regulation of this multimeric signaling complex at the membrane surface.
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Affiliation(s)
- Ningdi F. Liu
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
| | - Masahiro Enomoto
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
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4
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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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5
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Martins F, Machado AL, Ribeiro A, Oliveira SM, Carvalho J, Matthiesen R, Backman V, Velho S. KRAS silencing alters chromatin physical organization and transcriptional activity in colorectal cancer cells. RESEARCH SQUARE 2024:rs.3.rs-3752760. [PMID: 38410476 PMCID: PMC10896403 DOI: 10.21203/rs.3.rs-3752760/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Clinical data revealed that KRAS mutant tumors, while initially sensitive to treatment, rapidly bypass KRAS dependence to acquire a drug-tolerant phenotype. However, the mechanisms underlying the transition from a drug-sensitive to a drug-tolerant state still elude us. Here, we show that global chromatin reorganization is a recurrent and specific feature of KRAS-dependent cells that tolerated KRAS silencing. We show that KRAS-dependent cells undergo G0/G1 cell cycle arrest after KRAS silencing, presenting a transcriptomic signature of quiescence. Proteomic analysis showed upregulated chromatin-associated proteins and transcription-associated biological processes. Accordingly, these cells shifted euchromatin/heterochromatin states, gained topologically associating domains, and altered the nanoscale physical organization of chromatin, more precisely by downregulating chromatin packing domains, a feature associated with the induction of quiescence. In addition, they also accumulated transcriptional alterations over time leading to a diversification of biological processes, linking chromatin alterations to transcriptional performance. Overall, our observations pinpoint a novel molecular mechanism of tolerance to KRAS oncogenic loss driven not by specific gene alterations but by global reorganization of genomic information, in which cells transition chromatin domain structure towards a more quiescent state and gain transcriptional reprogramming capacity.
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Affiliation(s)
| | | | | | | | | | | | | | - Sérgia Velho
- i3S - Institute for Research and Innovation in Health
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6
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Nussinov R, Jang H. Direct K-Ras Inhibitors to Treat Cancers: Progress, New Insights, and Approaches to Treat Resistance. Annu Rev Pharmacol Toxicol 2024; 64:231-253. [PMID: 37524384 DOI: 10.1146/annurev-pharmtox-022823-113946] [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: 08/02/2023]
Abstract
Here we discuss approaches to K-Ras inhibition and drug resistance scenarios. A breakthrough offered a covalent drug against K-RasG12C. Subsequent innovations harnessed same-allele drug combinations, as well as cotargeting K-RasG12C with a companion drug to upstream regulators or downstream kinases. However, primary, adaptive, and acquired resistance inevitably emerge. The preexisting mutation load can explain how even exceedingly rare mutations with unobservable effects can promote drug resistance, seeding growth of insensitive cell clones, and proliferation. Statistics confirm the expectation that most resistance-related mutations are in cis, pointing to the high probability of cooperative, same-allele effects. In addition to targeted Ras inhibitors and drug combinations, bifunctional molecules and innovative tri-complex inhibitors to target Ras mutants are also under development. Since the identities and potential contributions of preexisting and evolving mutations are unknown, selecting a pharmacologic combination is taxing. Collectively, our broad review outlines considerations and provides new insights into pharmacology and resistance.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland, USA;
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland, USA;
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7
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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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8
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Tariq M, Ikeya T, Togashi N, Fairall L, Kamei S, Mayooramurugan S, Abbott LR, Hasan A, Bueno-Alejo C, Sukegawa S, Romartinez-Alonso B, Muro Campillo MA, Hudson AJ, Ito Y, Schwabe JW, Dominguez C, Tanaka K. Structural insights into the complex of oncogenic KRas4B G12V and Rgl2, a RalA/B activator. Life Sci Alliance 2024; 7:e202302080. [PMID: 37833074 PMCID: PMC10576006 DOI: 10.26508/lsa.202302080] [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: 04/06/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
About a quarter of total human cancers carry mutations in Ras isoforms. Accumulating evidence suggests that small GTPases, RalA, and RalB, and their activators, Ral guanine nucleotide exchange factors (RalGEFs), play an essential role in oncogenic Ras-induced signalling. We studied the interaction between human KRas4B and the Ras association (RA) domain of Rgl2 (Rgl2RA), one of the RA-containing RalGEFs. We show that the G12V oncogenic KRas4B mutation changes the interaction kinetics with Rgl2RA The crystal structure of the KRas4BG12V: Rgl2RA complex shows a 2:2 heterotetramer where the switch I and switch II regions of each KRasG12V interact with both Rgl2RA molecules. This structural arrangement is highly similar to the HRasE31K:RALGDSRA crystal structure and is distinct from the well-characterised Ras:Raf complex. Interestingly, the G12V mutation was found at the dimer interface of KRas4BG12V with its partner. Our study reveals a potentially distinct mode of Ras:effector complex formation by RalGEFs and offers a possible mechanistic explanation for how the oncogenic KRas4BG12V hyperactivates the RalA/B pathway.
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Affiliation(s)
- Mishal Tariq
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Teppei Ikeya
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Naoyuki Togashi
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Louise Fairall
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Shun Kamei
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Sannojah Mayooramurugan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Lauren R Abbott
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Anab Hasan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Carlos Bueno-Alejo
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Sakura Sukegawa
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Beatriz Romartinez-Alonso
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Miguel Angel Muro Campillo
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Andrew J Hudson
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Department of Chemistry, University of Leicester, Leicester, UK
| | - Yutaka Ito
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - John Wr Schwabe
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Cyril Dominguez
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Kayoko Tanaka
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
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9
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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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10
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Smith MJ. Defining bone fide effectors of RAS GTPases. Bioessays 2023; 45:e2300088. [PMID: 37401638 DOI: 10.1002/bies.202300088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
RAS GTPases play essential roles in normal development and are direct drivers of human cancers. Three decades of study have failed to wholly characterize pathways stimulated by activated RAS, driven by engagement with 'effector' proteins that have RAS binding domains (RBDs). Bone fide effectors must bind directly to RAS GTPases in a nucleotide-dependent manner, and this interaction must impart a clear change in effector activity. Despite this, for most proteins currently deemed effectors there is little mechanistic understanding of how binding to the GTPase alters protein function. There has also been limited effort to comprehensively resolve the specificity of effector binding to the full array of RAS superfamily GTPase proteins. This review will summarize what is known about RAS-driven activation for an array of potential effector proteins, focusing on structural and mechanistic effects and highlighting how little is still known regarding this key paradigm of cellular signal transduction.
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Affiliation(s)
- Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
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11
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Tomazini A, Shifman JM. Targeting Ras with protein engineering. Oncotarget 2023; 14:672-687. [PMID: 37395750 DOI: 10.18632/oncotarget.28469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Ras proteins are small GTPases that regulate cell growth and division. Mutations in Ras genes are associated with many types of cancer, making them attractive targets for cancer therapy. Despite extensive efforts, targeting Ras proteins with small molecules has been extremely challenging due to Ras's mostly flat surface and lack of small molecule-binding cavities. These challenges were recently overcome by the development of the first covalent small-molecule anti-Ras drug, sotorasib, highlighting the efficacy of Ras inhibition as a therapeutic strategy. However, this drug exclusively inhibits the Ras G12C mutant, which is not a prevalent mutation in most cancer types. Unlike the G12C variant, other Ras oncogenic mutants lack reactive cysteines, rendering them unsuitable for targeting via the same strategy. Protein engineering has emerged as a promising method to target Ras, as engineered proteins have the ability to recognize various surfaces with high affinity and specificity. Over the past few years, scientists have engineered antibodies, natural Ras effectors, and novel binding domains to bind to Ras and counteract its carcinogenic activities via a variety of strategies. These include inhibiting Ras-effector interactions, disrupting Ras dimerization, interrupting Ras nucleotide exchange, stimulating Ras interaction with tumor suppressor genes, and promoting Ras degradation. In parallel, significant advancements have been made in intracellular protein delivery, enabling the delivery of the engineered anti-Ras agents into the cellular cytoplasm. These advances offer a promising path for targeting Ras proteins and other challenging drug targets, opening up new opportunities for drug discovery and development.
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Affiliation(s)
- Atilio Tomazini
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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12
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Liu C, Ye D, Yang H, Chen X, Su Z, Li X, Ding M, Liu Y. RAS-targeted cancer therapy: Advances in drugging specific mutations. MedComm (Beijing) 2023; 4:e285. [PMID: 37250144 PMCID: PMC10225044 DOI: 10.1002/mco2.285] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/06/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
Rat sarcoma (RAS), as a frequently mutated oncogene, has been studied as an attractive target for treating RAS-driven cancers for over four decades. However, it is until the recent success of kirsten-RAS (KRAS)G12C inhibitor that RAS gets rid of the title "undruggable". It is worth noting that the therapeutic effect of KRASG12C inhibitors on different RAS allelic mutations or even different cancers with KRASG12C varies significantly. Thus, deep understanding of the characteristics of each allelic RAS mutation will be a prerequisite for developing new RAS inhibitors. In this review, the structural and biochemical features of different RAS mutations are summarized and compared. Besides, the pathological characteristics and treatment responses of different cancers carrying RAS mutations are listed based on clinical reports. In addition, the development of RAS inhibitors, either direct or indirect, that target the downstream components in RAS pathway is summarized as well. Hopefully, this review will broaden our knowledge on RAS-targeting strategies and trigger more intensive studies on exploiting new RAS allele-specific inhibitors.
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Affiliation(s)
- Cen Liu
- Beijing University of Chinese MedicineBeijingChina
| | - Danyang Ye
- Beijing University of Chinese MedicineBeijingChina
| | - Hongliu Yang
- Beijing University of Chinese MedicineBeijingChina
| | - Xu Chen
- Beijing University of Chinese MedicineBeijingChina
| | - Zhijun Su
- Beijing University of Chinese MedicineBeijingChina
| | - Xia Li
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Mei Ding
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yonggang Liu
- Beijing University of Chinese MedicineBeijingChina
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13
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Nussinov R, Tsai CJ, Jang H. A New View of Activating Mutations in Cancer. Cancer Res 2022; 82:4114-4123. [PMID: 36069825 PMCID: PMC9664134 DOI: 10.1158/0008-5472.can-22-2125] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/16/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022]
Abstract
A vast effort has been invested in the identification of driver mutations of cancer. However, recent studies and observations call into question whether the activating mutations or the signal strength are the major determinant of tumor development. The data argue that signal strength determines cell fate, not the mutation that initiated it. In addition to activating mutations, factors that can impact signaling strength include (i) homeostatic mechanisms that can block or enhance the signal, (ii) the types and locations of additional mutations, and (iii) the expression levels of specific isoforms of genes and regulators of proteins in the pathway. Because signal levels are largely decided by chromatin structure, they vary across cell types, states, and time windows. A strong activating mutation can be restricted by low expression, whereas a weaker mutation can be strengthened by high expression. Strong signals can be associated with cell proliferation, but too strong a signal may result in oncogene-induced senescence. Beyond cancer, moderate signal strength in embryonic neural cells may be associated with neurodevelopmental disorders, and moderate signals in aging may be associated with neurodegenerative diseases, like Alzheimer's disease. The challenge for improving patient outcomes therefore lies in determining signaling thresholds and predicting signal strength.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, NCI, Frederick, Maryland
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, NCI, Frederick, Maryland
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, NCI, Frederick, Maryland
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14
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The current state of the art and future trends in RAS-targeted cancer therapies. Nat Rev Clin Oncol 2022; 19:637-655. [PMID: 36028717 PMCID: PMC9412785 DOI: 10.1038/s41571-022-00671-9] [Citation(s) in RCA: 167] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2022] [Indexed: 12/18/2022]
Abstract
Despite being the most frequently altered oncogenic protein in solid tumours, KRAS has historically been considered ‘undruggable’ owing to a lack of pharmacologically targetable pockets within the mutant isoforms. However, improvements in drug design have culminated in the development of inhibitors that are selective for mutant KRAS in its active or inactive state. Some of these inhibitors have proven efficacy in patients with KRASG12C-mutant cancers and have become practice changing. The excitement associated with these advances has been tempered by drug resistance, which limits the depth and/or duration of responses to these agents. Improvements in our understanding of RAS signalling in cancer cells and in the tumour microenvironment suggest the potential for several novel combination therapies, which are now being explored in clinical trials. Herein, we provide an overview of the RAS pathway and review the development and current status of therapeutic strategies for targeting oncogenic RAS, as well as their potential to improve outcomes in patients with RAS-mutant malignancies. We then discuss challenges presented by resistance mechanisms and strategies by which they could potentially be overcome. The RAS oncogenes are among the most common drivers of tumour development and progression but have historically been considered undruggable. The development of direct KRAS inhibitors has changed this paradigm, although currently clinical use of these novel therapeutics is limited to a select subset of patients, and intrinsic or acquired resistance presents an inevitable challenge to cure. Herein, the authors provide an overview of the RAS pathway in cancer and review the ongoing efforts to develop effective therapeutic strategies for RAS-mutant cancers. They also discuss the current understanding of mechanisms of resistance to direct KRAS inhibitors and strategies by which they might be overcome. Owing to intrinsic and extrinsic factors, KRAS and other RAS isoforms have until recently been impervious to targeting with small-molecule inhibitors. Inhibitors of the KRASG12C variant constitute a potential breakthrough in the treatment of many cancer types, particularly non-small-cell lung cancer, for which such an agent has been approved by the FDA. Several forms of resistance to KRAS inhibitors have been defined, including primary, adaptive and acquired resistance; these resistance mechanisms are being targeted in studies that combine KRAS inhibitors with inhibitors of horizontal or vertical signalling pathways. Mutant KRAS has important effects on the tumour microenvironment, including the immunological milieu; these effects must be considered to fully understand resistance to KRAS inhibitors and when designing novel treatment strategies.
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15
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Huynh MV, Hobbs GA, Schaefer A, Pierobon M, Carey LM, Diehl JN, DeLiberty JM, Thurman RD, Cooke AR, Goodwin CM, Cook JH, Lin L, Waters AM, Rashid NU, Petricoin EF, Campbell SL, Haigis KM, Simeone DM, Lyssiotis CA, Cox AD, Der CJ. Functional and biological heterogeneity of KRAS Q61 mutations. Sci Signal 2022; 15:eabn2694. [PMID: 35944066 PMCID: PMC9534304 DOI: 10.1126/scisignal.abn2694] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Missense mutations at the three hotspots in the guanosine triphosphatase (GTPase) RAS-Gly12, Gly13, and Gln61 (commonly known as G12, G13, and Q61, respectively)-occur differentially among the three RAS isoforms. Q61 mutations in KRAS are infrequent and differ markedly in occurrence. Q61H is the predominant mutant (at 57%), followed by Q61R/L/K (collectively 40%), and Q61P and Q61E are the rarest (2 and 1%, respectively). Probability analysis suggested that mutational susceptibility to different DNA base changes cannot account for this distribution. Therefore, we investigated whether these frequencies might be explained by differences in the biochemical, structural, and biological properties of KRASQ61 mutants. Expression of KRASQ61 mutants in NIH 3T3 fibroblasts and RIE-1 epithelial cells caused various alterations in morphology, growth transformation, effector signaling, and metabolism. The relatively rare KRASQ61E mutant stimulated actin stress fiber formation, a phenotype distinct from that of KRASQ61H/R/L/P, which disrupted actin cytoskeletal organization. The crystal structure of KRASQ61E was unexpectedly similar to that of wild-type KRAS, a potential basis for its weak oncogenicity. KRASQ61H/L/R-mutant pancreatic ductal adenocarcinoma (PDAC) cell lines exhibited KRAS-dependent growth and, as observed with KRASG12-mutant PDAC, were susceptible to concurrent inhibition of ERK-MAPK signaling and of autophagy. Our results uncover phenotypic heterogeneity among KRASQ61 mutants and support the potential utility of therapeutic strategies that target KRASQ61 mutant-specific signaling and cellular output.
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Affiliation(s)
- Minh V. Huynh
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - G. Aaron Hobbs
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Leiah M. Carey
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan M. DeLiberty
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D. Thurman
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adelaide R. Cooke
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua H. Cook
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical
School, Boston, MA 02115, USA
| | - Lin Lin
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Andrew M. Waters
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Naim U. Rashid
- Department of Biostatistics, University of North Carolina
at Chapel Hill, NC 27955, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Sharon L. Campbell
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin M. Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
- Harvard Digestive Disease Center, Harvard Medical School,
Boston, MA 02115, USA
| | - Diane M. Simeone
- Perlmutter Cancer Center, New York University, New York,
NY10016, USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of
Gastroenterology, University of Michigan, Ann Arbor, MI 48198, USA
- University of Michigan Comprehensive Cancer Center, Ann
Arbor, MI 48109, USA
| | - Adrienne D. Cox
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North
Carolina at Chapel Hill, Chapel Hill, NC 2799, USA
| | - Channing J. Der
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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16
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Dias Carvalho P, Martins F, Carvalho J, Oliveira MJ, Velho S. Mutant KRAS-Associated Proteome Is Mainly Controlled by Exogenous Factors. Cells 2022; 11:1988. [PMID: 35805073 PMCID: PMC9265670 DOI: 10.3390/cells11131988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 02/06/2023] Open
Abstract
Understanding how mutant KRAS signaling is modulated by exogenous stimuli is of utmost importance to elucidate resistance mechanisms underlying pathway inhibition failure, and to uncover novel therapeutic targets for mutant KRAS patients. Hence, aiming at perceiving KRAS-autonomous versus -non autonomous mechanisms, we studied the response of two mutant KRAS colorectal cancer cell lines (HCT116 and LS174T) upon KRAS silencing and treatment with rhTGFβ1-activated fibroblasts secretome. A proteomic analysis revealed that rhTGFβ1-activated fibroblast-secreted factors triggered cell line-specific proteome alterations and that mutant KRAS governs 43% and 38% of these alterations in HCT116 and LS174T cells, respectively. These KRAS-dependent proteins were localized and displayed molecular functions that were common to both cell lines (e.g., extracellular exosome, RNA binding functions). Moreover, 67% and 78% of the KRAS-associated proteome of HCT116 and LS174T cells, respectively, was controlled in a KRAS-non-autonomous manner, being dependent on fibroblast-secreted factors. In HCT116 cells, KRAS-non-autonomously controlled proteins were mainly involved in proteoglycans in cancer, p53, and Rap1 signaling pathways; whereas in LS174T cells, they were associated with substrate adhesion-dependent cell-spreading and involved in metabolic processes. This work highlights the context-dependency of KRAS-associated signaling and reinforces the importance of integrating the tumor microenvironment in the study of KRAS-associated effects.
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Affiliation(s)
- Patrícia Dias Carvalho
- Instituto de Investigação e Inovação em Saúde (i3S), Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.D.C.); (F.M.); (J.C.); (M.J.O.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Flávia Martins
- Instituto de Investigação e Inovação em Saúde (i3S), Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.D.C.); (F.M.); (J.C.); (M.J.O.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Joana Carvalho
- Instituto de Investigação e Inovação em Saúde (i3S), Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.D.C.); (F.M.); (J.C.); (M.J.O.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
| | - Maria José Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.D.C.); (F.M.); (J.C.); (M.J.O.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Institute of Biomedical Engineering (INEB), University of Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - Sérgia Velho
- Instituto de Investigação e Inovação em Saúde (i3S), Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.D.C.); (F.M.); (J.C.); (M.J.O.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
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17
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Johnson C, Burkhart DL, Haigis KM. Classification of KRAS-Activating Mutations and the Implications for Therapeutic Intervention. Cancer Discov 2022; 12:913-923. [PMID: 35373279 PMCID: PMC8988514 DOI: 10.1158/2159-8290.cd-22-0035] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/02/2022] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
Abstract
Members of the family of RAS proto-oncogenes, discovered just over 40 years ago, were among the first cancer-initiating genes to be discovered. Of the three RAS family members, KRAS is the most frequently mutated in human cancers. Despite intensive biological and biochemical study of RAS proteins over the past four decades, we are only now starting to devise therapeutic strategies to target their oncogenic properties. Here, we highlight the distinct biochemical properties of common and rare KRAS alleles, enabling their classification into functional subtypes. We also discuss the implications of this functional classification for potential therapeutic avenues targeting mutant subtypes. SIGNIFICANCE Efforts in the recent past to inhibit KRAS oncogenicity have focused on kinases that function in downstream signal transduction cascades, although preclinical successes have not translated to patients with KRAS-mutant cancer. Recently, clinically effective covalent inhibitors of KRASG12C have been developed, establishing two principles that form a foundation for future efforts. First, KRAS is druggable. Second, each mutant form of KRAS is likely to have properties that make it uniquely druggable.
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Affiliation(s)
- Christian Johnson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Deborah L Burkhart
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
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18
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Johnson CW, Seo HS, Terrell EM, Yang MH, KleinJan F, Gebregiworgis T, Gasmi-Seabrook GMC, Geffken EA, Lakhani J, Song K, Bashyal P, Popow O, Paulo JA, Liu A, Mattos C, Marshall CB, Ikura M, Morrison DK, Dhe-Paganon S, Haigis KM. Regulation of GTPase function by autophosphorylation. Mol Cell 2022; 82:950-968.e14. [PMID: 35202574 PMCID: PMC8986090 DOI: 10.1016/j.molcel.2022.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/29/2021] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
Abstract
A unifying feature of the RAS superfamily is a conserved GTPase cycle by which these proteins transition between active and inactive states. We demonstrate that autophosphorylation of some GTPases is an intrinsic regulatory mechanism that reduces nucleotide hydrolysis and enhances nucleotide exchange, altering the on/off switch that forms the basis for their signaling functions. Using X-ray crystallography, nuclear magnetic resonance spectroscopy, binding assays, and molecular dynamics on autophosphorylated mutants of H-RAS and K-RAS, we show that phosphoryl transfer from GTP requires dynamic movement of the switch II region and that autophosphorylation promotes nucleotide exchange by opening the active site and extracting the stabilizing Mg2+. Finally, we demonstrate that autophosphorylated K-RAS exhibits altered effector interactions, including a reduced affinity for RAF proteins in mammalian cells. Thus, autophosphorylation leads to altered active site dynamics and effector interaction properties, creating a pool of GTPases that are functionally distinct from their non-phosphorylated counterparts.
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Affiliation(s)
- Christian W Johnson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Moon-Hee Yang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Ezekiel A Geffken
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jimit Lakhani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Puspalata Bashyal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Olesja Popow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, MD 21702, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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19
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Eves BJ, Gebregiworgis T, Gasmi-Seabrook GM, Kuntz DA, Privé GG, Marshall CB, Ikura M. Structures of RGL1 RAS-Association domain in complex with KRAS and the oncogenic G12V mutant. J Mol Biol 2022; 434:167527. [DOI: 10.1016/j.jmb.2022.167527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
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20
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Shen M, Qi R, Ren J, Lv D, Yang H. Characterization With KRAS Mutant Is a Critical Determinant in Immunotherapy and Other Multiple Therapies for Non-Small Cell Lung Cancer. Front Oncol 2022; 11:780655. [PMID: 35070984 PMCID: PMC8766810 DOI: 10.3389/fonc.2021.780655] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a frequent type of cancer, which is mainly characterized clinically by high aggressiveness and high mortality. KRAS oncoprotein is the most common molecular protein detected in NSCLC, accounting for 25% of all oncogenic mutations. Constitutive activation of the KRAS oncoprotein triggers an intracellular cascade in cancer cells, leading to uncontrolled cell proliferation of cancer cells and aberrant cell survival states. The results of multiple clinical trials have shown that different KRAS mutation subtypes exhibit different sensitivities to different chemotherapy regimens. Meanwhile, anti-angiogenic drugs have shown differential efficacy for different subtypes of KRAS mutated lung cancer. It was explored to find if the specificity of the KRAS mutation subtype would affect PD-L1 expression, so immunotherapy would be of potential clinical value for the treatment of some types of KRAS mutations. It was discovered that the specificity of the KRAS mutation affected PD-L1, which opened up immunotherapy as a potential clinical treatment option. After several breakthrough studies, the preliminary test data of many early clinical trials showed that it is possible to directly inhibit KRAS G12C mutation, which has been proved to be a targeted treatment that is suitable for about 10%-12% of patients with advanced NSCLC, having a significant impact on the prolongation of their survival and the improvement of their quality of life. This article reviews the latest progress of treatments for NSCLC with KRAS mutation, in order to gain insight into the biological diversity of lung cancer cells and their potential clinical implications, thereby enabling individualized treatment for patients with KRAS-mutant NSCLC.
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Affiliation(s)
- Mo Shen
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Rongbin Qi
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Respiratory Medicine, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
| | - Justin Ren
- Biological Sciences, Northwestern University, Evanston, Evanston, IL, United States
| | - Dongqing Lv
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Respiratory Medicine, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
| | - Haihua Yang
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Radiation Oncology, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
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21
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Singh A, Erijman A, Noronha A, Kumar H, Peleg Y, Yarden Y, Shifman JM. Engineered variants of the Ras effector protein RASSF5 (NORE1A) promote anticancer activities in lung adenocarcinoma. J Biol Chem 2021; 297:101353. [PMID: 34717958 PMCID: PMC8605244 DOI: 10.1016/j.jbc.2021.101353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/12/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
Within the superfamily of small GTPases, Ras appears to be the master regulator of such processes as cell cycle progression, cell division, and apoptosis. Several oncogenic Ras mutations at amino acid positions 12, 13, and 61 have been identified that lose their ability to hydrolyze GTP, giving rise to constitutive signaling and eventually development of cancer. While disruption of the Ras/effector interface is an attractive strategy for drug design to prevent this constitutive activity, inhibition of this interaction using small molecules is impractical due to the absence of a cavity to which such molecules could bind. However, proteins and especially natural Ras effectors that bind to the Ras/effector interface with high affinity could disrupt Ras/effector interactions and abolish procancer pathways initiated by Ras oncogene. Using a combination of computational design and in vitro evolution, we engineered high-affinity Ras-binding proteins starting from a natural Ras effector, RASSF5 (NORE1A), which is encoded by a tumor suppressor gene. Unlike previously reported Ras oncogene inhibitors, the proteins we designed not only inhibit Ras-regulated procancer pathways, but also stimulate anticancer pathways initiated by RASSF5. We show that upon introduction into A549 lung carcinoma cells, the engineered RASSF5 mutants decreased cell viability and mobility to a significantly greater extent than WT RASSF5. In addition, these mutant proteins induce cellular senescence by increasing acetylation and decreasing phosphorylation of p53. In conclusion, engineered RASSF5 variants provide an attractive therapeutic strategy able to oppose cancer development by means of inhibiting of procancer pathways and stimulating anticancer processes.
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Affiliation(s)
- Anamika Singh
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ariel Erijman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ashish Noronha
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Hemant Kumar
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yoav Peleg
- Life Sciences Core Facilities (LSCF) Structural Proteomics Unit (SPU), Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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22
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Fedele C, Li S, Teng KW, Foster CJR, Peng D, Ran H, Mita P, Geer MJ, Hattori T, Koide A, Wang Y, Tang KH, Leinwand J, Wang W, Diskin B, Deng J, Chen T, Dolgalev I, Ozerdem U, Miller G, Koide S, Wong KK, Neel BG. SHP2 inhibition diminishes KRASG12C cycling and promotes tumor microenvironment remodeling. J Exp Med 2021; 218:211451. [PMID: 33045063 PMCID: PMC7549316 DOI: 10.1084/jem.20201414] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 12/21/2022] Open
Abstract
KRAS is the most frequently mutated human oncogene, and KRAS inhibition has been a longtime goal. Recently, inhibitors were developed that bind KRASG12C-GDP and react with Cys-12 (G12C-Is). Using new affinity reagents to monitor KRASG12C activation and inhibitor engagement, we found that an SHP2 inhibitor (SHP2-I) increases KRAS-GDP occupancy, enhancing G12C-I efficacy. The SHP2-I abrogated RTK feedback signaling and adaptive resistance to G12C-Is in vitro, in xenografts, and in syngeneic KRASG12C-mutant pancreatic ductal adenocarcinoma (PDAC) and non-small cell lung cancer (NSCLC). SHP2-I/G12C-I combination evoked favorable but tumor site-specific changes in the immune microenvironment, decreasing myeloid suppressor cells, increasing CD8+ T cells, and sensitizing tumors to PD-1 blockade. Experiments using cells expressing inhibitor-resistant SHP2 showed that SHP2 inhibition in PDAC cells is required for PDAC regression and remodeling of the immune microenvironment but revealed direct inhibitory effects on tumor angiogenesis and vascularity. Our results demonstrate that SHP2-I/G12C-I combinations confer a substantial survival benefit in PDAC and NSCLC and identify additional potential combination strategies.
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Affiliation(s)
- Carmine Fedele
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Shuai Li
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Kai Wen Teng
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Connor J R Foster
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - David Peng
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Hao Ran
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Paolo Mita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Mitchell J Geer
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Takamitsu Hattori
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY.,Department of Medicine, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Yubao Wang
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Kwan Ho Tang
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Joshua Leinwand
- S. Arthur Localio Laboratory, Department of Surgery, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Wei Wang
- S. Arthur Localio Laboratory, Department of Surgery, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Brian Diskin
- S. Arthur Localio Laboratory, Department of Surgery, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Jiehui Deng
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Ting Chen
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Igor Dolgalev
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Ugur Ozerdem
- Department of Pathology, New York University School of Medicine, NYU Langone Health, New York, NY
| | - George Miller
- S. Arthur Localio Laboratory, Department of Surgery, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
| | - Benjamin G Neel
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY
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23
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RAS GTPase signalling to alternative effector pathways. Biochem Soc Trans 2021; 48:2241-2252. [PMID: 33125484 DOI: 10.1042/bst20200506] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023]
Abstract
RAS GTPases are fundamental regulators of development and drivers of an extraordinary number of human cancers. RAS oncoproteins constitutively signal through downstream effector proteins, triggering cancer initiation, progression and metastasis. In the absence of targeted therapeutics to mutant RAS itself, inhibitors of downstream pathways controlled by the effector kinases RAF and PI3K have become tools in the treatment of RAS-driven tumours. Unfortunately, the efficacy of this approach has been greatly minimized by the prevalence of acquired drug resistance. Decades of research have established that RAS signalling is highly complex, and in addition to RAF and PI3K these small GTPase proteins can interact with an array of alternative effectors that feature RAS binding domains. The consequence of RAS binding to these effectors remains relatively unexplored, but these pathways may provide targets for combinatorial therapeutics. We discuss here three candidate alternative effectors: RALGEFs, RASSF5 and AFDN, detailing their interaction with RAS GTPases and their biological significance. The metastatic nature of RAS-driven cancers suggests more attention should be granted to these alternate pathways, as they are highly implicated in the regulation of cell adhesion, polarity, cell size and cytoskeletal architecture.
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24
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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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25
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Ras Isoforms from Lab Benches to Lives-What Are We Missing and How Far Are We? Int J Mol Sci 2021; 22:ijms22126508. [PMID: 34204435 PMCID: PMC8233758 DOI: 10.3390/ijms22126508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/21/2022] Open
Abstract
The central protein in the oncogenic circuitry is the Ras GTPase that has been under intense scrutiny for the last four decades. From its discovery as a viral oncogene and its non-oncogenic contribution to crucial cellular functioning, an elaborate genetic, structural, and functional map of Ras is being created for its therapeutic targeting. Despite decades of research, there still exist lacunae in our understanding of Ras. The complexity of the Ras functioning is further exemplified by the fact that the three canonical Ras genes encode for four protein isoforms (H-Ras, K-Ras4A, K-Ras4B, and N-Ras). Contrary to the initial assessment that the H-, K-, and N-Ras isoforms are functionally similar, emerging data are uncovering crucial differences between them. These Ras isoforms exhibit not only cell-type and context-dependent functions but also activator and effector specificities on activation by the same receptor. Preferential localization of H-, K-, and N-Ras in different microdomains of the plasma membrane and cellular organelles like Golgi, endoplasmic reticulum, mitochondria, and endosome adds a new dimension to isoform-specific signaling and diverse functions. Herein, we review isoform-specific properties of Ras GTPase and highlight the importance of considering these towards generating effective isoform-specific therapies in the future.
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26
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Nomura TK, Heishima K, Sugito N, Sugawara R, Ueda H, Yukihiro A, Honda R. Specific inhibition of oncogenic RAS using cell-permeable RAS-binding domains. Cell Chem Biol 2021; 28:1581-1589.e6. [PMID: 33964212 DOI: 10.1016/j.chembiol.2021.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/17/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Oncogenic RAS proteins, common oncogenic drivers in many human cancers, have been refractory to conventional small-molecule and macromolecule inhibitors due to their intracellular localization and the lack of druggable pockets. Here, we present a feasible strategy for designing RAS inhibitors that involves intracellular delivery of RAS-binding domain (RBD), a nanomolar-affinity specific ligand of RAS. Screening of 51 different combinations of RBD and cell-permeable peptides has identified Pen-cRaf-v1 as a cell-permeable pan-RAS inhibitor capable of targeting both G12C and non-G12C RAS mutants. Pen-cRaf-v1 crosses the cell membrane via endocytosis, competitively inhibits RAS-effector interaction, and thereby exerts anticancer activity against several KRAS-mutant cancer cell lines. Moreover, Pen-cRaf-v1 exhibits excellent activity comparable with a leading pan-RAS inhibitor (BI-2852), as well as high target specificity in transcriptome analysis and alanine mutation analysis. These findings demonstrate that specific inhibition of oncogenic RAS, and possibly treatment of RAS-mutant cancer, is feasible by intracellular delivery of RBD.
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Affiliation(s)
- Teiko Komori Nomura
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Kazuki Heishima
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Nobuhiko Sugito
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Ryota Sugawara
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Hiroshi Ueda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Akao Yukihiro
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan.
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27
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Cook JH, Melloni GEM, Gulhan DC, Park PJ, Haigis KM. The origins and genetic interactions of KRAS mutations are allele- and tissue-specific. Nat Commun 2021; 12:1808. [PMID: 33753749 PMCID: PMC7985210 DOI: 10.1038/s41467-021-22125-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Mutational activation of KRAS promotes the initiation and progression of cancers, especially in the colorectum, pancreas, lung, and blood plasma, with varying prevalence of specific activating missense mutations. Although epidemiological studies connect specific alleles to clinical outcomes, the mechanisms underlying the distinct clinical characteristics of mutant KRAS alleles are unclear. Here, we analyze 13,492 samples from these four tumor types to examine allele- and tissue-specific genetic properties associated with oncogenic KRAS mutations. The prevalence of known mutagenic mechanisms partially explains the observed spectrum of KRAS activating mutations. However, there are substantial differences between the observed and predicted frequencies for many alleles, suggesting that biological selection underlies the tissue-specific frequencies of mutant alleles. Consistent with experimental studies that have identified distinct signaling properties associated with each mutant form of KRAS, our genetic analysis reveals that each KRAS allele is associated with a distinct tissue-specific comutation network. Moreover, we identify tissue-specific genetic dependencies associated with specific mutant KRAS alleles. Overall, this analysis demonstrates that the genetic interactions of oncogenic KRAS mutations are allele- and tissue-specific, underscoring the complexity that drives their clinical consequences.
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Affiliation(s)
- Joshua H Cook
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Giorgio E M Melloni
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
- Harvard Digestive Disease Center, Harvard Medical School, Boston, MA, USA.
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28
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Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V. Inhibition of Nonfunctional Ras. Cell Chem Biol 2021; 28:121-133. [PMID: 33440168 PMCID: PMC7897307 DOI: 10.1016/j.chembiol.2020.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Intuitively, functional states should be targeted; not nonfunctional ones. So why could drugging the inactive K-Ras4BG12Cwork-but drugging the inactive kinase will likely not? The reason is the distinct oncogenic mechanisms. Kinase driver mutations work by stabilizing the active state and/or destabilizing the inactive state. Either way, oncogenic kinases are mostly in the active state. Ras driver mutations work by quelling its deactivation mechanisms, GTP hydrolysis, and nucleotide exchange. Covalent inhibitors that bind to the inactive GDP-bound K-Ras4BG12C conformation can thus work. By contrast, in kinases, allosteric inhibitors work by altering the active-site conformation to favor orthosteric drugs. From the translational standpoint this distinction is vital: it expedites effective pharmaceutical development and extends the drug classification based on the mechanism of action. Collectively, here we postulate that drug action relates to blocking the mechanism of activation, not to whether the protein is in the active or inactive state.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
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29
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Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
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30
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Cui Y, Ma L, Schacke S, Yin JC, Hsueh YP, Jin H, Morrison H. Merlin cooperates with neurofibromin and Spred1 to suppress the Ras-Erk pathway. Hum Mol Genet 2020; 29:3793-3806. [PMID: 33331896 DOI: 10.1093/hmg/ddaa263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022] Open
Abstract
The Ras-Erk pathway is frequently overactivated in human tumors. Neurofibromatosis types 1 and 2 (NF1, NF2) are characterized by multiple tumors of Schwann cell origin. The NF1 tumor suppressor neurofibromin is a principal Ras-GAP accelerating Ras inactivation, whereas the NF2 tumor suppressor merlin is a scaffold protein coordinating multiple signaling pathways. We have previously reported that merlin interacts with Ras and p120RasGAP. Here, we show that merlin can also interact with the neurofibromin/Spred1 complex via merlin-binding sites present on both proteins. Further, merlin can directly bind to the Ras-binding domain (RBD) and the kinase domain (KiD) of Raf1. As the third component of the neurofibromin/Spred1 complex, merlin cannot increase the Ras-GAP activity; rather, it blocks Ras binding to Raf1 by functioning as a 'selective Ras barrier'. Merlin-deficient Schwann cells require the Ras-Erk pathway activity for proliferation. Accordingly, suppression of the Ras-Erk pathway likely contributes to merlin's tumor suppressor activity. Taken together, our results, and studies by others, support targeting or co-targeting of this pathway as a therapy for NF2 inactivation-related tumors.
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Affiliation(s)
- Yan Cui
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Lin Ma
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.,College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Stephan Schacke
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Jiani C Yin
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou 310016, China
| | - Helen Morrison
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Germany
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31
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Marshall CB, KleinJan F, Gebregiworgis T, Lee KY, Fang Z, Eves BJ, Liu NF, Gasmi-Seabrook GMC, Enomoto M, Ikura M. NMR in integrated biophysical drug discovery for RAS: past, present, and future. JOURNAL OF BIOMOLECULAR NMR 2020; 74:531-554. [PMID: 32804298 DOI: 10.1007/s10858-020-00338-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Mutations in RAS oncogenes occur in ~ 30% of human cancers, with KRAS being the most frequently altered isoform. RAS proteins comprise a conserved GTPase domain and a C-terminal lipid-modified tail that is unique to each isoform. The GTPase domain is a 'switch' that regulates multiple signaling cascades that drive cell growth and proliferation when activated by binding GTP, and the signal is terminated by GTP hydrolysis. Oncogenic RAS mutations disrupt the GTPase cycle, leading to accumulation of the activated GTP-bound state and promoting proliferation. RAS is a key target in oncology, however it lacks classic druggable pockets and has been extremely challenging to target. RAS signaling has thus been targeted indirectly, by harnessing key downstream effectors as well as upstream regulators, or disrupting the proper membrane localization required for signaling, by inhibiting either lipid modification or 'carrier' proteins. As a small (20 kDa) protein with multiple conformers in dynamic equilibrium, RAS is an excellent candidate for NMR-driven characterization and screening for direct inhibitors. Several molecules have been discovered that bind RAS and stabilize shallow pockets through conformational selection, and recent compounds have achieved substantial improvements in affinity. NMR-derived insight into targeting the RAS-membrane interface has revealed a new strategy to enhance the potency of small molecules, while another approach has been development of peptidyl inhibitors that bind through large interfaces rather than deep pockets. Remarkable progress has been made with mutation-specific covalent inhibitors that target the thiol of a G12C mutant, and these are now in clinical trials. Here we review the history of RAS inhibitor development and highlight the utility of NMR and integrated biophysical approaches in RAS drug discovery.
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Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Zhenhao Fang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Ben J Eves
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ningdi F Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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32
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Vatansever S, Erman B, Gümüş ZH. Comparative effects of oncogenic mutations G12C, G12V, G13D, and Q61H on local conformations and dynamics of K-Ras. Comput Struct Biotechnol J 2020; 18:1000-1011. [PMID: 32373288 PMCID: PMC7191603 DOI: 10.1016/j.csbj.2020.04.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 03/05/2020] [Accepted: 04/04/2020] [Indexed: 12/25/2022] Open
Abstract
K-Ras is the most frequently mutated protein in human cancers. However, until very recently, its oncogenic mutants were viewed as undruggable. To develop inhibitors that directly target oncogenic K-Ras mutants, we need to understand both their mutant-specific and pan-mutant dynamics and conformations. Recently, we have investigated how the most frequently observed K-Ras mutation in cancer patients, G12D, changes its local dynamics and conformations (Vatansever et al., 2019). Here, we extend our analysis to study and compare the local effects of other frequently observed oncogenic mutations, G12C, G12V, G13D and Q61H. For this purpose, we have performed Molecular Dynamics (MD) simulations of each mutant when active (GTP-bound) and inactive (GDP-bound), analyzed their trajectories, and compared how each mutant changes local residue conformations, inter-protein distance distributions, local flexibility and residue pair correlated motions. Our results reveal that in the four active oncogenic mutants we have studied, the α2 helix moves closer to the C-terminal of the α3 helix. However, P-loop mutations cause α3 helix to move away from Loop7, and only G12 mutations change the local conformational state populations of the protein. Furthermore, the motions of coupled residues are mutant-specific: G12 mutations lead to new negative correlations between residue motions, while Q61H destroys them. Overall, our findings on the local conformational states and protein dynamics of oncogenic K-Ras mutants can provide insights for both mutant-selective and pan-mutant targeted inhibition efforts.
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Affiliation(s)
- Sezen Vatansever
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, New York, NY, United States
| | - Burak Erman
- Department of Chemical and Biological Engineering, College of Engineering, Koç University, Istanbul, Turkey
| | - Zeynep H. Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, New York, NY, United States
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Liu Z, Wang M, Wang H, Fang L, Gou S. Targeting RAS-RAF pathway significantly improves antitumor activity of Rigosertib-derived platinum(IV) complexes and overcomes cisplatin resistance. Eur J Med Chem 2020; 194:112269. [PMID: 32248002 DOI: 10.1016/j.ejmech.2020.112269] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/22/2020] [Accepted: 03/22/2020] [Indexed: 02/07/2023]
Abstract
RAS-RAF pathway presents a valuable target for the cancer treatment due to its important roles in the regulation of tumor proliferation, apoptosis and the obtained resistance. To explore such target a RAS/CRAF interference agent, was therefore conjugated with Pt(IV) prodrugs via ester bond, resulting in total eleven multifunctional Pt(IV) complexes. The complexes could target genomic DNA and disrupt the signaling transduction from RAS protein to CRAF so that block the mitogen-activated protein kinase (MAPK) signaling pathway. Experiments in vitro indicated that all of the Pt(IV) complexes showed potent anti-tumor activity with IC50 values ranged from 8 nM to 22.55 μM, which were significantly improved as compared with cisplatin (CDDP) whose IC50 values ranged from 5.45 μM to 9.05 μM. Among them, 26 exerted the best anti-tumor activity in vitro, which not only exhibited excellent cytotoxicity against normal tumor cells, but also against CDDP-resistance cell lines (e.g. A549/CDDP and SKOV-3/CDDP). Importantly, 26 only showed little effect on normal cell lines such as HUEVC and LO2. Besides, the following biological mechanisms studies demonstrated that 26 could efficiently enter. A549 cells, significantly arrest cell cycle at G2/M phase, disrupt the signaling pathway and trigger endogenous caspase apoptosis pathway. Furthermore, results of a xenograft subcutaneous model of A549 tumor showed that 26 could effectively decrease tumor growth rates without causing loss of bodyweight.
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Affiliation(s)
- Zhikun Liu
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, 211189, China; Pharmaceutical Research Center, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Meng Wang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin, 541004, China
| | - Hengshan Wang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin, 541004, China
| | - Lei Fang
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, 211189, China; Pharmaceutical Research Center, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| | - Shaohua Gou
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, 211189, China; Pharmaceutical Research Center, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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Ibáňez Gaspar V, Catozzi S, Ternet C, Luthert PJ, Kiel C. Analysis of Ras-effector interaction competition in large intestine and colorectal cancer context. Small GTPases 2020; 12:209-225. [PMID: 32057289 PMCID: PMC7939564 DOI: 10.1080/21541248.2020.1724596] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cancer is the second leading cause of death globally, and colorectal cancer (CRC) is among the five most common cancers. The small GTPase KRAS is an oncogene that is mutated in ~30% of all CRCs. Pharmacological treatments of CRC are currently unsatisfactory, but much hope rests on network-centric approaches to drug development and cancer treatment. These approaches, however, require a better understanding of how networks downstream of Ras oncoproteins are connected in a particular tissue context – here colon and CRC. Previously we have shown that competition for binding to a ‘hub’ protein, such as Ras, can induce a rewiring of signal transduction networks. In this study, we analysed 56 established and predicted effectors that contain a structural domain with the potential ability to bind to Ras oncoproteins and their link to pathways coordinating intestinal homoeostasis and barrier function. Using protein concentrations in colon tissue and Ras-effector binding affinities, a computational network model was generated that predicted how effectors differentially and competitively bind to Ras in colon context. The model also predicted both qualitative and quantitative changes in Ras-effector complex formations with increased levels of active Ras – to simulate its upregulation in cancer – simply as an emergent property of competition for the same binding interface on the surface of Ras. We also considered how the number of Ras-effector complexes at the membrane can be increased by additional domains present in some effectors that are recruited to the membrane in response to specific conditions (inputs/stimuli/growth factors) in colon context and CRC.
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Affiliation(s)
- Verónica Ibáňez Gaspar
- Systems Biology Ireland, and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Ireland
| | - Simona Catozzi
- Systems Biology Ireland, and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Ireland
| | - Camille Ternet
- Systems Biology Ireland, and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Ireland
| | - Philip J Luthert
- UCL Institute of Ophthalmology, and NIHR Moorfields Biomedical Research Centre, University College London, London, UK
| | - Christina Kiel
- Systems Biology Ireland, and UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Ireland
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Hobbs GA, Baker NM, Miermont AM, Thurman RD, Pierobon M, Tran TH, Anderson AO, Waters AM, Diehl JN, Papke B, Hodge RG, Klomp JE, Goodwin CM, DeLiberty JM, Wang J, Ng RWS, Gautam P, Bryant KL, Esposito D, Campbell SL, Petricoin EF, Simanshu DK, Aguirre AJ, Wolpin BM, Wennerberg K, Rudloff U, Cox AD, Der CJ. Atypical KRAS G12R Mutant Is Impaired in PI3K Signaling and Macropinocytosis in Pancreatic Cancer. Cancer Discov 2020; 10:104-123. [PMID: 31649109 PMCID: PMC6954322 DOI: 10.1158/2159-8290.cd-19-1006] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022]
Abstract
Allele-specific signaling by different KRAS alleles remains poorly understood. The KRAS G12R mutation displays uneven prevalence among cancers that harbor the highest occurrence of KRAS mutations: It is rare (∼1%) in lung and colorectal cancers, yet relatively common (∼20%) in pancreatic ductal adenocarcinoma (PDAC), suggesting context-specific properties. We evaluated whether KRASG12R is functionally distinct from the more common KRASG12D- or KRASG12V-mutant proteins (KRASG12D/V). We found that KRASG12D/V but not KRASG12R drives macropinocytosis and that MYC is essential for macropinocytosis in KRASG12D/V- but not KRASG12R-mutant PDAC. Surprisingly, we found that KRASG12R is defective for interaction with a key effector, p110α PI3K (PI3Kα), due to structural perturbations in switch II. Instead, upregulated KRAS-independent PI3Kγ activity was able to support macropinocytosis in KRASG12R-mutant PDAC. Finally, we determined that KRASG12R-mutant PDAC displayed a distinct drug sensitivity profile compared with KRASG12D-mutant PDAC but is still responsive to the combined inhibition of ERK and autophagy. SIGNIFICANCE: We determined that KRASG12R is impaired in activating a key effector, p110α PI3K. As such, KRASG12R is impaired in driving macropinocytosis. However, overexpression of PI3Kγ in PDAC compensates for this deficiency, providing one basis for the prevalence of this otherwise rare KRAS mutant in pancreatic cancer but not other cancers.See related commentary by Falcomatà et al., p. 23.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- G Aaron Hobbs
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nicole M Baker
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Ryan D Thurman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | | | - Andrew M Waters
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - J Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Bjoern Papke
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Richard G Hodge
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jennifer E Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Craig M Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jonathan M DeLiberty
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Junning Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Raymond W S Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Prson Gautam
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Kirsten L Bryant
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Sharon L Campbell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Udo Rudloff
- Thoracic and GI Oncology Branch, NCI, Bethesda, Maryland.
- Rare Tumor Initiative, Pediatric Oncology Branch, NCI, Bethesda, Maryland
| | - Adrienne D Cox
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Channing J Der
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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36
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Pantsar T. The current understanding of KRAS protein structure and dynamics. Comput Struct Biotechnol J 2019; 18:189-198. [PMID: 31988705 PMCID: PMC6965201 DOI: 10.1016/j.csbj.2019.12.004] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 01/10/2023] Open
Abstract
One of the most common drivers in human cancer is the mutant KRAS protein. Not so long ago KRAS was considered as an undruggable oncoprotein. After a long struggle, however, we finally see some light at the end of the tunnel as promising KRAS targeted therapies are in or approaching clinical trials. In recent years, together with the promising progress in RAS drug discovery, our understanding of KRAS has increased tremendously. This progress has been accompanied with a resurgence of publicly available KRAS structures, which were limited to nine structures less than ten years ago. Furthermore, the ever-increasing computational capacity has made biologically relevant timescales accessible, enabling molecular dynamics (MD) simulations to study the dynamics of KRAS protein in more detail at the atomistic level. In this minireview, my aim is to provide the reader an overview of the publicly available KRAS structural data, insights to conformational dynamics revealed by experiments and what we have learned from MD simulations. Also, I will discuss limitations of the current data and provide suggestions for future research related to KRAS, which would fill out the existing gaps in our knowledge and provide guidance in deciphering this enigmatic oncoprotein.
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Affiliation(s)
- Tatu Pantsar
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
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37
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Li X, Dai J, Ni D, He X, Zhang H, Zhang J, Fu Q, Liu Y, Lu S. Insight into the mechanism of allosteric activation of PI3Kα by oncoprotein K-Ras4B. Int J Biol Macromol 2019; 144:643-655. [PMID: 31816384 DOI: 10.1016/j.ijbiomac.2019.12.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 12/16/2022]
Abstract
Ras is a key member in the superfamily of small GTPase. Transforming between GTP-bound active state and GDP-bound inactive state in response to exogenous signals, Ras serves as a binary switch in various signaling pathways. One of its downstream effectors is phosphatidylinositol-4,5-bisphosphate 3-kinase α (PI3Kα), which phosphorylates phosphatidylinositol 4,5-bisphosphate into phosphatidylinositol 3,4,5-trisphosphate in the PI3K/Akt/mTOR pathway and mediates an array of important cellular activities including cell growth, migration and survival. Hyperactivation of PI3Kα induced by the Ras isoform K-Ras4B has been unveiled as a key event during the oncogenesis of pancreatic ductal adenocarcinoma, but the underlying mechanism of how K-Ras4B allosterically activates PI3Kα still remains largely unsolved. Here, we employed accelerated molecular dynamic simulations and allosteric pathway analysis to explore into the activation process of PI3Kα by K-Ras4B and unraveled the underlying structural mechanisms. We found that K-Ras4B binding induced more conformational dynamics within PI3Kα and triggered its step-wise transition from a self-inhibited state towards an activated state. Moreover, K-Ras4B binding markedly disrupted the interactions along the p110/p85 interface, especially the ones between nSH2 in p85 and its nearby functional domains in p110 like C2, helical, and kinase domains. The altered inter-domain interactions exposed the kinase domain, which promoted the membrane association and substrate phosphorylation of PI3Kα, thereby facilitating its activation. In particular, the community networks and allosteric pathways analysis further revealed that in PI3Kα/K-Ras4B system, allosteric signaling regulating p110/p85 interaction was rewired from the helical domain to the kinase domain and several important residues and their related allosteric pathways mediating PI3Kα autoinhibition were bypassed. The obtained structural mechanisms provide an in-depth mechanistic insight into the allosteric activation of PI3Kα by K-Ras4B as well as shed light on its drug discovery.
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Affiliation(s)
- Xinyi Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jinyuan Dai
- Chemical Engineering and Technology, School of Chemical Engineering, East China University of Science and Technology, Shanghai 201424, China
| | - Duan Ni
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xinheng He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Hao Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Qiang Fu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China.
| | - Yaqin Liu
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China; Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.
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38
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Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FHT. Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis. Nat Methods 2019; 16:743-749. [PMID: 31363225 PMCID: PMC6837886 DOI: 10.1038/s41592-019-0495-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Cellular behavior is controlled by the interplay of diverse biomolecules. Most experimental methods, however, can only monitor a single molecule class or reaction type at a time. We developed an in vitro nuclear magnetic resonance spectroscopy (NMR) approach, which permitted dynamic quantification of an entire 'heterotypic' network-simultaneously monitoring three distinct molecule classes (metabolites, proteins and RNA) and all elementary reaction types (bimolecular interactions, catalysis, unimolecular changes). Focusing on an eight-reaction co-transcriptional RNA folding network, in a single sample we recorded over 35 time points with over 170 observables each, and accurately determined five core reaction constants in multiplex. This reconstruction revealed unexpected cross-talk between the different reactions. We further observed dynamic phase-separation in a system of five distinct RNA-binding domains in the course of the RNA transcription reaction. Our Systems NMR approach provides a deeper understanding of biological network dynamics by combining the dynamic resolution of biochemical assays and the multiplexing ability of 'omics'.
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Affiliation(s)
- Yaroslav Nikolaev
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Nina Ripin
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Soste
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
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Murugan AK, Grieco M, Tsuchida N. RAS mutations in human cancers: Roles in precision medicine. Semin Cancer Biol 2019; 59:23-35. [PMID: 31255772 DOI: 10.1016/j.semcancer.2019.06.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 05/13/2019] [Accepted: 06/07/2019] [Indexed: 02/07/2023]
Abstract
Ras proteins play a crucial role as a central component of the cellular networks controlling a variety of signaling pathways that regulate growth, proliferation, survival, differentiation, adhesion, cytoskeletal rearrangements and motility of a cell. Almost, 4 decades passed since Ras research was started and ras genes were originally discovered as retroviral oncogenes. Later on, mutations of the human RAS genes were linked to tumorigenesis. Genetic analyses found that RAS is one of the most deregulated oncogenes in human cancers. In this review, we summarize the pioneering works which allowed the discovery of RAS oncogenes, the finding of frequent mutations of RAS in various human cancers, the role of these mutations in tumorigenesis and mutation-activated signaling networks. We further describe the importance of RAS mutations in personalized or precision medicine particularly in molecular targeted therapy, as well as their use as diagnostic and prognostic markers as therapeutic determinants in human cancers.
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Affiliation(s)
- Avaniyapuram Kannan Murugan
- Department of Molecular Cellular Oncology and Microbiology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549 Japan.
| | - Michele Grieco
- DiSTABiF, Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, Caserta 81100 Italy
| | - Nobuo Tsuchida
- Department of Molecular Cellular Oncology and Microbiology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549 Japan.
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40
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Molt RW, Pellegrini E, Jin Y. A GAP-GTPase-GDP-P i Intermediate Crystal Structure Analyzed by DFT Shows GTP Hydrolysis Involves Serial Proton Transfers. Chemistry 2019; 25:8484-8488. [PMID: 31038818 PMCID: PMC6771576 DOI: 10.1002/chem.201901627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/28/2019] [Indexed: 01/01/2023]
Abstract
Cell signaling by small G proteins uses an ON to OFF signal based on conformational changes following the hydrolysis of GTP to GDP and release of dihydrogen phosphate (Pi ). The catalytic mechanism of GTP hydrolysis by RhoA is strongly accelerated by a GAP protein and is now well defined, but timing of inorganic phosphate release and signal change remains unresolved. We have generated a quaternary complex for RhoA-GAP-GDP-Pi . Its 1.75 Å crystal structure shows geometry for ionic and hydrogen bond coordination of GDP and Pi in an intermediate state. It enables the selection of a QM core for DFT exploration of a 20 H-bonded network. This identifies serial locations of the two mobile protons from the original nucleophilic water molecule, showing how they move in three rational steps to form a stable quaternary complex. It also suggests how two additional proton transfer steps can facilitate Pi release.
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Affiliation(s)
- Robert W. Molt
- Department of Biochemistry & Molecular BiologyIndiana University School of MedicineIndianapolisIndiana46202USA
- ENSCO, Inc.4849 North Wickham RoadMelbourneFlorida32940USA
| | - Erika Pellegrini
- 9 European Molecular Biology Laboratory71 Avenue des Martyrs, CS 9018138042Grenoble, Cedex 9France
| | - Yi Jin
- Cardiff Catalysis InstituteSchool of ChemistryCardiff UniversityCardiffCF10 3ATUK
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41
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Killoran RC, Smith MJ. Conformational resolution of nucleotide cycling and effector interactions for multiple small GTPases determined in parallel. J Biol Chem 2019; 294:9937-9948. [PMID: 31088913 DOI: 10.1074/jbc.ra119.008653] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/09/2019] [Indexed: 12/31/2022] Open
Abstract
Small GTPases alternatively bind GDP/GTP guanine nucleotides to gate signaling pathways that direct most cellular processes. Numerous GTPases are implicated in oncogenesis, particularly the three RAS isoforms HRAS, KRAS, and NRAS and the RHO family GTPase RAC1. Signaling networks comprising small GTPases are highly connected, and there is some evidence of direct biochemical cross-talk between their functional G-domains. The activation potential of a given GTPase is contingent on a codependent interaction with the nucleotide and a Mg2+ ion, which bind to individual variants with distinct affinities coordinated by residues in the GTPase nucleotide-binding pocket. Here, we utilized a selective-labeling strategy coupled with real-time NMR spectroscopy to monitor nucleotide exchange, GTP hydrolysis, and effector interactions of multiple small GTPases in a single complex system. We provide insight into nucleotide preference and the role of Mg2+ in activating both WT and oncogenic mutant enzymes. Multiplexing revealed guanine nucleotide exchange factor (GEF), GTPase-activating protein (GAP), and effector-binding specificities in mixtures of GTPases and resolved that the three related RAS isoforms are biochemically equivalent. This work establishes that direct quantitation of the nucleotide-bound conformation is required to accurately determine an activation potential for any given GTPase, as small GTPases such as RAS-like proto-oncogene A (RALA) or the G12C mutant of KRAS display fast exchange kinetics but have a high affinity for GDP. Furthermore, we propose that the G-domains of small GTPases behave autonomously in solution and that nucleotide cycling proceeds independently of protein concentration but is highly impacted by Mg2+ abundance.
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Affiliation(s)
- Ryan C Killoran
- From the Institute for Research in Immunology and Cancer and
| | - Matthew J Smith
- From the Institute for Research in Immunology and Cancer and .,Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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42
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Erickson KE, Rukhlenko OS, Posner RG, Hlavacek WS, Kholodenko BN. New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling. Semin Cancer Biol 2019; 54:162-173. [PMID: 29518522 PMCID: PMC6123307 DOI: 10.1016/j.semcancer.2018.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/13/2018] [Accepted: 02/22/2018] [Indexed: 01/04/2023]
Abstract
RAS is the most frequently mutated gene across human cancers, but developing inhibitors of mutant RAS has proven to be challenging. Given the difficulties of targeting RAS directly, drugs that impact the other components of pathways where mutant RAS operates may potentially be effective. However, the system-level features, including different localizations of RAS isoforms, competition between downstream effectors, and interlocking feedback and feed-forward loops, must be understood to fully grasp the opportunities and limitations of inhibiting specific targets. Mathematical modeling can help us discern the system-level impacts of these features in normal and cancer cells. New technologies enable the acquisition of experimental data that will facilitate development of realistic models of oncogenic RAS behavior. In light of the wealth of empirical data accumulated over decades of study and the advancement of experimental methods for gathering new data, modelers now have the opportunity to advance progress toward realization of targeted treatment for mutant RAS-driven cancers.
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Affiliation(s)
- Keesha E Erickson
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Richard G Posner
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - William S Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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43
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Kano Y, Gebregiworgis T, Marshall CB, Radulovich N, Poon BPK, St-Germain J, Cook JD, Valencia-Sama I, Grant BMM, Herrera SG, Miao J, Raught B, Irwin MS, Lee JE, Yeh JJ, Zhang ZY, Tsao MS, Ikura M, Ohh M. Tyrosyl phosphorylation of KRAS stalls GTPase cycle via alteration of switch I and II conformation. Nat Commun 2019; 10:224. [PMID: 30644389 PMCID: PMC6333830 DOI: 10.1038/s41467-018-08115-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
Deregulation of the RAS GTPase cycle due to mutations in the three RAS genes is commonly associated with cancer development. Protein tyrosine phosphatase SHP2 promotes RAF-to-MAPK signaling pathway and is an essential factor in RAS-driven oncogenesis. Despite the emergence of SHP2 inhibitors for the treatment of cancers harbouring mutant KRAS, the mechanism underlying SHP2 activation of KRAS signaling remains unclear. Here we report tyrosyl-phosphorylation of endogenous RAS and demonstrate that KRAS phosphorylation via Src on Tyr32 and Tyr64 alters the conformation of switch I and II regions, which stalls multiple steps of the GTPase cycle and impairs binding to effectors. In contrast, SHP2 dephosphorylates KRAS, a process that is required to maintain dynamic canonical KRAS GTPase cycle. Notably, Src- and SHP2-mediated regulation of KRAS activity extends to oncogenic KRAS and the inhibition of SHP2 disrupts the phosphorylation cycle, shifting the equilibrium of the GTPase cycle towards the stalled ‘dark state’. Deregulation of the RAS GTPase cycle due to mutations in RAS genes is commonly associated with cancer development. Here authors use NMR and mass spectrometry to shows that KRAS phosphorylation via Src alters the conformation of switch I and II regions and thereby impacts the GTPase cycle.
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Affiliation(s)
- Yoshihito Kano
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network and Department of Pathology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Betty P K Poon
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Jonathan D Cook
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Ivette Valencia-Sama
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, 5G OA4, Canada
| | - Benjamin M M Grant
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Silvia Gabriela Herrera
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jinmin Miao
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN, 47907, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Meredith S Irwin
- Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, 5G OA4, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Surgery, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN, 47907, USA
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network and Department of Pathology, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada. .,Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.
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44
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Abstract
K-Ras is the undisputed champion of oncogenes, yet our ability to interfere with its oncogenic function is hampered by insufficient mechanistic understanding. In this issue of Cell, Ambrogio and colleagues connect the ability of K-Ras to dimerize to the ability of wild-type K-Ras to limit the oncogenic properties of the mutant.
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Affiliation(s)
- Yi-Jang Lin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kevin M Haigis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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45
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Fang Z, Marshall CB, Nishikawa T, Gossert AD, Jansen JM, Jahnke W, Ikura M. Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site. Cell Chem Biol 2018; 25:1327-1336.e4. [DOI: 10.1016/j.chembiol.2018.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/21/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022]
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46
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Pantsar T, Rissanen S, Dauch D, Laitinen T, Vattulainen I, Poso A. Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling. PLoS Comput Biol 2018; 14:e1006458. [PMID: 30199525 PMCID: PMC6147662 DOI: 10.1371/journal.pcbi.1006458] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 09/20/2018] [Accepted: 08/22/2018] [Indexed: 12/29/2022] Open
Abstract
A mutated KRAS protein is frequently observed in human cancers. Traditionally, the oncogenic properties of KRAS missense mutants at position 12 (G12X) have been considered as equal. Here, by assessing the probabilities of occurrence of all KRAS G12X mutations and KRAS dynamics we show that this assumption does not hold true. Instead, our findings revealed an outstanding mutational bias. We conducted a thorough mutational analysis of KRAS G12X mutations and assessed to what extent the observed mutation frequencies follow a random distribution. Unique tissue-specific frequencies are displayed with specific mutations, especially with G12R, which cannot be explained by random probabilities. To clarify the underlying causes for the nonrandom probabilities, we conducted extensive atomistic molecular dynamics simulations (170 μs) to study the differences of G12X mutations on a molecular level. The simulations revealed an allosteric hydrophobic signaling network in KRAS, and that protein dynamics is altered among the G12X mutants and as such differs from the wild-type and is mutation-specific. The shift in long-timescale conformational dynamics was confirmed with Markov state modeling. A G12X mutation was found to modify KRAS dynamics in an allosteric way, which is especially manifested in the switch regions that are responsible for the effector protein binding. The findings provide a basis to understand better the oncogenic properties of KRAS G12X mutants and the consequences of the observed nonrandom frequencies of specific G12X mutations. The oncogene KRAS is frequently mutated in various cancers. When the amino acid glycine 12 is mutated, KRAS protein acquires oncogenic properties that result in tumor cell-growth and cancer progression. These mutations prevail especially in the pancreatic ductal adenocarcinoma, which is a cancer with an exceptionally dismal prognosis. To date, there is a limited understanding of the different mutations at the position 12, also regarding whether the different mutations would have different consequences. These discrepancies could have major implications for the future drug therapies targeting KRAS mutant harboring tumors. In this study, we made a critical assessment of the observed frequency of KRAS G12X mutations and the underlying causes for these frequencies. We also assessed KRAS G12X mutant discrepancies on an atomistic level by utilizing state-of-the-art molecular dynamics simulations. We found that the dynamics of the mutants does not only differ from the wild-type protein, but there is also a profound difference among the different mutants. These results emphasize that the different KRAS G12X mutations are not equal, and thereby they suggest that the future research related to mutant KRAS biology should account for these observations.
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Affiliation(s)
- Tatu Pantsar
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- * E-mail: (TP); (AP)
| | - Sami Rissanen
- Laboratory of Physics, Tampere University of Technology, Tampere, Finland
| | - Daniel Dauch
- Department of Internal Medicine VIII, University Hospital Tuebingen, Tuebingen, Germany
- Department of Physiology I, Institute of Physiology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Tuomo Laitinen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology, Tampere, Finland
- Department of Physics, University of Helsinki, Helsinki, Finland
- MEMPHYS-Center for Biomembrane Physics, Helsinki, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Department of Internal Medicine VIII, University Hospital Tuebingen, Tuebingen, Germany
- * E-mail: (TP); (AP)
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47
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Parker JA, Mattos C. The K-Ras, N-Ras, and H-Ras Isoforms: Unique Conformational Preferences and Implications for Targeting Oncogenic Mutants. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031427. [PMID: 29038336 DOI: 10.1101/cshperspect.a031427] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ras controls a multitude of cellular signaling processes, including cell proliferation, differentiation, and apoptosis. Deregulation of Ras cycling often promotes tumorigenesis and various other developmental disorders, termed RASopothies. Although the structure of Ras has been known for many decades, it is still one of the most highly sought-after drug targets today, and is often referred to as "undruggable." At the center of this paradoxical protein is a lack of understanding of fundamental differences in the G domains between the highly similar Ras isoforms and common oncogenic mutations, despite the immense wealth of knowledge accumulated about this protein to date. A shift in the field during the past few years toward a high-resolution understanding of the structure confirms the hypothesis that each isoform and oncogenic mutation must be considered individually, and that not all Ras mutations are created equal. For the first time in Ras history, we have the ability to directly compare the structures of each wild-type isoform to construct a "base-line" understanding, which can then be used as a springboard for analyzing the effects of oncogenic mutations on the structure-function relationship in Ras. This is a fundamental and large step toward the goal of developing personalized therapies for patients with Ras-driven cancers and diseases.
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Affiliation(s)
- Jillian A Parker
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
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48
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Krygowska AA, Castellano E. PI3K: A Crucial Piece in the RAS Signaling Puzzle. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031450. [PMID: 28847905 DOI: 10.1101/cshperspect.a031450] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RAS proteins are key signaling switches essential for control of proliferation, differentiation, and survival of eukaryotic cells. RAS proteins are mutated in 30% of human cancers. In addition, mutations in upstream or downstream signaling components also contribute to oncogenic activation of the pathway. RAS proteins exert their functions through activation of several signaling pathways and dissecting the contributions of these effectors in normal cells and in cancer is an ongoing challenge. In this review, we summarize our current knowledge about how RAS regulates type I phosphatidylinositol 3-kinase (PI3K), one of the main RAS effectors. RAS signaling through PI3K is necessary for normal lymphatic vasculature development and for RAS-induced transformation in vitro and in vivo, especially in lung cancer, where it is essential for tumor initiation and necessary for tumor maintenance.
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Affiliation(s)
- Agata Adelajda Krygowska
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Esther Castellano
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
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49
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Han CW, Jeong MS, Jang SB. Structure, signaling and the drug discovery of the Ras oncogene protein. BMB Rep 2018; 50:355-360. [PMID: 28571593 PMCID: PMC5584742 DOI: 10.5483/bmbrep.2017.50.7.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 01/04/2023] Open
Abstract
Mutations in Ras GTPase are among the most common genetic alterations in human cancers. Despite extensive research investigating Ras proteins, their functions still remain a challenge over a long period of time. The currently available data suggests that solving the outstanding issues regarding Ras could lead to development of effective drugs that could have a significant impact on cancer treatment. Developing a better understanding of their biochemical properties or modes of action, along with improvements in their pharmacologic profiles, clinical design and scheduling will enable the development of more effective therapies.
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Affiliation(s)
- Chang Woo Han
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Mi Suk Jeong
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
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50
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Evolution of AF6-RAS association and its implications in mixed-lineage leukemia. Nat Commun 2017; 8:1099. [PMID: 29062045 PMCID: PMC5653649 DOI: 10.1038/s41467-017-01326-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/09/2017] [Indexed: 12/31/2022] Open
Abstract
Elucidation of activation mechanisms governing protein fusions is essential for therapeutic development. MLL undergoes rearrangement with numerous partners, including a recurrent translocation fusing the epigenetic regulator to a cytoplasmic RAS effector, AF6/afadin. We show here that AF6 employs a non-canonical, evolutionarily conserved α-helix to bind RAS, unique to AF6 and the classical RASSF effectors. Further, all patients with MLL-AF6 translocations express fusion proteins missing only this helix from AF6, resulting in exposure of hydrophobic residues that induce dimerization. We provide evidence that oligomerization is the dominant mechanism driving oncogenesis from rare MLL translocation partners and employ our mechanistic understanding of MLL-AF6 to examine how dimers induce leukemia. Proteomic data resolve association of dimerized MLL with gene expression modulators, and inhibiting dimerization disrupts formation of these complexes while completely abrogating leukemogenesis in mice. Oncogenic gene translocations are thus selected under pressure from protein structure/function, underscoring the complex nature of chromosomal rearrangements. Several rearrangements of the MLL gene are associated with acute leukemia, including the fusion of MLL with a RAS effector protein, AF6. Here the authors show that the truncated AF6 can induce AF6-MLL dimerization and drive its oncogenic activity.
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