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Fink JC, Landry D, Webb LJ. Probing the Electrostatic Effects of H-Ras Tyrosine 32 Mutations on Intrinsic GTP Hydrolysis Using Vibrational Stark Effect Spectroscopy of a Thiocyanate Probe. Biochemistry 2024; 63:1752-1760. [PMID: 38967549 DOI: 10.1021/acs.biochem.4c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The wildtype H-Ras protein functions as a molecular switch in a variety of cell signaling pathways, and mutations to key residues result in a constitutively active oncoprotein. However, there is some debate regarding the mechanism of the intrinsic GTPase activity of H-Ras. It has been hypothesized that ordered water molecules are coordinated at the active site by Q61, a highly transforming amino acid site, and Y32, a position that has not previously been investigated. Here, we examine the electrostatic contribution of the Y32 position to GTP hydrolysis by comparing the rate of GTP hydrolysis of Y32X mutants to the vibrational energy shift of each mutation measured by a nearby thiocyanate vibrational probe to estimate changes in the electrostatic environment caused by changes at the Y32 position. We further compared vibrational energy shifts for each mutation to the hydration potential of the respective side chain and demonstrated that Y32 is less critical for recruiting water molecules into the active site to promote hydrolysis than Q61. Our results show a clear interplay between a steric contribution from Y32 and an electrostatic contribution from Q61 that are both critical for intrinsic GTP hydrolysis.
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Affiliation(s)
- Jackson C Fink
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Danielle Landry
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
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2
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Moore S, Kulkarni V, Moore A, Landes JR, Simonette R, He Q, Rady PL, Tyring SK. Tirbanibulin decreases cell proliferation and downregulates protein expression of oncogenic pathways in human papillomavirus containing HeLa cells. Arch Dermatol Res 2024; 316:455. [PMID: 38967656 DOI: 10.1007/s00403-024-03205-8] [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: 05/11/2024] [Revised: 06/18/2024] [Accepted: 06/23/2024] [Indexed: 07/06/2024]
Abstract
Tirbanibulin 1% ointment is a synthetic antiproliferative agent approved in 2021 by the European Union for treating actinic keratoses (AK). Topical tirbanibulin has clinically resolved HPV-57 ( +) squamous cell carcinoma (SCC), HPV-16 ( +) vulvar high-grade squamous intraepithelial lesion, epidermodysplasia verruciformis, and condyloma. We examined how tirbanibulin might affect HPV oncoprotein expression and affect other cellular pathways involved in cell proliferation and transformation. We treated the HeLa cell line, containing integrated HPV-18, with increasing doses of tirbanibulin to determine the effects on cell proliferation. Immunoblotting was performed with antibodies against the Src canonical pathway, HPV 18 E6 and E7 transcription regulation, apoptosis, and invasion and metastasis pathways. Cell proliferation assays with tirbanibulin determined the half-maximal inhibitory concentration (IC50) of HeLa cells to be 31.49 nmol/L. Increasing concentrations of tirbanibulin downregulates the protein expression of Src (p < 0.001), phospho-Src (p < 0.001), Ras (p < 0.01), c-Raf (p < 0.001), ERK1 (p < 0.001), phospho-ERK1 (p < 0.001), phospho-ERK2 (p < 0.01), phospho-Mnk1 (p < 0.001), eIF4E (p < 0.01), phospho-eIF4E (p < 0.001), E6 (p < 0.01), E7 (p < 0.01), Rb (p < 0.01), phospho-Rb (p < 0.001), MDM2 (p < 0.01), E2F1 (p < 0.001), phospho-FAK (p < 0.001), phospho-p130 Cas (p < 0.001), Mcl-1 (p < 0.01), and Bcl-2 (p < 0.001), but upregulates cPARP (p < 0.001), and cPARP/fPARP (p < 0.001). These results demonstrate that tirbanibulin may impact expression of HPV oncoproteins via the Src- MEK- pathway. Tirbanibulin significantly downregulates oncogenic proteins related to cell cycle regulation and cell proliferation while upregulating apoptosis pathways.
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Affiliation(s)
- Stephen Moore
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Veda Kulkarni
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA
| | - Angela Moore
- Department of Dermatology, Baylor University Medical Center Part of Baylor Scott and White, Dallas, TX, USA
| | - Jennifer R Landes
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA
| | - Rebecca Simonette
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA
| | - Qin He
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA
| | - Peter L Rady
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA
| | - Stephen K Tyring
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA.
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3
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Chen J, Wang J, Yang W, Zhao L, Zhao J, Hu G. Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning. Molecules 2024; 29:2317. [PMID: 38792177 PMCID: PMC11123822 DOI: 10.3390/molecules29102317] [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: 04/23/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the phosphorylation-mediated effect on conformational dynamics of the GTP-bound KRAS. The DL finds that the switch domains are involved in obvious differences in conformation contacts and suggests that the switch domains play a key role in the function of KRAS. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of pY32, pY64, and pY137 leads to more disordered states of the switch domains than the wild-type (WT) KRAS and induces conformational transformations between the closed and open states. The results from principal component analysis (PCA) indicate that principal motions PC1 and PC2 are responsible for the closed and open states of the phosphorylated KRAS. Interaction networks were analyzed and the results verify that the phosphorylation alters interactions of GTP and magnesium ion Mg2+ with the switch domains. It is concluded that the phosphorylation pY32, pY64, and pY137 tune the activity of KRAS through changing conformational dynamics and interactions of the switch domains. We anticipated that this work could provide theoretical aids for deeply understanding the function of KRAS.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jian Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Juan Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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4
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Weeks R, Mehta S, Zhang J. Genetically encodable biosensors for Ras activity. RSC Chem Biol 2024; 5:312-320. [PMID: 38576721 PMCID: PMC10989514 DOI: 10.1039/d3cb00185g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/02/2024] [Indexed: 04/06/2024] Open
Abstract
Genetically encoded Ras biosensors have been instrumental in illuminating the spatiotemporal dynamics of Ras activity since the beginning of the imaging revolution of the early 21st century. In general, these sensors employ Ras sensing units coupled with fluorescent proteins. These biosensors have not only helped elucidate Ras signalling dynamics at the plasma membrane but also revealed novel roles for Ras signalling within subcellular compartments such as the Golgi apparatus. In this review, we discuss the different classes of biosensors used to measure Ras activity and discuss their importance in uncovering new roles for Ras activity in cellular signalling and behavior.
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Affiliation(s)
- Ryan Weeks
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla CA 92093 USA +1 (858) 246-0602
- Department of Pharmacology, University of California, San Diego La Jolla CA 92093 USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego La Jolla CA 92093 USA
| | - Jin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla CA 92093 USA +1 (858) 246-0602
- Department of Pharmacology, University of California, San Diego La Jolla CA 92093 USA
- Department of Bioengineering, University of California, San Diego La Jolla CA 92093 USA
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5
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Baumann P, Jin Y. Far-reaching effects of tyrosine64 phosphorylation on Ras revealed with BeF 3- complexes. Commun Chem 2024; 7:19. [PMID: 38297137 PMCID: PMC10830474 DOI: 10.1038/s42004-024-01105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Tyrosine phosphorylation on Ras by Src kinase is known to uncouple Ras from upstream regulation and downstream communication. However, the mechanisms by which phosphorylation modulates these interactions have not been detailed. Here, the major mono-phosphorylation level on tyrosine64 is quantified by 31P NMR and mutagenesis. Crystal structures of unphosphorylated and tyrosine64-phosphorylated Ras in complex with a BeF3- ground state analogue reveal "closed" Ras conformations very different from those of the "open" conformations previously observed for non-hydrolysable GTP analogue structures of Ras. They deliver new mechanistic and conformational insights into intrinsic GTP hydrolysis. Phosphorylation of tyrosine64 delivers conformational changes distant from the active site, showing why phosphorylated Ras has reduced affinity to its downstream effector Raf. 19F NMR provides evidence for changes in the intrinsic GTPase and nucleotide exchange rate and identifies the concurrent presence of a major "closed" conformation alongside a minor yet functionally important "open" conformation at the ground state of Ras. This study expands the application of metal fluoride complexes in revealing major and minor conformational changes of dynamic and modified Ras proteins.
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Affiliation(s)
- Patrick Baumann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yi Jin
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK.
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Nelson AR, Christiansen SL, Naegle KM, Saucerman JJ. Logic-based mechanistic machine learning on high-content images reveals how drugs differentially regulate cardiac fibroblasts. Proc Natl Acad Sci U S A 2024; 121:e2303513121. [PMID: 38266046 PMCID: PMC10835125 DOI: 10.1073/pnas.2303513121] [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: 03/01/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024] Open
Abstract
Fibroblasts are essential regulators of extracellular matrix deposition following cardiac injury. These cells exhibit highly plastic responses in phenotype during fibrosis in response to environmental stimuli. Here, we test whether and how candidate anti-fibrotic drugs differentially regulate measures of cardiac fibroblast phenotype, which may help identify treatments for cardiac fibrosis. We conducted a high-content microscopy screen of human cardiac fibroblasts treated with 13 clinically relevant drugs in the context of TGFβ and/or IL-1β, measuring phenotype across 137 single-cell features. We used the phenotypic data from our high-content imaging to train a logic-based mechanistic machine learning model (LogiMML) for fibroblast signaling. The model predicted how pirfenidone and Src inhibitor WH-4-023 reduce actin filament assembly and actin-myosin stress fiber formation, respectively. Validating the LogiMML model prediction that PI3K partially mediates the effects of Src inhibition, we found that PI3K inhibition reduces actin-myosin stress fiber formation and procollagen I production in human cardiac fibroblasts. In this study, we establish a modeling approach combining the strengths of logic-based network models and regularized regression models. We apply this approach to predict mechanisms that mediate the differential effects of drugs on fibroblasts, revealing Src inhibition acting via PI3K as a potential therapy for cardiac fibrosis.
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Affiliation(s)
- Anders R. Nelson
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA22903
| | - Steven L. Christiansen
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA22903
- Department of Biochemistry, Brigham Young University, Provo, UT84602
| | - Kristen M. Naegle
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA22903
| | - Jeffrey J. Saucerman
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA22903
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7
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Banerjee R, Mukherjee A, Adhikary A, Sharma S, Hussain MS, Ali ME, Nagotu S. Insights into the role of the conserved GTPase domain residues T62 and S277 in yeast Dnm1. Int J Biol Macromol 2023; 253:127381. [PMID: 37838106 DOI: 10.1016/j.ijbiomac.2023.127381] [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: 06/08/2023] [Revised: 09/10/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
Mitochondrial division is a highly regulated process. The master regulator of this process is the multi-domain, conserved protein called Dnm1 in yeast. In this study, we systematically analyzed two residues, T62 and S277, reported to be putatively phosphorylated in the GTPase domain of the protein. These residues lie in the G2 and G5 motifs of the GTPase domain. Both residues are important for the function of the protein, as evident from in vivo and in vitro analysis of the non-phosphorylatable and phosphomimetic variants. Dnm1T62A/D and Dnm1S277A/D showed differences with respect to the protein localization and puncta dynamics in vivo, albeit both were non-functional as assessed by mitochondrial morphology and GTPase activity. Overall, the secondary structure of the protein variants was unaltered, but local conformational changes were observed. Interestingly, both Dnm1T62A/D and Dnm1S277A/D exhibited dominant-negative behavior when expressed in cells containing endogenous Dnm1. To our knowledge, we report for the first time a single residue (S277) change that does not alter the localization of Dnm1 but makes it non-functional in a dominant-negative manner. Intriguingly, the two residues analyzed in this study are present in the same domain but exhibit variable effects when mutated to alanine or aspartic acid.
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Affiliation(s)
- Riddhi Banerjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Agradeep Mukherjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ankita Adhikary
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shikha Sharma
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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8
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Nelson AR, Christiansen SL, Naegle KM, Saucerman JJ. Logic-based mechanistic machine learning on high-content images reveals how drugs differentially regulate cardiac fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530599. [PMID: 36909540 PMCID: PMC10002757 DOI: 10.1101/2023.03.01.530599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fibroblasts are essential regulators of extracellular matrix deposition following cardiac injury. These cells exhibit highly plastic responses in phenotype during fibrosis in response to environmental stimuli. Here, we test whether and how candidate anti-fibrotic drugs differentially regulate measures of cardiac fibroblast phenotype, which may help identify treatments for cardiac fibrosis. We conducted a high content microscopy screen of human cardiac fibroblasts treated with 13 clinically relevant drugs in the context of TGFβ and/or IL-1β, measuring phenotype across 137 single-cell features. We used the phenotypic data from our high content imaging to train a logic-based mechanistic machine learning model (LogiMML) for fibroblast signaling. The model predicted how pirfenidone and Src inhibitor WH-4-023 reduce actin filament assembly and actin-myosin stress fiber formation, respectively. Validating the LogiMML model prediction that PI3K partially mediates the effects of Src inhibition, we found that PI3K inhibition reduces actin-myosin stress fiber formation and procollagen I production in human cardiac fibroblasts. In this study, we establish a modeling approach combining the strengths of logic-based network models and regularized regression models, apply this approach to predict mechanisms that mediate the differential effects of drugs on fibroblasts, revealing Src inhibition acting via PI3K as a potential therapy for cardiac fibrosis.
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Affiliation(s)
- Anders R. Nelson
- University of Virginia School of Medicine, Charlottesville, VA 22903
| | - Steven L. Christiansen
- University of Virginia School of Medicine, Charlottesville, VA 22903
- Brigham Young University Department of Biochemistry, Provo, UT 84602
| | - Kristen M. Naegle
- University of Virginia School of Medicine, Charlottesville, VA 22903
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9
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Simão S, Agostinho RR, Martínez-Ruiz A, Araújo IM. Regulation of Ras Signaling by S-Nitrosylation. Antioxidants (Basel) 2023; 12:1562. [PMID: 37627556 PMCID: PMC10451275 DOI: 10.3390/antiox12081562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Ras are a family of small GTPases that function as signal transduction mediators and are involved in cell proliferation, migration, differentiation and survival. The significance of Ras is further evidenced by the fact that Ras genes are among the most mutated oncogenes in different types of cancers. After translation, Ras proteins can be targets of post-translational modifications (PTM), which can alter the intracellular dynamics of the protein. In this review, we will focus on how S-nitrosylation of Ras affects the way these proteins interact with membranes, its cellular localization, and its activity. S-Nitrosylation occurs when a nitrosyl moiety of nitric oxide (NO) is covalently attached to a thiol group of a cysteine residue in a target protein. In Ras, the conserved Cys118 is the most surface-exposed Cys and the preferable residue for NO action, leading to the initiation of transduction events. Ras transduces the mitogen-activated protein kinases (MAPK), the phosphoinositide-3 kinase (PI3K) and the RalGEF cellular pathways. S-Nitrosylation of elements of the RalGEF cascade remains to be identified. On the contrary, it is well established that several components of the MAPK and PI3K pathways, as well as different proteins associated with these cascades, can be modified by S-nitrosylation. Overall, this review presents a better understanding of Ras S-nitrosylation, increasing the knowledge on the dynamics of these proteins in the presence of NO and the underlying implications in cellular signaling.
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Affiliation(s)
- Sónia Simão
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139 Faro, Portugal;
- Faculty of Medicine and Biomedical Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Rafaela Ribeiro Agostinho
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139 Faro, Portugal;
- Faculty of Medicine and Biomedical Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Antonio Martínez-Ruiz
- Unidad de Investigación, Hospital Universitario Santa Cristina, Instituto de Investigación Sanitaria Princesa, 28009 Madrid, Spain;
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Inês Maria Araújo
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139 Faro, Portugal;
- Faculty of Medicine and Biomedical Sciences, University of Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, 1400-038 Lisbon, Portugal
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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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11
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Yin G, Huang J, Petela J, Jiang H, Zhang Y, Gong S, Wu J, Liu B, Shi J, Gao Y. Targeting small GTPases: emerging grasps on previously untamable targets, pioneered by KRAS. Signal Transduct Target Ther 2023; 8:212. [PMID: 37221195 DOI: 10.1038/s41392-023-01441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 05/25/2023] Open
Abstract
Small GTPases including Ras, Rho, Rab, Arf, and Ran are omnipresent molecular switches in regulating key cellular functions. Their dysregulation is a therapeutic target for tumors, neurodegeneration, cardiomyopathies, and infection. However, small GTPases have been historically recognized as "undruggable". Targeting KRAS, one of the most frequently mutated oncogenes, has only come into reality in the last decade due to the development of breakthrough strategies such as fragment-based screening, covalent ligands, macromolecule inhibitors, and PROTACs. Two KRASG12C covalent inhibitors have obtained accelerated approval for treating KRASG12C mutant lung cancer, and allele-specific hotspot mutations on G12D/S/R have been demonstrated as viable targets. New methods of targeting KRAS are quickly evolving, including transcription, immunogenic neoepitopes, and combinatory targeting with immunotherapy. Nevertheless, the vast majority of small GTPases and hotspot mutations remain elusive, and clinical resistance to G12C inhibitors poses new challenges. In this article, we summarize diversified biological functions, shared structural properties, and complex regulatory mechanisms of small GTPases and their relationships with human diseases. Furthermore, we review the status of drug discovery for targeting small GTPases and the most recent strategic progress focused on targeting KRAS. The discovery of new regulatory mechanisms and development of targeting approaches will together promote drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Jing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Johnny Petela
- Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuetong Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Siqi Gong
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jiaxin Wu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Bei Liu
- National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, 100871, China
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, 610072, China.
| | - Yijun Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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Gall CM, Le AA, Lynch G. Sex differences in synaptic plasticity underlying learning. J Neurosci Res 2023; 101:764-782. [PMID: 33847004 PMCID: PMC10337639 DOI: 10.1002/jnr.24844] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 11/09/2022]
Abstract
Although sex differences in learning behaviors are well documented, sexual dimorphism in the synaptic processes of encoding is only recently appreciated. Studies in male rodents have built upon the discovery of long-term potentiation (LTP), and acceptance of this activity-dependent increase in synaptic strength as a mechanism of encoding, to identify synaptic receptors and signaling activities that coordinate the activity-dependent remodeling of the subsynaptic actin cytoskeleton that is critical for enduring potentiation and memory. These molecular substrates together with other features of LTP, as characterized in males, have provided an explanation for a range of memory phenomena including multiple stages of consolidation, the efficacy of spaced training, and the location of engrams at the level of individual synapses. In the present report, we summarize these findings and describe more recent results from our laboratories showing that in females the same actin regulatory mechanisms are required for hippocampal LTP and memory but, in females only, the engagement of both modulatory receptors such as TrkB and synaptic signaling intermediaries including Src and ERK1/2 requires neuron-derived estrogen and signaling through membrane-associated estrogen receptor α (ERα). Moreover, in association with the additional ERα involvement, females exhibit a higher threshold for hippocampal LTP and spatial learning. We propose that the distinct LTP threshold in females contributes to as yet unappreciated sex differences in information processing and features of learning and memory.
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Affiliation(s)
- Christine M. Gall
- Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Aliza A. Le
- Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Gary Lynch
- Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
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13
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Poh AR, Ernst M. Functional roles of SRC signaling in pancreatic cancer: Recent insights provide novel therapeutic opportunities. Oncogene 2023:10.1038/s41388-023-02701-x. [PMID: 37120696 DOI: 10.1038/s41388-023-02701-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignant disease with a 5-year survival rate of <10%. Aberrant activation or elevated expression of the tyrosine kinase c-SRC (SRC) is frequently observed in PDAC and is associated with a poor prognosis. Preclinical studies have revealed a multifaceted role for SRC activation in PDAC, including promoting chronic inflammation, tumor cell proliferation and survival, cancer cell stemness, desmoplasia, hypoxia, angiogenesis, invasion, metastasis, and drug resistance. Strategies to inhibit SRC signaling include suppressing its catalytic activity, inhibiting protein stability, or by interfering with signaling components of the SRC signaling pathway including suppressing protein interactions of SRC. In this review, we discuss the molecular and immunological mechanisms by which aberrant SRC activity promotes PDAC tumorigenesis. We also provide a comprehensive update of SRC inhibitors in the clinic, and discuss the clinical challenges associated with targeting SRC in pancreatic cancer.
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Affiliation(s)
- Ashleigh R Poh
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, VIC, 3084, Australia.
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Melbourne, VIC, 3084, Australia.
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14
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Jensen NR, Kelly RR, Kelly KD, Khoo SK, Sidles SJ, LaRue AC. From Stem to Sternum: The Role of Shp2 in the Skeleton. Calcif Tissue Int 2023; 112:403-421. [PMID: 36422682 DOI: 10.1007/s00223-022-01042-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/05/2022] [Indexed: 11/25/2022]
Abstract
Src homology-2 domain-containing phosphatase 2 (SHP2) is a ubiquitously expressed phosphatase that is vital for skeletal development and maintenance of chondrocytes, osteoblasts, and osteoclasts. Study of SHP2 function in small animal models has led to insights in phenotypes observed in SHP2-mutant human disease, such as Noonan syndrome. In recent years, allosteric SHP2 inhibitors have been developed to specifically target the protein in neoplastic processes. These inhibitors are highly specific and have great potential for disease modulation in cancer and other pathologies, including bone disorders. In this review, we discuss the importance of SHP2 and related signaling pathways (e.g., Ras/MEK/ERK, JAK/STAT, PI3K/Akt) in skeletal development. We review rodent models of pathologic processes caused by germline mutations that activate SHP2 enzymatic activity, with a focus on the skeletal phenotype seen in these patients. Finally, we discuss SHP2 inhibitors in development and their potential for disease modulation in these genetic diseases, particularly as it relates to the skeleton.
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Affiliation(s)
- Nathaniel R Jensen
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan R Kelly
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Kirsten D Kelly
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA
| | - Stephanie K Khoo
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA
| | - Sara J Sidles
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Amanda C LaRue
- Ralph H. Johnson VA Health Care System, Research Service, Charleston, SC, USA.
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA.
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15
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Jiang H, Zu S, Lu Y, Sun Z, Adeerjiang A, Guo Q, Zhang H, Dong C, Wu Q, Ding H, Du D, Wang M, Liu C, Tang Y, Liang Z, Luo C. A RhoA structure with switch II flipped outward revealed the conformational dynamics of switch II region. J Struct Biol 2023; 215:107942. [PMID: 36781028 DOI: 10.1016/j.jsb.2023.107942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/23/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Small GTPase RhoA switches from GTP-bound state to GDP-bound state by hydrolyzing GTP, which is accelerated by GTPases activating proteins (GAPs). However, less study of RhoA structural dynamic changes was conducted during this process, which is essential for understanding the molecular mechanism of GAP dissociation. Here, we solved a RhoA structure in GDP-bound state with switch II flipped outward. Because lacking the intermolecular interactions with guanine nucleotide, we proposed this conformation of RhoA could be an intermediate after GAP dissociation. Further molecular dynamics simulations found the conformational changes of switch regions are indeed existing in RhoA and involved in the regulation of GAP dissociation and GEF recognition. Besides, the guanine nucleotide binding pocket extended to switch II region, indicating a potential "druggable" cavity for RhoA. Taken together, our study provides a deeper understanding of the dynamic properties of RhoA switch regions and highlights the direction for future drug development.
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Affiliation(s)
- Hao Jiang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Shijia Zu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Yu Lu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Zhongya Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Akejiang Adeerjiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Qiao Guo
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Huimin Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China
| | - Chen Dong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Qiqi Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Daohai Du
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mingliang Wang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Yong Tang
- Ensem Therapeutics, Inc, 200 Boston Ave, Medford, MA 02155, USA
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China.
| | - Cheng Luo
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China.
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16
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Dynamic regulation of RAS and RAS signaling. Biochem J 2023; 480:1-23. [PMID: 36607281 PMCID: PMC9988006 DOI: 10.1042/bcj20220234] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023]
Abstract
RAS proteins regulate most aspects of cellular physiology. They are mutated in 30% of human cancers and 4% of developmental disorders termed Rasopathies. They cycle between active GTP-bound and inactive GDP-bound states. When active, they can interact with a wide range of effectors that control fundamental biochemical and biological processes. Emerging evidence suggests that RAS proteins are not simple on/off switches but sophisticated information processing devices that compute cell fate decisions by integrating external and internal cues. A critical component of this compute function is the dynamic regulation of RAS activation and downstream signaling that allows RAS to produce a rich and nuanced spectrum of biological outputs. We discuss recent findings how the dynamics of RAS and its downstream signaling is regulated. Starting from the structural and biochemical properties of wild-type and mutant RAS proteins and their activation cycle, we examine higher molecular assemblies, effector interactions and downstream signaling outputs, all under the aspect of dynamic regulation. We also consider how computational and mathematical modeling approaches contribute to analyze and understand the pleiotropic functions of RAS in health and disease.
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17
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Pieroni S, Castelli M, Piobbico D, Ferracchiato S, Scopetti D, Di-Iacovo N, Della-Fazia MA, Servillo G. The Four Homeostasis Knights: In Balance upon Post-Translational Modifications. Int J Mol Sci 2022; 23:ijms232214480. [PMID: 36430960 PMCID: PMC9696182 DOI: 10.3390/ijms232214480] [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: 10/13/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
A cancer outcome is a multifactorial event that comes from both exogenous injuries and an endogenous predisposing background. The healthy state is guaranteed by the fine-tuning of genes controlling cell proliferation, differentiation, and development, whose alteration induces cellular behavioral changes finally leading to cancer. The function of proteins in cells and tissues is controlled at both the transcriptional and translational level, and the mechanism allowing them to carry out their functions is not only a matter of level. A major challenge to the cell is to guarantee that proteins are made, folded, assembled and delivered to function properly, like and even more than other proteins when referring to oncogenes and onco-suppressors products. Over genetic, epigenetic, transcriptional, and translational control, protein synthesis depends on additional steps of regulation. Post-translational modifications are reversible and dynamic processes that allow the cell to rapidly modulate protein amounts and function. Among them, ubiquitination and ubiquitin-like modifications modulate the stability and control the activity of most of the proteins that manage cell cycle, immune responses, apoptosis, and senescence. The crosstalk between ubiquitination and ubiquitin-like modifications and post-translational modifications is a keystone to quickly update the activation state of many proteins responsible for the orchestration of cell metabolism. In this light, the correct activity of post-translational machinery is essential to prevent the development of cancer. Here we summarize the main post-translational modifications engaged in controlling the activity of the principal oncogenes and tumor suppressors genes involved in the development of most human cancers.
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18
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Ryan A, Janosko CP, Courtney TM, Deiters A. Engineering SHP2 Phosphatase for Optical Control. Biochemistry 2022; 61:2687-2697. [DOI: 10.1021/acs.biochem.2c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chasity P. Janosko
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Taylor M. Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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19
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Lepeta K, Roubinet C, Bauer M, Vigano MA, Aguilar G, Kanca O, Ochoa-Espinosa A, Bieli D, Cabernard C, Caussinus E, Affolter M. Engineered kinases as a tool for phosphorylation of selected targets in vivo. J Cell Biol 2022; 221:213463. [PMID: 36102907 PMCID: PMC9477969 DOI: 10.1083/jcb.202106179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 05/19/2022] [Accepted: 07/27/2022] [Indexed: 11/22/2022] Open
Abstract
Reversible protein phosphorylation by kinases controls a plethora of processes essential for the proper development and homeostasis of multicellular organisms. One main obstacle in studying the role of a defined kinase–substrate interaction is that kinases form complex signaling networks and most often phosphorylate multiple substrates involved in various cellular processes. In recent years, several new approaches have been developed to control the activity of a given kinase. However, most of them fail to regulate a single protein target, likely hiding the effect of a unique kinase–substrate interaction by pleiotropic effects. To overcome this limitation, we have created protein binder-based engineered kinases that permit a direct, robust, and tissue-specific phosphorylation of fluorescent fusion proteins in vivo. We show the detailed characterization of two engineered kinases based on Rho-associated protein kinase (ROCK) and Src. Expression of synthetic kinases in the developing fly embryo resulted in phosphorylation of their respective GFP-fusion targets, providing for the first time a means to direct the phosphorylation to a chosen and tagged target in vivo. We presume that after careful optimization, the novel approach we describe here can be adapted to other kinases and targets in various eukaryotic genetic systems to regulate specific downstream effectors.
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Affiliation(s)
| | - Chantal Roubinet
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK 2
| | - Milena Bauer
- Biozentrum, University of Basel, Basel, Switzerland 1
| | | | | | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 3
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20
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Wang J, Yao N, Hu Y, Lei M, Wang M, Yang L, Patel S, Li X, Liu K, Dong Z. PHLDA1 promotes glioblastoma cell growth via sustaining the activation state of Ras. Cell Mol Life Sci 2022; 79:520. [DOI: 10.1007/s00018-022-04538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/09/2022] [Accepted: 08/29/2022] [Indexed: 11/03/2022]
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21
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Protein Tyrosine Kinase 6 regulates activation of SRC kinase. J Biol Chem 2022; 298:102584. [DOI: 10.1016/j.jbc.2022.102584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 11/07/2022] Open
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22
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Weeks R, Zhou X, Yuan TL, Zhang J. Fluorescent Biosensor for Measuring Ras Activity in Living Cells. J Am Chem Soc 2022; 144:17432-17440. [PMID: 36122391 PMCID: PMC10031818 DOI: 10.1021/jacs.2c05203] [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] [Indexed: 11/29/2022]
Abstract
The small GTPase Ras is a critical regulator of cell growth and proliferation. Its activity is frequently dysregulated in cancers, prompting decades of work to pharmacologically target Ras. Understanding Ras biology and developing effective Ras therapeutics both require probing Ras activity in its native context, yet tools to measure its activities in cellulo are limited. Here, we developed a ratiometric Ras activity reporter (RasAR) that provides quantitative measurement of Ras activity in living cells with high spatiotemporal resolution. We demonstrated that RasAR can probe live-cell activities of all the primary isoforms of Ras. Given that the functional roles of different isoforms of Ras are intimately linked to their subcellular distribution and regulation, we interrogated the spatiotemporal regulation of Ras utilizing subcellularly targeted RasAR and uncovered the role of Src kinase as an upstream regulator to inhibit HRas. Furthermore, we showed that RasAR enables capture of KRasG12C inhibition dynamics in living cells upon treatment with KRasG12C covalent inhibitors, including ARS1620, Sotorasib, and Adagrasib. We found in living cells a residual Ras activity lingers for hours in the presence of these inhibitors. Together, RasAR represents a powerful molecular tool to enable live-cell interrogation of Ras activity and facilitate the development of Ras inhibitors.
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Affiliation(s)
- Ryan Weeks
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tina L. Yuan
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Correspondence: Jin Zhang, 9500 Gilman Drive, BRF-II 1120, La Jolla, CA 92093-0702, phone (858) 246-0602,
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23
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Garmendia I, Redin E, Montuenga LM, Calvo A. YES1: a novel therapeutic target and biomarker in cancer. Mol Cancer Ther 2022; 21:1371-1380. [PMID: 35732509 DOI: 10.1158/1535-7163.mct-21-0958] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/09/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022]
Abstract
YES1 is a non-receptor tyrosine kinase that belongs to the SRC family of kinases (SFKs) and controls multiple cancer signaling pathways. YES1 is amplified and overexpressed in many tumor types, where it promotes cell proliferation, survival and invasiveness. Therefore, YES1 has been proposed as an emerging target in solid tumors. In addition, studies have shown that YES1 is a prognostic biomarker and a predictor of dasatinib activity. Several SFKs-targeting drugs have been developed and some of them have reached clinical trials. However, these drugs have encountered challenges to their utilization in the clinical practice in unselected patients due to toxicity and lack of efficacy. In the case of YES1, novel specific inhibitors have been developed and tested in preclinical models, with impressive antitumor effects. In this review, we summarize the structure and activation of YES1 and describe its role in cancer as a target and prognostic and companion biomarker. We also address the efficacy of SFKs inhibitors that are currently in clinical trials, highlighting the main hindrances for their clinical use. Current available information strongly suggests that inhibiting YES1 in tumors with high expression of this protein is a promising strategy against cancer.
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Affiliation(s)
- Irati Garmendia
- INSERM UMRS1138. Centre de Recherche des Cordeliers, Paris, France
| | | | - Luis M Montuenga
- CIMA and Clinica Universidad de Navarra, Pamplona, Navarra, Spain
| | - Alfonso Calvo
- Center for Applied Medical Research (CIMA), Pamplona, Spain
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24
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Chinigò G, Grolez GP, Audero M, Bokhobza A, Bernardini M, Cicero J, Toillon RA, Bailleul Q, Visentin L, Ruffinatti FA, Brysbaert G, Lensink MF, De Ruyck J, Cantelmo AR, Fiorio Pla A, Gkika D. TRPM8-Rap1A Interaction Sites as Critical Determinants for Adhesion and Migration of Prostate and Other Epithelial Cancer Cells. Cancers (Basel) 2022; 14:2261. [PMID: 35565390 PMCID: PMC9102551 DOI: 10.3390/cancers14092261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Emerging evidence indicates that the TRPM8 channel plays an important role in prostate cancer (PCa) progression, by impairing the motility of these cancer cells. Here, we reveal a novel facet of PCa motility control via direct protein-protein interaction (PPI) of the channel with the small GTPase Rap1A. The functional interaction of the two proteins was assessed by active Rap1 pull-down assays and live-cell imaging experiments. Molecular modeling analysis allowed the identification of four putative residues involved in TRPM8-Rap1A interaction. Point mutations of these sites impaired PPI as shown by GST-pull-down, co-immunoprecipitation, and PLA experiments and revealed their key functional role in the adhesion and migration of PC3 prostate cancer cells. More precisely, TRPM8 inhibits cell migration and adhesion by trapping Rap1A in its GDP-bound inactive form, thus preventing its activation at the plasma membrane. In particular, residues E207 and Y240 in the sequence of TRPM8 and Y32 in that of Rap1A are critical for the interaction between the two proteins not only in PC3 cells but also in cervical (HeLa) and breast (MCF-7) cancer cells. This study deepens our knowledge of the mechanism through which TRPM8 would exert a protective role in cancer progression and provides new insights into the possible use of TRPM8 as a new therapeutic target in cancer treatment.
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Affiliation(s)
- Giorgia Chinigò
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Guillaume P. Grolez
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Madelaine Audero
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Alexandre Bokhobza
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Michela Bernardini
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
| | - Julien Cicero
- CNRS, INSERM, CHU Lille, Centre Oscar Lambret, UMR 9020-UMR 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, F-59000 Lille, France; (J.C.); (R.-A.T.)
- UR 2465—Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University of Artois, F-62300 Lens, France
| | - Robert-Alain Toillon
- CNRS, INSERM, CHU Lille, Centre Oscar Lambret, UMR 9020-UMR 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, F-59000 Lille, France; (J.C.); (R.-A.T.)
| | - Quentin Bailleul
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Luca Visentin
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
| | - Federico Alessandro Ruffinatti
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
| | - Guillaume Brysbaert
- CNRS UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, 59000 Lille, France; (G.B.); (M.F.L.); (J.D.R.)
| | - Marc F. Lensink
- CNRS UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, 59000 Lille, France; (G.B.); (M.F.L.); (J.D.R.)
| | - Jerome De Ruyck
- CNRS UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, 59000 Lille, France; (G.B.); (M.F.L.); (J.D.R.)
| | - Anna Rita Cantelmo
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Alessandra Fiorio Pla
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Dimitra Gkika
- CNRS, INSERM, CHU Lille, Centre Oscar Lambret, UMR 9020-UMR 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, F-59000 Lille, France; (J.C.); (R.-A.T.)
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Institut Universitaire de France (IUF), 75231 Paris, France
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Genomic and Epigenomic Landscape of Juvenile Myelomonocytic Leukemia. Cancers (Basel) 2022; 14:cancers14051335. [PMID: 35267643 PMCID: PMC8909150 DOI: 10.3390/cancers14051335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Juvenile myelomonocytic leukemia (JMML) is a rare pediatric myelodysplastic/myeloproliferative neoplasm characterized by the constitutive activation of the RAS pathway. In spite of the recent progresses in the molecular characterization of JMML, this disease is still a clinical challenge due to its heterogeneity, difficult diagnosis, poor prognosis, and the lack of curative treatment options other than hematopoietic stem cell transplantation (HSCT). In this review, we will provide a detailed overview of the genetic and epigenetic alterations occurring in JMML, and discuss their clinical relevance in terms of disease prognosis and risk of relapse after HSCT. We will also present the most recent advances on novel preclinical and clinical therapeutic approaches directed against JMML molecular targets. Finally, we will outline future research perspectives to further explore the oncogenic mechanism driving JMML leukemogenesis and progression, with special attention to the application of single-cell next-generation sequencing technologies. Abstract Juvenile myelomonocytic leukemia (JMML) is a rare myelodysplastic/myeloproliferative neoplasm of early childhood. Most of JMML patients experience an aggressive clinical course of the disease and require hematopoietic stem cell transplantation, which is currently the only curative treatment. JMML is characterized by RAS signaling hyperactivation, which is mainly driven by mutations in one of five genes of the RAS pathway, including PTPN11, KRAS, NRAS, NF1, and CBL. These driving mutations define different disease subtypes with specific clinico-biological features. Secondary mutations affecting other genes inside and outside the RAS pathway contribute to JMML pathogenesis and are associated with a poorer prognosis. In addition to these genetic alterations, JMML commonly presents aberrant epigenetic profiles that strongly correlate with the clinical outcome of the patients. This observation led to the recent publication of an international JMML stratification consensus, which defines three JMML clinical groups based on DNA methylation status. Although the characterization of the genomic and epigenomic landscapes in JMML has significantly contributed to better understand the molecular mechanisms driving the disease, our knowledge on JMML origin, cell identity, and intratumor and interpatient heterogeneity is still scarce. The application of new single-cell sequencing technologies will be critical to address these questions in the future.
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Bose M, Grover P, Sanders AJ, Zhou R, Ahmad M, Shwartz S, Lala P, Nath S, Yazdanifar M, Brouwer C, Mukherjee P. Overexpression of MUC1 Induces Non-Canonical TGF-β Signaling in Pancreatic Ductal Adenocarcinoma. Front Cell Dev Biol 2022; 10:821875. [PMID: 35237602 PMCID: PMC8883581 DOI: 10.3389/fcell.2022.821875] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal human cancers. Transforming Growth Factor Beta (TGF-β) is a cytokine that switches from a tumor-suppressor at early stages to a tumor promoter in the late stages of tumor development, by yet unknown mechanisms. Tumor associated MUC1 is aberrantly glycosylated and overexpressed in >80% of PDAs and is associated with poor prognosis. MUC1 expression is found in the early stages of PDA development with subsequent increase in later stages. Analysis of human PDA samples from TCGA database showed significant differences in gene expression and survival profiles between low and high MUC1 samples. Further, high MUC1 expression was found to positively correlate to TGF-βRII expression and negatively correlate to TGF-βRI expression in PDA cell lines. We hypothesized that MUC1 overexpression induces TGF-β mediated non-canonical signaling pathways which is known to be associated with poor prognosis. In this study, we report that MUC1 overexpression in PDA cells directly activates the JNK pathway in response to TGF-β, and leads to increased cell viability via up-regulation and stabilization of c-Myc. Conversely, in low MUC1 expressing PDA cells, TGF-β preserves its tumor-suppressive function and inhibits phosphorylation of JNK and stabilization of c-Myc. Knockdown of MUC1 in PDA cells also results in decreased phosphorylation of JNK and c-Myc in response to TGF-β treatment. Taken together, the results indicate that overexpression of MUC1 plays a significant role in switching the TGF-β function from a tumor-suppressor to a tumor promoter by directly activating JNK. Lastly, we report that high-MUC1 PDA tumors respond to TGF-β neutralizing antibody in vivo showing significantly reduced tumor growth while low-MUC1 tumors do not respond to TGF-β neutralizing antibody further confirming our hypothesis.
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Affiliation(s)
- Mukulika Bose
- Department of Biological Sciences, UNC Charlotte, Charlotte, NC, United States
| | - Priyanka Grover
- Department of Biological Sciences, UNC Charlotte, Charlotte, NC, United States
| | - Alexa J Sanders
- Department of Bioinformatics, UNC Charlotte, Charlotte, NC, United States
| | - Ru Zhou
- Department of Biological Sciences, UNC Charlotte, Charlotte, NC, United States
| | - Mohammad Ahmad
- Department of Biological Sciences, UNC Charlotte, Charlotte, NC, United States
| | - Sophia Shwartz
- Department of Biological Sciences, UNC Charlotte, Charlotte, NC, United States
| | - Priyanka Lala
- Department of Biological Sciences, UNC Charlotte, Charlotte, NC, United States
| | - Sritama Nath
- Department of Biological Sciences, UNC Charlotte, Charlotte, NC, United States
| | | | - Cory Brouwer
- Department of Bioinformatics, UNC Charlotte, Charlotte, NC, United States
| | - Pinku Mukherjee
- Department of Biological Sciences, UNC Charlotte, Charlotte, NC, United States
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27
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Chou YT, Bivona TG. Inhibition of SHP2 as an approach to block RAS-driven cancers. Adv Cancer Res 2022; 153:205-236. [PMID: 35101231 DOI: 10.1016/bs.acr.2021.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The non-receptor protein tyrosine phosphatase SHP2 (encoded by PTPN11) is a critical component of RAS/MAPK signaling by acting upstream of RAS to promote oncogenic signaling and tumor growth. Over three decades, SHP2 was considered "undruggable" because enzymatic active-site inhibitors generally showed off-target inhibition of other proteins and low membrane permeability. More recently, allosteric SHP2 inhibitors with striking inhibitory potency have been developed. These small molecules effectively block the signal transduction between receptor tyrosine kinases (RTKs) and RAS/MAPK signaling and show efficacy in preclinical cancer models. Moreover, clinical evaluation of these allosteric SHP2 inhibitors is ongoing. RAS proteins which harbor transforming properties by gain-of-function mutations are present in various cancer types. While inhibitors of KRASG12C show early clinical promise, resistance remains a challenge and other forms of oncogenic RAS remain to be selectively inhibited. Here, we summarize the role of SHP2 in RAS-driven cancers and the therapeutic potential of allosteric SHP2 inhibitors as a strategy to block RAS-driven cancers.
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Affiliation(s)
- Yu-Ting Chou
- Department of Medicine, Division of Hematology and Oncology, and The Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, United States
| | - Trever G Bivona
- Department of Medicine, Division of Hematology and Oncology, and The Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, United States.
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Ilter M, Kasmer R, Jalalypour F, Atilgan C, Topcu O, Karakas N, Sensoy O. Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS. eLife 2022; 11:79747. [PMID: 36458814 PMCID: PMC9762712 DOI: 10.7554/elife.79747] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
Undruggability of RAS proteins has necessitated alternative strategies for the development of effective inhibitors. In this respect, phosphorylation has recently come into prominence as this reversible post-translational modification attenuates sensitivity of RAS towards RAF. As such, in this study, we set out to unveil the impact of phosphorylation on dynamics of HRASWT and aim to invoke similar behavior in HRASG12D mutant by means of small therapeutic molecules. To this end, we performed molecular dynamics (MD) simulations using phosphorylated HRAS and showed that phosphorylation of Y32 distorted Switch I, hence the RAS/RAF interface. Consequently, we targeted Switch I in HRASG12D by means of approved therapeutic molecules and showed that the ligands enabled detachment of Switch I from the nucleotide-binding pocket. Moreover, we demonstrated that displacement of Switch I from the nucleotide-binding pocket was energetically more favorable in the presence of the ligand. Importantly, we verified computational findings in vitro where HRASG12D/RAF interaction was prevented by the ligand in HEK293T cells that expressed HRASG12D mutant protein. Therefore, these findings suggest that targeting Switch I, hence making Y32 accessible might open up new avenues in future drug discovery strategies that target mutant RAS proteins.
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Affiliation(s)
- Metehan Ilter
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol UniversityIstanbulTurkey
| | - Ramazan Kasmer
- Medical Biology and Genetics Program, Graduate School for Health Sciences, Istanbul Medipol UniversityIstanbulTurkey,Cancer Research Center, Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
| | - Farzaneh Jalalypour
- Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbulTurkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbulTurkey
| | - Ozan Topcu
- Medical Biology and Genetics Program, Graduate School for Health Sciences, Istanbul Medipol UniversityIstanbulTurkey
| | - Nihal Karakas
- Medical Biology and Genetics Program, Graduate School for Health Sciences, Istanbul Medipol UniversityIstanbulTurkey,Department of Medical Biology, International School of Medicine, Istanbul Medipol UniversityIstanbulTurkey
| | - Ozge Sensoy
- Department of Computer Engineering, School of Engineering and Natural Sciences, Istanbul Medipol UniversityIstanbulTurkey,Regenerative and Restorative Medicine Research Center (REMER), Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
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The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors. Nat Commun 2021; 12:6274. [PMID: 34725361 PMCID: PMC8560773 DOI: 10.1038/s41467-021-26526-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/23/2021] [Indexed: 12/31/2022] Open
Abstract
Cancer cells bearing distinct KRAS mutations exhibit variable sensitivity to SHP2 inhibitors (SHP2i). Here we show that cells harboring KRAS Q61H are uniquely resistant to SHP2i, and investigate the underlying mechanisms using biophysics, molecular dynamics, and cell-based approaches. Q61H mutation impairs intrinsic and GAP-mediated GTP hydrolysis, and impedes activation by SOS1, but does not alter tyrosyl phosphorylation. Wild-type and Q61H-mutant KRAS are both phosphorylated by Src on Tyr32 and Tyr64 and dephosphorylated by SHP2, however, SHP2i does not reduce ERK phosphorylation in KRAS Q61H cells. Phosphorylation of wild-type and Gly12-mutant KRAS, which are associated with sensitivity to SHP2i, confers resistance to regulation by GAP and GEF activities and impairs binding to RAF, whereas the near-complete GAP/GEF-resistance of KRAS Q61H remains unaltered, and high-affinity RAF interaction is retained. SHP2 can stimulate KRAS signaling by modulating GEF/GAP activities and dephosphorylating KRAS, processes that fail to regulate signaling of the Q61H mutant. SHP2 promotes RAS-driven MAPK signalling, but it is unclear why cancer cells with distinct KRAS mutations exhibit differential sensitivity to SHP2 inhibition. Here the authors show that KRAS Q61H is decoupled from SHP2- mediated upstream regulation, thus Q61H pancreatic cancer cells maintain MAPK signalling and are refractory to SHP2 inhibitors.
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Qiu Y, Wang Y, Chai Z, Ni D, Li X, Pu J, Chen J, Zhang J, Lu S, Lv C, Ji M. Targeting RAS phosphorylation in cancer therapy: Mechanisms and modulators. Acta Pharm Sin B 2021; 11:3433-3446. [PMID: 34900528 PMCID: PMC8642438 DOI: 10.1016/j.apsb.2021.02.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/26/2021] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
RAS, a member of the small GTPase family, functions as a binary switch by shifting between inactive GDP-loaded and active GTP-loaded state. RAS gain-of-function mutations are one of the leading causes in human oncogenesis, accounting for ∼19% of the global cancer burden. As a well-recognized target in malignancy, RAS has been intensively studied in the past decades. Despite the sustained efforts, many failures occurred in the earlier exploration and resulted in an ‘undruggable’ feature of RAS proteins. Phosphorylation at several residues has been recently determined as regulators for wild-type and mutated RAS proteins. Therefore, the development of RAS inhibitors directly targeting the RAS mutants or towards upstream regulatory kinases supplies a novel direction for tackling the anti-RAS difficulties. A better understanding of RAS phosphorylation can contribute to future therapeutic strategies. In this review, we comprehensively summarized the current advances in RAS phosphorylation and provided mechanistic insights into the signaling transduction of associated pathways. Importantly, the preclinical and clinical success in developing anti-RAS drugs targeting the upstream kinases and potential directions of harnessing allostery to target RAS phosphorylation sites were also discussed.
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Key Words
- ABL, Abelson
- APC, adenomatous polyposis coli
- Allostery
- CK1, casein kinase 1
- CML, chronic myeloid leukemia
- ER, endoplasmic reticulum
- GAPs, GTPase-activating proteins
- GEFs, guanine nucleotide exchange-factors
- GSK3, glycogen synthase kinase 3
- HVR, hypervariable region
- IP3R, inositol trisphosphate receptors
- LRP6, lipoprotein-receptor-related protein 6
- OMM, outer mitochondrial membrane
- PI3K, phosphatidylinositol 3-kinase
- PKC, protein kinase C
- PPIs, protein−protein interactions
- Phosphorylation
- Protein kinases
- RAS
- RIN1, RAB-interacting protein 1
- SHP2, SRC homology 2 domain containing phosphatase 2
- SOS, Son of Sevenless
- STK19, serine/threonine-protein kinase 19
- TKIs, tyrosine kinase inhibitors
- Undruggable
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Affiliation(s)
- Yuran Qiu
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai 200003, China
- 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
| | - Yuanhao Wang
- 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
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, 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
| | - 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
| | - Jun Pu
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200120, China
| | - Jie Chen
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai 200003, 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
- Corresponding authors.
| | - 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
- Corresponding authors.
| | - Chuan Lv
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, Shanghai 200438, China
- Corresponding authors.
| | - Mingfei Ji
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai 200003, China
- Corresponding authors.
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Fowlkes JL, Thrailkill KM, Bunn RC. RASopathies: The musculoskeletal consequences and their etiology and pathogenesis. Bone 2021; 152:116060. [PMID: 34144233 PMCID: PMC8316423 DOI: 10.1016/j.bone.2021.116060] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 01/07/2023]
Abstract
The RASopathies comprise an ever-growing number of clinical syndromes resulting from germline mutations in components of the RAS/MAPK signaling pathway. While multiple organs and tissues may be affected by these mutations, this review will focus on how these mutations specifically impact the musculoskeletal system. Herein, we review the genetics and musculoskeletal phenotypes of these syndromes in humans. We discuss how mutations in the RASopathy syndromes have been studied in translational mouse models. Finally, we discuss how signaling molecules within the RAS/MAPK pathway are involved in normal and abnormal bone biology in the context of osteoblasts, osteoclasts and chondrocytes.
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Affiliation(s)
- John L Fowlkes
- University of Kentucky Barnstable Brown Diabetes Center, Department of Pediatrics, University of Kentucky College of Medicine, Lexington, KY 40536, United States of America.
| | - Kathryn M Thrailkill
- University of Kentucky Barnstable Brown Diabetes Center, Department of Pediatrics, University of Kentucky College of Medicine, Lexington, KY 40536, United States of America
| | - R Clay Bunn
- University of Kentucky Barnstable Brown Diabetes Center, Department of Pediatrics, University of Kentucky College of Medicine, Lexington, KY 40536, United States of America
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Rozengurt E, Eibl G. Crosstalk between KRAS, SRC and YAP Signaling in Pancreatic Cancer: Interactions Leading to Aggressive Disease and Drug Resistance. Cancers (Basel) 2021; 13:5126. [PMID: 34680275 PMCID: PMC8533944 DOI: 10.3390/cancers13205126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), the predominant form of pancreatic cancer, remains a devastating disease. The purpose of this review is to highlight recent literature on mechanistic and translational developments that advance our understanding of a complex crosstalk between KRAS, YAP and Src tyrosine kinase family (SFK) in PDAC development and maintenance. We discuss recent studies indicating the importance of RAS dimerization in signal transduction and new findings showing that the potent pro-oncogenic members of the SFK phosphorylate and inhibit RAS function. These surprising findings imply that RAS may not play a crucial role in maintaining certain subtypes of PDAC. In support of this interpretation, current evidence indicates that the survival of the basal-like subtype of PDAC is less dependent on RAS but relies, at least in part, on the activity of YAP/TAZ. Based on current evidence, we propose that SFK propels PDAC cells to a state of high metastasis, epithelial-mesenchymal transition (EMT) and reduced dependence on KRAS signaling, salient features of the aggressive basal-like/squamous subtype of PDAC. Strategies for PDAC treatment should consider the opposite effects of tyrosine phosphorylation on KRAS and SFK/YAP in the design of drug combinations that target these novel crosstalk mechanisms and overcome drug resistance.
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Affiliation(s)
- Enrique Rozengurt
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Guido Eibl
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA;
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33
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KRASG12C inhibitor: combing for combination. Biochem Soc Trans 2021; 48:2691-2701. [PMID: 33242077 DOI: 10.1042/bst20200473] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022]
Abstract
Oncogenic mutation in KRAS is one of the most common alterations in human cancer. After decades of extensive research and unsuccessful drug discovery programs, therapeutic targeting of KRAS mutant tumour is at an exciting juncture. The discovery of mutation-specific inhibitors of KRASG12C and early positive findings from clinical trials has raised the hope of finally having a drug to treat a significant segment of KRAS mutant cancer patients. Crucially, it has also re-energized the RAS field to look beyond G12C mutation and find new innovative targeting opportunities. However, the early clinical trial data also indicates that there is significant variation in response among patients and that monotherapy treatment with KRASG12C inhibitors (G12Ci) alone is unlikely to be sufficient to elicit a sustained response. Understanding the molecular mechanism of variation in patient response and identifying possible combination opportunities, which could be exploited to achieve durable and significant responses and delay emergence of resistance, is central to the success of G12Ci therapy. Given the specificity of G12Ci, toxicity is expected to be minimal. Therefore, it might be possible to combine G12Ci with other targeted agents which have previously been explored to tackle KRAS mutant cancer but deemed too toxic, e.g. MEK inhibitor. Ongoing clinical trials will shed light on clinical resistance to G12C inhibitors, however extensive work is already ongoing to identify the best combination partners. This review provides an update on combination opportunities which could be explored to maximize the benefit of this new exciting drug.
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34
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Campbell SL, Philips MR. Post-translational modification of RAS proteins. Curr Opin Struct Biol 2021; 71:180-192. [PMID: 34365229 DOI: 10.1016/j.sbi.2021.06.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022]
Abstract
Mutations of RAS genes drive cancer more frequently than any other oncogene. RAS proteins integrate signals from a wide array of receptors and initiate downstream signaling through pathways that control cellular growth. RAS proteins are fundamentally binary molecular switches in which the off/on state is determined by the binding of GDP or GTP, respectively. As such, the intrinsic and regulated nucleotide-binding and hydrolytic properties of the RAS GTPase were historically believed to account for the entirety of the regulation of RAS signaling. However, it is increasingly clear that RAS proteins are also regulated by a vast array of post-translational modifications (PTMs). The current challenge is to understand what are the functional consequences of these modifications and which are physiologically relevant. Because PTMs are catalyzed by enzymes that may offer targets for drug discovery, the study of RAS PTMs has been a high priority for RAS biologists.
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Affiliation(s)
| | - Mark R Philips
- Perlmutter Cancer Center, NYU Grossman School of Medicine, USA
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35
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Rezaei Adariani S, Kazemein Jasemi NS, Bazgir F, Wittich C, Amin E, Seidel CAM, Dvorsky R, Ahmadian MR. A comprehensive analysis of RAS-effector interactions reveals interaction hotspots and new binding partners. J Biol Chem 2021; 296:100626. [PMID: 33930461 PMCID: PMC8163975 DOI: 10.1016/j.jbc.2021.100626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
RAS effectors specifically interact with GTP-bound RAS proteins to link extracellular signals to downstream signaling pathways. These interactions rely on two types of domains, called RAS-binding (RB) and RAS association (RA) domains, which share common structural characteristics. Although the molecular nature of RAS-effector interactions is well-studied for some proteins, most of the RA/RB-domain-containing proteins remain largely uncharacterized. Here, we searched through human proteome databases, extracting 41 RA domains in 39 proteins and 16 RB domains in 14 proteins, each of which can specifically select at least one of the 25 members in the RAS family. We next comprehensively investigated the sequence–structure–function relationship between different representatives of the RAS family, including HRAS, RRAS, RALA, RAP1B, RAP2A, RHEB1, and RIT1, with all members of RA domain family proteins (RASSFs) and the RB-domain-containing CRAF. The binding affinity for RAS-effector interactions, determined using fluorescence polarization, broadly ranged between high (0.3 μM) and very low (500 μM) affinities, raising interesting questions about the consequence of these variable binding affinities in the regulation of signaling events. Sequence and structural alignments pointed to two interaction hotspots in the RA/RB domains, consisting of an average of 19 RAS-binding residues. Moreover, we found novel interactions between RRAS1, RIT1, and RALA and RASSF7, RASSF9, and RASSF1, respectively, which were systematically explored in sequence–structure–property relationship analysis, and validated by mutational analysis. These data provide a set of distinct functional properties and putative biological roles that should now be investigated in the cellular context.
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Affiliation(s)
- Soheila Rezaei Adariani
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Neda S Kazemein Jasemi
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Farhad Bazgir
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Christoph Wittich
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Ehsan Amin
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany; Medical Faculty, Institute of Neural and Sensory Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Claus A M Seidel
- Chair of Molecular Physical Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Radovan Dvorsky
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany.
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Chen J, Zhang S, Wang W, Pang L, Zhang Q, Liu X. Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis. J Chem Inf Model 2021; 61:1954-1969. [PMID: 33739090 DOI: 10.1021/acs.jcim.0c01470] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mutations yield significant effect on the structural flexibility of two switch domains, SW1 and SW2, in K-Ras, which is considered as an important target of anticancer drug design. To unveil a molecular mechanism with regard to mutation-mediated tuning on the activity of K-Ras, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations followed by analysis of free energy landscapes (FELs) are performed on the GDP- and GTP-bound wild-type (WT), G12V, and D33E K-Ras. The results suggest that G12V and D33E not only evidently change the flexibility of SW1 and SW2 but also greatly affect correlated motions of SW1 and SW2 separately relative to the P-loop and SW1, which exerts a certain tuning on the activity of K-Ras. The information stemming from the analyses of FELs reveals that the conformations of SW1 and SW2 are in high disorders in the GDP- and GTP-associated WT and mutated K-Ras, possibly producing significant effect on binding of guanine nucleotide exchange factors or effectors to K-Ras. The interaction networks of GDP and GTP with K-Ras are identified and the results uncover that the instability in hydrogen-bonding interactions of SW1 with GDP and GTP is mostly responsible for conformational disorder of SW1 and SW2 as well as tunes the activity of oncogenic K-Ras.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
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Wang Y, Ji D, Lei C, Chen Y, Qiu Y, Li X, Li M, Ni D, Pu J, Zhang J, Fu Q, Liu Y, Lu S. Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins. Comput Struct Biotechnol J 2021; 19:1184-1199. [PMID: 33680360 PMCID: PMC7902900 DOI: 10.1016/j.csbj.2021.01.044] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ras undergoes interconversion between the active GTP-bound state and the inactive GDP-bound state. This GTPase cycle, which controls the activities of Ras, is accelerated by Ras GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (SOS). Oncogenic Ras mutations could affect the GTPase cycle and impair Ras functions. Additionally, Src-induced K-Ras Y32/64 dual phosphorylation has been reported to disrupt GTPase cycle and hinder Ras downstream signaling. However, the underlying mechanisms remain unclear. To address this, we performed molecular dynamics simulations (~30 μs in total) on unphosphorylated and phosphorylated K-Ras4B in GTP- and GDP-bound states, and on their complexes with GTPase cycle regulators (GAP and SOS) and the effector protein Raf. We found that K-Ras4B dual phosphorylation mainly alters the conformation at the nucleotide binding site and creates disorder at the catalytic site, resulting in the enlargement of GDP binding pocket and the retard of Ras-GTP intrinsic hydrolysis. We observed phosphorylation-induced shift in the distribution of Ras-GTP inactive-active sub-states and recognized potential druggable pockets in the phosphorylated Ras-GTP. Moreover, decreased catalytic competence or signal delivery abilities due to reduced binding affinities and/or distorted catalytic conformations of GAP, SOS and Raf were observed. In addition, the allosteric pathway from Ras/Raf interface to the distal Raf L4 loop was compromised by Ras phosphorylation. These results reveal the mechanisms by which phosphorylation influences the intrinsic or GAP/SOS catalyzed transformations between GTP- and GDP-bound states of Ras and its signal transduction to Raf. Our findings project Ras phosphorylation as a target for cancer drug discovery.
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Affiliation(s)
- Yuanhao Wang
- 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
| | - Dong Ji
- Department of Anesthesiology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, China
| | - Chaoyu Lei
- 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
| | - Yingfei Chen
- 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
| | - Yuran Qiu
- 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
| | - 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
| | - Mingyu 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
| | - 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
- The Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Jun Pu
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200120, 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
- Medicinal Chemistry and Bioinformatics Centre, 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 Chemistry and Bioinformatics Centre, 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 Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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38
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Kiel C, Matallanas D, Kolch W. The Ins and Outs of RAS Effector Complexes. Biomolecules 2021; 11:236. [PMID: 33562401 PMCID: PMC7915224 DOI: 10.3390/biom11020236] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
RAS oncogenes are among the most commonly mutated proteins in human cancers. They regulate a wide range of effector pathways that control cell proliferation, survival, differentiation, migration and metabolic status. Including aberrations in these pathways, RAS-dependent signaling is altered in more than half of human cancers. Targeting mutant RAS proteins and their downstream oncogenic signaling pathways has been elusive. However, recent results comprising detailed molecular studies, large scale omics studies and computational modeling have painted a new and more comprehensive portrait of RAS signaling that helps us to understand the intricacies of RAS, how its physiological and pathophysiological functions are regulated, and how we can target them. Here, we review these efforts particularly trying to relate the detailed mechanistic studies with global functional studies. We highlight the importance of computational modeling and data integration to derive an actionable understanding of RAS signaling that will allow us to design new mechanism-based therapies for RAS mutated cancers.
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Affiliation(s)
- Christina Kiel
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; (C.K.); (D.M.)
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - David Matallanas
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; (C.K.); (D.M.)
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; (C.K.); (D.M.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
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39
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Yin C, Zhu B, Li X, Goding CR, Cui R. A Reply to ''Evidence that STK19 Is Not an NRAS-Dependent Melanoma Driver". Cell 2020; 181:1406-1409.e2. [PMID: 32531246 DOI: 10.1016/j.cell.2020.04.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/02/2020] [Accepted: 04/16/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Chengqian Yin
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Bo Zhu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Xin Li
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Colin R Goding
- Ludwig Institute for Cancer Research, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Rutao Cui
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA.
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40
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Attur M, Lu C, Zhang X, Han T, Alexandre C, Valacca C, Zheng S, Meikle S, Dabovic BB, Tassone E, Yang Q, Kolupaeva V, Yakar S, Abramson S, Mignatti P. Membrane-type 1 Matrix Metalloproteinase Modulates Tissue Homeostasis by a Non-proteolytic Mechanism. iScience 2020; 23:101789. [PMID: 33294797 PMCID: PMC7695985 DOI: 10.1016/j.isci.2020.101789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/31/2020] [Accepted: 11/06/2020] [Indexed: 12/26/2022] Open
Abstract
Membrane-type 1 matrix metalloproteinase (MT1-MMP, MMP-14), a transmembrane proteinase with a short cytoplasmic tail, is a major effector of extracellular matrix remodeling. Genetic silencing of MT1-MMP in mouse (Mmp14 -/- ) and man causes dwarfism, osteopenia, arthritis, and lipodystrophy, abnormalities ascribed to defective collagen turnover. We have previously shown non-proteolytic functions of MT1-MMP mediated by its cytoplasmic tail, where the unique tyrosine (Y573) controls intracellular signaling. The Y573D mutation blocks TIMP-2/MT1-MMP-induced Erk1/2 and Akt signaling without affecting proteolytic activity. Here, we report that a mouse with the MT1-MMP Y573D mutation (Mmp14 Y573D/Y573D ) shows abnormalities similar to but also different from those of Mmp14 -/- mice. Skeletal stem cells (SSC) of Mmp14 Y573D/Y573D mice show defective differentiation consistent with the mouse phenotype, which is rescued by wild-type SSC transplant. These results provide the first in vivo demonstration that MT1-MMP modulates bone, cartilage, and fat homeostasis by controlling SSC differentiation through a mechanism independent of proteolysis.
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Affiliation(s)
- Mukundan Attur
- Department of Medicine, Division of Rheumatology, NYU School of Medicine, 301 East 17th Street, Suite 1612A, NY 10003, USA
| | - Cuijie Lu
- Department of Medicine, Division of Rheumatology, NYU School of Medicine, 301 East 17th Street, Suite 1612A, NY 10003, USA
| | - Xiaodong Zhang
- Department of Cardiothoracic Surgery, NYU School of Medicine, 550 First Avenue, NY 10016, USA
| | - Tianzhen Han
- Department of Medicine, Division of Rheumatology, NYU School of Medicine, 301 East 17th Street, Suite 1612A, NY 10003, USA
| | - Cassidy Alexandre
- Department of Cardiothoracic Surgery, NYU School of Medicine, 550 First Avenue, NY 10016, USA
| | - Cristina Valacca
- Department of Cardiothoracic Surgery, NYU School of Medicine, 550 First Avenue, NY 10016, USA
| | - Shuai Zheng
- Department of Cardiothoracic Surgery, NYU School of Medicine, 550 First Avenue, NY 10016, USA
| | - Sarina Meikle
- Department of Cardiothoracic Surgery, NYU School of Medicine, 550 First Avenue, NY 10016, USA
| | | | - Evelyne Tassone
- Department of Cardiothoracic Surgery, NYU School of Medicine, 550 First Avenue, NY 10016, USA
| | - Qing Yang
- Department of Medicine, Division of Rheumatology, NYU School of Medicine, 301 East 17th Street, Suite 1612A, NY 10003, USA
| | - Victoria Kolupaeva
- Department of Microbiology, NYU School of Medicine, 550 First Avenue, NY 10016, USA
| | - Shoshana Yakar
- Department of Basic Science & Craniofacial Biology, NYU College of Dentistry, 345 E. 24th Street, NY 10010, USA
| | - Steven Abramson
- Department of Medicine, Division of Rheumatology, NYU School of Medicine, 301 East 17th Street, Suite 1612A, NY 10003, USA
| | - Paolo Mignatti
- Department of Medicine, Division of Rheumatology, NYU School of Medicine, 301 East 17th Street, Suite 1612A, NY 10003, USA
- Department of Cardiothoracic Surgery, NYU School of Medicine, 550 First Avenue, NY 10016, USA
- Department of Cell Biology, NYU School of Medicine, 550 First Avenue, NY 10016, USA
- Corresponding author
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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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42
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Buday L, Vas V. Novel regulation of Ras proteins by direct tyrosine phosphorylation and dephosphorylation. Cancer Metastasis Rev 2020; 39:1067-1073. [PMID: 32936431 PMCID: PMC7680326 DOI: 10.1007/s10555-020-09918-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 06/19/2020] [Indexed: 12/01/2022]
Abstract
Somatic mutations in the RAS genes are frequent in human tumors, especially in pancreatic, colorectal, and non-small-cell lung cancers. Such mutations generally decrease the ability of Ras to hydrolyze GTP, maintaining the protein in a constitutively active GTP-bound form that drives uncontrolled cell proliferation. Efforts to develop drugs that target Ras oncoproteins have been unsuccessful. Recent emerging data suggest that Ras regulation is more complex than the scientific community has believed for decades. In this review, we summarize advances in the "textbook" view of Ras activation. We also discuss a novel type of Ras regulation that involves direct phosphorylation and dephosphorylation of Ras tyrosine residues. The discovery that pharmacological inhibition of the tyrosine phosphoprotein phosphatase SHP2 maintains mutant Ras in an inactive state suggests that SHP2 could be a novel drug target for the treatment of Ras-driven human cancers.
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Affiliation(s)
- László Buday
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary.
- Department of Medical Chemistry, Semmelweis University Medical School, Budapest, 1094, Hungary.
| | - Virág Vas
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary
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43
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Abstract
RAS was identified as a human oncogene in the early 1980s and subsequently found to be mutated in nearly 30% of all human cancers. More importantly, RAS plays a central role in driving tumor development and maintenance. Despite decades of effort, there remain no FDA approved drugs that directly inhibit RAS. The prevalence of RAS mutations in cancer and the lack of effective anti-RAS therapies stem from RAS' core role in growth factor signaling, unique structural features, and biochemistry. However, recent advances have brought promising new drugs to clinical trials and shone a ray of hope in the field. Here, we will exposit the details of RAS biology that illustrate its key role in cell signaling and shed light on the difficulties in therapeutically targeting RAS. Furthermore, past and current efforts to develop RAS inhibitors will be discussed in depth.
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Affiliation(s)
- J Matthew Rhett
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States
| | - Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States.
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44
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Valencia-Sama I, Ladumor Y, Kee L, Adderley T, Christopher G, Robinson CM, Kano Y, Ohh M, Irwin MS. NRAS Status Determines Sensitivity to SHP2 Inhibitor Combination Therapies Targeting the RAS-MAPK Pathway in Neuroblastoma. Cancer Res 2020; 80:3413-3423. [PMID: 32586982 DOI: 10.1158/0008-5472.can-19-3822] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/08/2020] [Accepted: 06/22/2020] [Indexed: 11/16/2022]
Abstract
Survival for high-risk neuroblastoma remains poor and treatment for relapsed disease rarely leads to long-term cures. Large sequencing studies of neuroblastoma tumors from diagnosis have not identified common targetable driver mutations other than the 10% of tumors that harbor mutations in the anaplastic lymphoma kinase (ALK) gene. However, at neuroblastoma recurrence, more frequent mutations in genes in the RAS-MAPK pathway have been detected. The PTPN11-encoded tyrosine phosphatase SHP2 is an activator of the RAS pathway, and we and others have shown that pharmacologic inhibition of SHP2 suppresses the growth of various tumor types harboring KRAS mutations such as pancreatic and lung cancers. Here we report inhibition of growth and downstream RAS-MAPK signaling in neuroblastoma cells in response to treatment with the SHP2 inhibitors SHP099, II-B08, and RMC-4550. However, neuroblastoma cell lines harboring endogenous NRAS Q61K mutation (which is commonly detected at relapse) or isogenic neuroblastoma cells engineered to overexpress NRASQ61K were distinctly resistant to SHP2 inhibitors. Combinations of SHP2 inhibitors with other RAS pathway inhibitors such as trametinib, vemurafenib, and ulixertinib were synergistic and reversed resistance to SHP2 inhibition in neuroblastoma in vitro and in vivo. These results suggest for the first time that combination therapies targeting SHP2 and other components of the RAS-MAPK pathway may be effective against conventional therapy-resistant relapsed neuroblastoma, including those that have acquired NRAS mutations. SIGNIFICANCE: These findings suggest that conventional therapy-resistant, relapsed neuroblastoma may be effectively treated via combined inhibition of SHP2 and MEK or ERK of the RAS-MAPK pathway.
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Affiliation(s)
- Ivette Valencia-Sama
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Yagnesh Ladumor
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Lynn Kee
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Teresa Adderley
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | | | - Claire M Robinson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Yoshihito Kano
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada.,Department of Clinical Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada. .,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Meredith S Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada. .,Cell Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Pediatrics, The Hospital for Sick Children, Toronto, Canada
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45
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Washington C, Chernet R, Gokhale RH, Martino-Cortez Y, Liu HY, Rosenberg AM, Shahar S, Pfleger CM. A conserved, N-terminal tyrosine signal directs Ras for inhibition by Rabex-5. PLoS Genet 2020; 16:e1008715. [PMID: 32559233 PMCID: PMC7329146 DOI: 10.1371/journal.pgen.1008715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 07/01/2020] [Accepted: 03/13/2020] [Indexed: 01/08/2023] Open
Abstract
Dysregulation of the Ras oncogene in development causes developmental disorders, "Rasopathies," whereas mutational activation or amplification of Ras in differentiated tissues causes cancer. Rabex-5 (also called RabGEF1) inhibits Ras by promoting Ras mono- and di-ubiquitination. We report here that Rabex-5-mediated Ras ubiquitination requires Ras Tyrosine 4 (Y4), a site of known phosphorylation. Ras substitution mutants insensitive to Y4 phosphorylation did not undergo Rabex-5-mediated ubiquitination in cells and exhibited Ras gain-of-function phenotypes in vivo. Ras Y4 phosphomimic substitution increased Rabex-5-mediated ubiquitination in cells. Y4 phosphomimic substitution in oncogenic Ras blocked the morphological phenotypes associated with oncogenic Ras in vivo dependent on the presence of Rabex-5. We developed polyclonal antibodies raised against an N-terminal Ras peptide phosphorylated at Y4. These anti-phospho-Y4 antibodies showed dramatic recognition of recombinant wild-type Ras and RasG12V proteins when incubated with JAK2 or SRC kinases but not of RasY4F or RasY4F,G12V recombinant proteins suggesting that JAK2 and SRC could promote phosphorylation of Ras proteins at Y4 in vitro. Anti-phospho-Y4 antibodies also showed recognition of RasG12V protein, but not wild-type Ras, when incubated with EGFR. A role for JAK2, SRC, and EGFR (kinases with well-known roles to activate signaling through Ras), to promote Ras Y4 phosphorylation could represent a feedback mechanism to limit Ras activation and thus establish Ras homeostasis. Notably, rare variants of Ras at Y4 have been found in cerebellar glioblastomas. Therefore, our work identifies a physiologically relevant Ras ubiquitination signal and highlights a requirement for Y4 for Ras inhibition by Rabex-5 to maintain Ras pathway homeostasis and to prevent tissue transformation.
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Affiliation(s)
- Chalita Washington
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Rachel Chernet
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Rewatee H. Gokhale
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yesenia Martino-Cortez
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Hsiu-Yu Liu
- Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ashley M. Rosenberg
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Columbia University, New York, New York, United States of America
| | - Sivan Shahar
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- New York Medical College, Valhalla, New York, United States of America
| | - Cathie M. Pfleger
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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46
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Mo GCH, Posner C, Rodriguez EA, Sun T, Zhang J. A rationally enhanced red fluorescent protein expands the utility of FRET biosensors. Nat Commun 2020; 11:1848. [PMID: 32296061 PMCID: PMC7160135 DOI: 10.1038/s41467-020-15687-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/20/2020] [Indexed: 11/30/2022] Open
Abstract
Genetically encoded Förster Resonance Energy Transfer (FRET)-based biosensors are powerful tools to illuminate spatiotemporal regulation of cell signaling in living cells, but the utility of the red spectrum for biosensing was limited due to a lack of bright and stable red fluorescent proteins. Here, we rationally improve the photophysical characteristics of the coral-derived fluorescent protein TagRFP-T. We show that a new single-residue mutant, super-TagRFP (stagRFP) has nearly twice the molecular brightness of TagRFP-T and negligible photoactivation. stagRFP facilitates significant improvements on multiple green-red biosensors as a FRET acceptor and is an efficient FRET donor that supports red/far-red FRET biosensing. Capitalizing on the ability of stagRFP to couple with multiple FRET partners, we develop a novel multiplex method to examine the confluence of signaling activities from three kinases simultaneously in single living cells, providing evidence for a role of Src family kinases in regulating growth factor induced Akt and ERK activities.
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Affiliation(s)
- Gary C H Mo
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Clara Posner
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Erik A Rodriguez
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Tengqian Sun
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
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A Non-Canonical Calmodulin Target Motif Comprising a Polybasic Region and Lipidated Terminal Residue Regulates Localization. Int J Mol Sci 2020; 21:ijms21082751. [PMID: 32326637 PMCID: PMC7216078 DOI: 10.3390/ijms21082751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 12/12/2022] Open
Abstract
Calmodulin (CaM) is a Ca2+-sensor that regulates a wide variety of target proteins, many of which interact through short basic helical motifs bearing two hydrophobic ‘anchor’ residues. CaM comprises two globular lobes, each containing a pair of EF-hand Ca2+-binding motifs that form a Ca2+-induced hydrophobic pocket that binds an anchor residue. A central flexible linker allows CaM to accommodate diverse targets. Several reported CaM interactors lack these anchors but contain Lys/Arg-rich polybasic sequences adjacent to a lipidated N- or C-terminus. Ca2+-CaM binds the myristoylated N-terminus of CAP23/NAP22 with intimate interactions between the lipid and a surface comprised of the hydrophobic pockets of both lobes, while the basic residues make electrostatic interactions with the negatively charged surface of CaM. Ca2+-CaM binds farnesylcysteine, derived from the farnesylated polybasic C-terminus of KRAS4b, with the lipid inserted into the C-terminal lobe hydrophobic pocket. CaM sequestration of the KRAS4b farnesyl moiety disrupts KRAS4b membrane association and downstream signaling. Phosphorylation of basic regions of N-/C-terminal lipidated CaM targets can reduce affinity for both CaM and the membrane. Since both N-terminal myristoylated and C-terminal prenylated proteins use a Singly Lipidated Polybasic Terminus (SLIPT) for CaM binding, we propose these polybasic lipopeptide elements comprise a non-canonical CaM-binding motif.
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Wong RW, Balachandran A, Cheung PK, Cheng R, Pan Q, Stoilov P, Harrigan PR, Blencowe BJ, Branch DR, Cochrane A. An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing. PLoS Pathog 2020; 16:e1008307. [PMID: 32069328 PMCID: PMC7048317 DOI: 10.1371/journal.ppat.1008307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/28/2020] [Accepted: 01/06/2020] [Indexed: 12/17/2022] Open
Abstract
The ability of HIV-1 to evolve resistance to combined antiretroviral therapies (cARTs) has stimulated research into alternative means of controlling this infection. We assayed >60 modulators of RNA alternative splicing (AS) to identify new inhibitors of HIV-1 RNA processing-a segment of the viral lifecycle not targeted by current drugs-and discovered compound N-[4-chloro-3-(trifluoromethyl)phenyl]-7-nitro-2,1,3-benzoxadiazol-4-amine (5342191) as a potent inhibitor of both wild-type (Ba-L, NL4-3, LAI, IIIB, and N54) and drug-resistant strains of HIV-1 (IC50: ~700 nM) with no significant effect on cell viability at doses tested. 5342191 blocks expression of four essential HIV-1 structural and regulatory proteins (Gag, Env, Tat, and Rev) without affecting total protein synthesis of the cell. This response is associated with altered unspliced (US) and singly-spliced (SS) HIV-1 RNA accumulation (~60% reduction) and transport to the cytoplasm (loss of Rev) whereas parallel analysis of cellular RNAs revealed less than a 0.7% of host alternative splicing (AS) events (0.25-0.67% by ≥ 10-20%), gene expression (0.01-0.46% by ≥ 2-5 fold), and protein abundance (0.02-0.34% by ≥ 1.5-2 fold) being affected. Decreased expression of Tat, but not Gag/Env, upon 5342191 treatment was reversed by a proteasome inhibitor, suggesting that this compound alters the synthesis/degradation of this key viral factor. Consistent with an affect on HIV-1 RNA processing, 5342191 treatment of cells altered the abundance and phosphorylation of serine/arginine-rich splicing factor (SRSF) 1, 3, and 4. Despite the activation of several intracellular signaling pathways by 5342191 (Ras, MEK1/2-ERK1/2, and JNK1/2/3), inhibition of HIV-1 gene expression by this compound could be reversed by pre-treatment with either a G-protein α-subunit inhibitor or two different MEK1/2 inhibitors. These observations demonstrate enhanced sensitivity of HIV-1 gene expression to small changes in host RNA processing and highlights the potential of modulating host intracellular signaling as an alternative approach for controlling HIV-1 infection.
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Affiliation(s)
- Raymond W. Wong
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ahalya Balachandran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Peter K. Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Ran Cheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Qun Pan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Peter Stoilov
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Benjamin J. Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Donald R. Branch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Advanced Diagnostics, Infection and Immunity Group, Toronto General Hospital Research Institute, Toronto, Ontario, Canada
- Centre for Innovation, Canadian Blood Services, Toronto, Ontario, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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Khan I, Rhett JM, O'Bryan JP. Therapeutic targeting of RAS: New hope for drugging the "undruggable". BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118570. [PMID: 31678118 PMCID: PMC6937383 DOI: 10.1016/j.bbamcr.2019.118570] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/01/2019] [Accepted: 10/14/2019] [Indexed: 12/18/2022]
Abstract
RAS is the most frequently mutated oncogene in cancer and a critical driver of oncogenesis. Therapeutic targeting of RAS has been a goal of cancer research for more than 30 years due to its essential role in tumor formation and maintenance. Yet the quest to inhibit this challenging foe has been elusive. Although once considered "undruggable", the struggle to directly inhibit RAS has seen recent success with the development of pharmacological agents that specifically target the KRAS(G12C) mutant protein, which include the first direct RAS inhibitor to gain entry to clinical trials. However, the limited applicability of these inhibitors to G12C-mutant tumors demands further efforts to identify more broadly efficacious RAS inhibitors. Understanding allosteric influences on RAS may open new avenues to inhibit RAS. Here, we provide a brief overview of RAS biology and biochemistry, discuss the allosteric regulation of RAS, and summarize the various approaches to develop RAS inhibitors.
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Affiliation(s)
- Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States of America; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, United States of America
| | - J Matthew Rhett
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States of America; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, United States of America
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States of America; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, United States of America.
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Parker MI, Nikonova AS, Sun D, Golemis EA. Proliferative signaling by ERBB proteins and RAF/MEK/ERK effectors in polycystic kidney disease. Cell Signal 2019; 67:109497. [PMID: 31830556 DOI: 10.1016/j.cellsig.2019.109497] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 12/24/2022]
Abstract
A primary pathological feature of polycystic kidney disease (PKD) is the hyperproliferation of epithelial cells in renal tubules, resulting in formation of fluid-filled cysts. The proliferative aspects of the two major forms of PKD-autosomal dominant PKD (ADPKD), which arises from mutations in the polycystins PKD1 and PKD2, and autosomal recessive PKD (ARPKD), which arises from mutations in PKHD1-has encouraged investigation into protein components of the core cell proliferative machinery as potential drivers of PKD pathogenesis. In this review, we examine the role of signaling by ERBB proteins and their effectors, with a primary focus on ADPKD. The ERBB family of receptor tyrosine kinases (EGFR/ERBB1, HER2/ERBB2, ERBB3, and ERBB4) are activated by extracellular ligands, inducing multiple pro-growth signaling cascades; among these, activation of signaling through the RAS GTPase, and the RAF, MEK1/2, and ERK1/2 kinases enhance cell proliferation and restrict apoptosis during renal tubuloepithelial cyst formation. Characteristics of PKD include overexpression and mislocalization of the ERBB receptors and ligands, leading to enhanced activation and increased activity of downstream signaling proteins. The altered regulation of ERBBs and their effectors in PKD is influenced by enhanced activity of SRC kinase, which is promoted by the loss of cytoplasmic Ca2+ and an increase in cAMP-dependent PKA kinase activity that stimulates CFTR, driving the secretory phenotype of ADPKD. We discuss the interplay between ERBB/SRC signaling, and polycystins and their depending signaling, with emphasis on thes changes that affect cell proliferation in cyst expansion, as well as the inflammation-associated fibrogenesis, which characterizes progressive disease. We summarize the current progress of preclinical and clinical trials directed at inhibiting this signaling axis, and discuss potential future strategies that may be productive for controlling PKD.
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Affiliation(s)
- Mitchell I Parker
- Program in Molecular Therapeutics, Fox Chase Cancer Center, 19111, USA; Molecular & Cell Biology & Genetics (MCBG) Program, Drexel University College of Medicine, 19102, USA
| | - Anna S Nikonova
- Program in Molecular Therapeutics, Fox Chase Cancer Center, 19111, USA
| | - Danlin Sun
- Program in Molecular Therapeutics, Fox Chase Cancer Center, 19111, USA; Institute of Life Science, Jiangsu University, Jingkou District, Zhenjiang, Jiangsu 212013, China
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, 19111, USA.
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