1
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Aravind A, Nandakumar R, Ahmed M, Nisar M, Palollathil A, Kanichery A, Sreelan S, Sinan KM, Balaya RDA, Vijayakumar M, Prasad TSK, Raju R. REMEMProt: a resource of membrane-enriched proteome profiles, their disease associations, and biomarker status. Life Sci Alliance 2024; 7:e202302443. [PMID: 38719747 PMCID: PMC11077588 DOI: 10.26508/lsa.202302443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
The differential expression of plasma membrane proteins is integrally analyzed for their diagnosis, prognosis, and therapeutic applications in diverse clinical manifestations. Necessarily, distinct membrane protein enrichment methods and mass spectrometry platforms are employed for their global and relative quantitation. First of its kind to explore, we compiled membrane-associated proteomes in human and mouse systems into a database named, Resource of Experimental Membrane-Enriched Mass spectrometry-derived Proteome (REMEMProt). It currently hosts 14,626 proteins (9,507 proteins in Homo sapiens; 5,119 proteins in Mus musculus) with information on their membrane-protein enrichment methods, experimental/physiological context of detection in cells or tissues, transmembrane domain analysis, and their current attribution as biomarkers. Based on these annotations and the transmembrane domain analysis in proteins or their binary/complex protein-protein interactors, REMEMProt facilitates the assessment of the plasma membrane localization potential of proteins through batch query. A cross-study enrichment analysis platform is enabled in REMEMProt for comparative analysis of proteomes using novel/modified membrane enrichment methods and evaluation of methods for targeted enrichment of membrane proteins. REMEMProt data are made freely accessible to explore and download at https://rememprot.ciods.in/.
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Affiliation(s)
- Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Revathy Nandakumar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Mukhtar Ahmed
- https://ror.org/02f81g417 Department of Zoology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, India
| | - Akhina Palollathil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Anagha Kanichery
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sourav Sreelan
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, India
- Yenepoya Institute of Technology, Yenepoya (Deemed to be University), Mangalore, India
| | - Kp Munavvar Sinan
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, India
- Yenepoya Institute of Technology, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Manavalan Vijayakumar
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, India
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2
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Hussain MS, Moglad E, Afzal M, Bansal P, Kaur H, Deorari M, Ali H, Shahwan M, Hassan Almalki W, Kazmi I, Alzarea SI, Singh SK, Dua K, Gupta G. Circular RNAs in the KRAS pathway: Emerging players in cancer progression. Pathol Res Pract 2024; 256:155259. [PMID: 38503004 DOI: 10.1016/j.prp.2024.155259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
Circular RNAs (circRNAs) have been recognized as key components in the intricate regulatory network of the KRAS pathway across various cancers. The KRAS pathway, a central signalling cascade crucial in tumorigenesis, has gained substantial emphasis as a possible therapeutic target. CircRNAs, a subgroup of non-coding RNAs known for their closed circular arrangement, play diverse roles in gene regulation, contributing to the intricate landscape of cancer biology. This review consolidates existing knowledge on circRNAs within the framework of the KRAS pathway, emphasizing their multifaceted functions in cancer progression. Notable circRNAs, such as Circ_GLG1 and circITGA7, have been identified as pivotal regulators in colorectal cancer (CRC), influencing KRAS expression and the Ras signaling pathway. Aside from their significance in gene regulation, circRNAs contribute to immune evasion, apoptosis, and drug tolerance within KRAS-driven cancers, adding complexity to the intricate interplay. While our comprehension of circRNAs in the KRAS pathway is evolving, challenges such as the diverse landscape of KRAS mutant tumors and the necessity for synergistic combination therapies persist. Integrating cutting-edge technologies, including deep learning-based prediction methods, holds the potential for unveiling disease-associated circRNAs and identifying novel therapeutic targets. Sustained research efforts are crucial to comprehensively unravel the molecular mechanisms governing the intricate interplay between circRNAs and the KRAS pathway, offering insights that could potentially revolutionize cancer diagnostics and treatment strategies.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, Jaipur, Rajasthan 302017, India
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Bengaluru, Karnataka 560069, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh 247341, India; Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand 831001, India
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Moyad Shahwan
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates; Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman 346, United Arab Emirates
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology, Ultimo, Sydney, NSW 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology, Ultimo, Sydney, NSW 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology, Ultimo, Sydney, NSW 2007, Australia
| | - Gaurav Gupta
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India.
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3
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Pehkonen H, Filippou A, Väänänen J, Lindfors I, Vänttinen M, Ianevski P, Mäkelä A, Munne P, Klefström J, Toppila‐Salmi S, Grénman R, Hagström J, Mäkitie AA, Karhemo P, Monni O. Liprin-α1 contributes to oncogenic MAPK signaling by counteracting ERK activity. Mol Oncol 2024; 18:662-676. [PMID: 38264964 PMCID: PMC10920090 DOI: 10.1002/1878-0261.13593] [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: 07/05/2023] [Revised: 12/15/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024] Open
Abstract
PTPRF interacting protein alpha 1 (PPFIA1) encodes for liprin-α1, a member of the leukocyte common antigen-related protein tyrosine phosphatase (LAR-RPTPs)-interacting protein family. Liprin-α1 localizes to adhesive and invasive structures in the periphery of cancer cells, where it modulates migration and invasion in head and neck squamous cell carcinoma (HNSCC) and breast cancer. To study the possible role of liprin-α1 in anticancer drug responses, we screened a library of oncology compounds in cell lines with high endogenous PPFIA1 expression. The compounds with the highest differential responses between high PPFIA1-expressing and silenced cells across cell lines were inhibitors targeting mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinases (ERK) signaling. KRAS proto-oncogene, GTPase (KRAS)-mutated MDA-MB-231 cells were more resistant to trametinib upon PPFIA1 knockdown compared with control cells. In contrast, liprin-α1-depleted HNSCC cells with low RAS activity showed a context-dependent response to MEK/ERK inhibitors. Importantly, we showed that liprin-α1 depletion leads to increased p-ERK1/2 levels in all our studied cell lines independent of KRAS mutational status, suggesting a role of liprin-α1 in the regulation of MAPK oncogenic signaling. Furthermore, liprin-α1 depletion led to more pronounced redistribution of RAS proteins to the cell membrane. Our data suggest that liprin-α1 is an important contributor to oncogenic RAS/MAPK signaling, and the status of liprin-α1 may assist in predicting drug responses in cancer cells in a context-dependent manner.
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Affiliation(s)
- Henna Pehkonen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Artemis Filippou
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Juho Väänänen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Iida Lindfors
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Mira Vänttinen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Philipp Ianevski
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiFinland
| | - Anne Mäkelä
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Pauliina Munne
- Finnish Cancer Institute, FICAN South Helsinki University Hospital & Translational Cancer Medicine, Medical FacultyUniversity of HelsinkiFinland
| | - Juha Klefström
- Finnish Cancer Institute, FICAN South Helsinki University Hospital & Translational Cancer Medicine, Medical FacultyUniversity of HelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
| | - Sanna Toppila‐Salmi
- Skin and Allergy HospitalHelsinki University Hospital and University of HelsinkiFinland
- Department of Otorhinolaryngology, Kuopio University Hospital and School of Medicine, Institute of Clinical MedicineUniversity of Eastern FinlandKuopioFinland
| | - Reidar Grénman
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of Turku and Turku University HospitalFinland
| | - Jaana Hagström
- Department of PathologyUniversity of Helsinki and Helsinki University HospitalFinland
- Institute of DentistryUniversity of TurkuFinland
| | - Antti A. Mäkitie
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
- Department of Otorhinolaryngology‐Head and Neck Surgery, Research Program in Systems OncologyUniversity of Helsinki and Helsinki University HospitalFinland
| | - Piia‐Riitta Karhemo
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
| | - Outi Monni
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
- Department of Oncology, Faculty of MedicineUniversity of HelsinkiFinland
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4
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Hu M, Li H, Zhu K, Guo L, Zhao M, Zhan H, Devreotes PN, Qing Q. Electric field modulation of ERK dynamics shows dependency on waveform and timing. Sci Rep 2024; 14:3167. [PMID: 38326365 PMCID: PMC10850077 DOI: 10.1038/s41598-024-53018-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
Different exogenous electric fields (EF) can guide cell migration, disrupt proliferation, and program cell development. Studies have shown that many of these processes were initiated at the cell membrane, but the mechanism has been unclear, especially for conventionally non-excitable cells. In this study, we focus on the electrostatic aspects of EF coupling with the cell membrane by eliminating Faradaic processes using dielectric-coated microelectrodes. Our data unveil a distinctive biphasic response of the ERK signaling pathway of epithelial cells (MCF10A) to alternate current (AC) EF. The ERK signal exhibits both inhibition and activation phases, with the former triggered by a lower threshold of AC EF, featuring a swifter peaking time and briefer refractory periods than the later-occurring activation phase, induced at a higher threshold. Interestingly, the biphasic ERK responses are sensitive to the waveform and timing of EF stimulation pulses, depicting the characteristics of electrostatic and dissipative interactions. Blocker tests and correlated changes of active Ras on the cell membrane with ERK signals indicated that both EGFR and Ras were involved in the rich ERK dynamics induced by EF. We propose that the frequency-dependent dielectric relaxation process could be an important mechanism to couple EF energy to the cell membrane region and modulate membrane protein-initiated signaling pathways, which can be further explored to precisely control cell behavior and fate with high temporal and spatial resolution.
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Affiliation(s)
- Minxi Hu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Houpu Li
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Kan Zhu
- Department of Dermatology, University of California, Davis, CA, 95616, USA
| | - Liang Guo
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Min Zhao
- Department of Dermatology, University of California, Davis, CA, 95616, USA
- Department of Ophthalmology and Vision Science, University of California, Davis, CA, 95616, USA
| | - Huiwang Zhan
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Peter N Devreotes
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Quan Qing
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA.
- Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.
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5
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Bteich F, Mohammadi M, Li T, Bhat MA, Sofianidi A, Wei N, Kuang C. Targeting KRAS in Colorectal Cancer: A Bench to Bedside Review. Int J Mol Sci 2023; 24:12030. [PMID: 37569406 PMCID: PMC10418782 DOI: 10.3390/ijms241512030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease with a myriad of alterations at the cellular and molecular levels. Kristen rat sarcoma (KRAS) mutations occur in up to 40% of CRCs and serve as both a prognostic and predictive biomarker. Oncogenic mutations in the KRAS protein affect cellular proliferation and survival, leading to tumorigenesis through RAS/MAPK pathways. Until recently, only indirect targeting of the pathway had been investigated. There are now several KRAS allele-specific inhibitors in late-phase clinical trials, and many newer agents and targeting strategies undergoing preclinical and early-phase clinical testing. The adequate treatment of KRAS-mutated CRC will inevitably involve combination therapies due to the existence of robust adaptive resistance mechanisms in these tumors. In this article, we review the most recent understanding and findings related to targeting KRAS mutations in CRC, mechanisms of resistance to KRAS inhibitors, as well as evolving treatment strategies for KRAS-mutated CRC patients.
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Affiliation(s)
- Fernand Bteich
- Department of Medical Oncology, Montefiore Medical Center, Bronx, NY 10467, USA;
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
| | - Mahshid Mohammadi
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Terence Li
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Muzaffer Ahmed Bhat
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amalia Sofianidi
- Oncology Unit, Third Department of Internal Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Ning Wei
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Chaoyuan Kuang
- Department of Medical Oncology, Montefiore Medical Center, Bronx, NY 10467, USA;
- Department of Medical Oncology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (M.M.); (T.L.); (M.A.B.); (N.W.)
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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6
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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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7
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Rosen JC, Sacher A, Tsao MS. Direct GDP-KRAS G12C inhibitors and mechanisms of resistance: the tip of the iceberg. Ther Adv Med Oncol 2023; 15:17588359231160141. [PMID: 36950276 PMCID: PMC10026147 DOI: 10.1177/17588359231160141] [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: 10/08/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog mutations are observed in 25% of lung adenocarcinoma and 40% of these are G12C mutations. Historically, no approved targeted agents were available for patients with any KRAS mutation, and response rates to standard-of-care therapies were suboptimal. Newly developed inhibitors directed toward KRASG12C have been successful in clinical trials with overall response rates ranging between 32% and 46%, and two FDA approvals were granted in May 2021 and December 2022 as second-line or later monotherapies. However, rapid tumor resistance complicates their use as a monotherapy. With the rapid development of this novel class of inhibitors, it is important to discern the different types of tumor resistance that may arise and how each can differently contribute to tumor growth and survival. G12C inhibitor resistance is under investigation and combinations of therapies with G12C inhibitors have been proposed. Much of this insight is gleaned from preclinical investigations, as our knowledge of clinical resistance is in its infancy. In this review, we summarize the preclinical development of KRASG12C inhibitors, their clinical evaluations, different types of resistance mechanisms to these compounds, and ways of overcoming them. Finally, we underscore the importance of basic and translational investigations of these molecules in a landscape where their clinical evaluations garner the most attention, and we set the stage for what is to come.
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Affiliation(s)
- Joshua C. Rosen
- Princess Margaret Hospital Cancer Centre,
University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and
Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto,
ON, Canada
| | - Adrian Sacher
- Princess Margaret Hospital Cancer Centre,
University Health Network, Toronto, ON, Canada
- Division of Medical Oncology, Department of
Medicine, Princess Margaret Cancer Centre, Temerty Faculty of Medicine,
University of Toronto, Toronto, ON, Canada
- Department of Immunology, Temerty Faculty of
Medicine, University of Toronto, Toronto, ON, Canada
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8
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Volmar AY, Guterres H, Zhou H, Reid D, Pavlopoulos S, Makowski L, Mattos C. Mechanisms of isoform-specific residue influence on GTP-bound HRas, KRas, and NRas. Biophys J 2022; 121:3616-3629. [PMID: 35794829 PMCID: PMC9617160 DOI: 10.1016/j.bpj.2022.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/04/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
HRas, KRas, and NRas are GTPases with a common set of effectors that control many cell-signaling pathways, including proliferation through Raf kinase. Their G-domains are nearly identical in sequence, with a few isoform-specific residues that have an effect on dynamics and biochemical properties. Here, we use accelerated molecular dynamics (aMD) simulations consistent with solution x-ray scattering experiments to elucidate mechanisms through which isoform-specific residues associated with each Ras isoform affects functionally important regions connected to the active site. HRas-specific residues cluster in loop 8 to stabilize the nucleotide-binding pocket, while NRas-specific residues on helix 3 directly affect the conformations of switch I and switch II. KRas, the most globally flexible of the isoforms, shows greatest fluctuations in the switch regions enhanced by a KRas-specific residue in loop 7 and a highly dynamic loop 8 region. The analysis of isoform-specific residue effects on Ras proteins is supported by NMR experiments and is consistent with previously published biochemical data.
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Affiliation(s)
- Alicia Y Volmar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Hugo Guterres
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Hao Zhou
- Department of Electrical and Computing Engineering, Northeastern University, Boston, Massachusetts
| | - Derion Reid
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Spiro Pavlopoulos
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts
| | - Lee Makowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts; Department of Bioengineering, Northeastern University, Boston, Massachusetts
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.
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9
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Lu H, Martí J. Predicting the conformational variability of oncogenic GTP-bound G12D mutated KRas-4B proteins at zwitterionic model cell membranes. NANOSCALE 2022; 14:3148-3158. [PMID: 35142321 DOI: 10.1039/d1nr07622a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
KRas proteins are the largest family of mutated Ras isoforms, participating in a wide variety of cancers. Due to their importance, large effort is being carried out on drug development by small-molecule inhibitors. However, understanding protein conformational variability remains a challenge in drug discovery. In the case of the Ras family, their multiple conformational states can affect the binding of potential drug inhibitors. To overcome this challenge, we propose a computational framework based on combined all-atom Molecular Dynamics and Metadynamics simulations in order to accurately access conformational variants of the target protein. We tested the methodology using a G12D mutated GTP bound oncogenic KRas-4B protein located at the interface of a DOPC/DOPS/cholesterol model anionic cell membrane. Two main orientations of KRas-4B at the anionic membrane have been determined. The corresponding torsional angles are taken as reliable reaction coordinates so that free-energy landscapes are obtained by well-tempered metadynamics simulations, revealing local and global minima of the free-energy hypersurface and unveiling reactive paths of the system between the two preferential orientations. We have observed that GTP-binding to KRas-4B has huge influence on the stabilisation of the protein and it can potentially help to open Switch I/II druggable pockets, lowering energy barriers between stable states and resulting in cumulative conformers of KRas-4B. This may highlight new opportunities for targeting the unique meta-stable states through the design of new efficient drugs.
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Affiliation(s)
- Huixia Lu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
| | - Jordi Martí
- Department of Physics, Polytechnical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
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10
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Mu H, Zeng Y, Zhuang Y, Gao W, Zhou Y, Rajalingam K, Zhao W. Patterning of Oncogenic Ras Clustering in Live Cells Using Vertically Aligned Nanostructure Arrays. NANO LETTERS 2022; 22:1007-1016. [PMID: 35044178 DOI: 10.1021/acs.nanolett.1c03886] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As a dominant oncogenic protein, Ras is well-known to segregate into clusters on the plasma membrane for activating downstream signaling. However, current technologies for direct measurements of Ras clustering are limited to sophisticated high-resolution techniques like electron microscopy and fluorescence lifetime imaging. To further promote fundamental investigations and the related drug development, we hereby introduce a nanobar-based platform which effectively guides Ras clusters into quantifiable patterns in live cells that is resolvable under conventional microscopy. Major Ras isoforms, K-Ras, H-Ras, and N-Ras, were differentiated, as well as their highly prevalent oncogenic mutants G12V and G13D. Moreover, the isoform specificity and the sensitivity of a Ras inhibitor were successfully characterized on nanobars. We envision that this nanobar-based platform will serve as an effective tool to read Ras clustering on the plasma membrane, enabling a novel avenue both to decipher Ras regulations and to facilitate anti-Ras drug development.
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Affiliation(s)
- Huanwen Mu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore
- Ageing Research Institute for Society and Education, Nanyang Technological University, Singapore 637335, Singapore
| | - Yongpeng Zeng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore
| | - Yinyin Zhuang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore
| | - Weibo Gao
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- The Photonics Institute and Centre for Disruptive Photonic Technologies, Nanyang Technological University, Singapore 637371, Singapore
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center, Houston, Texas 77030, United States
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, United States
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
- University Cancer Center Mainz, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Wenting Zhao
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore
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11
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Ozdemir ES, Koester AM, Nan X. Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Genes (Basel) 2022; 13:219. [PMID: 35205266 PMCID: PMC8872464 DOI: 10.3390/genes13020219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Formation of Ras multimers, including dimers and nanoclusters, has emerged as an exciting, new front of research in the 'old' field of Ras biomedicine. With significant advances made in the past few years, we are beginning to understand the structure of Ras multimers and, albeit preliminary, mechanisms that regulate their formation in vitro and in cells. Here we aim to synthesize the knowledge accrued thus far on Ras multimers, particularly the presence of multiple globular (G-) domain interfaces, and discuss how membrane nanodomain composition and structure would influence Ras multimer formation. We end with some general thoughts on the potential implications of Ras multimers in basic and translational biology.
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Affiliation(s)
- E. Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
| | - Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
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12
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Components of the phosphatidylserine endoplasmic reticulum to plasma membrane transport mechanism as targets for KRAS inhibition in pancreatic cancer. Proc Natl Acad Sci U S A 2021; 118:2114126118. [PMID: 34903667 DOI: 10.1073/pnas.2114126118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
KRAS is mutated in 90% of human pancreatic ductal adenocarcinomas (PDACs). To function, KRAS must localize to the plasma membrane (PM) via a C-terminal membrane anchor that specifically engages phosphatidylserine (PtdSer). This anchor-binding specificity renders KRAS-PM localization and signaling capacity critically dependent on PM PtdSer content. We now show that the PtdSer lipid transport proteins, ORP5 and ORP8, which are essential for maintaining PM PtdSer levels and hence KRAS PM localization, are required for KRAS oncogenesis. Knockdown of either protein, separately or simultaneously, abrogated growth of KRAS-mutant but not KRAS-wild-type pancreatic cancer cell xenografts. ORP5 or ORP8 knockout also abrogated tumor growth in an immune-competent orthotopic pancreatic cancer mouse model. Analysis of human datasets revealed that all components of this PtdSer transport mechanism, including the PM-localized EFR3A-PI4KIIIα complex that generates phosphatidylinositol-4-phosphate (PI4P), and endoplasmic reticulum (ER)-localized SAC1 phosphatase that hydrolyzes counter transported PI4P, are significantly up-regulated in pancreatic tumors compared to normal tissue. Taken together, these results support targeting PI4KIIIα in KRAS-mutant cancers to deplete the PM-to-ER PI4P gradient, reducing PM PtdSer content. We therefore repurposed the US Food and Drug Administration-approved hepatitis C antiviral agent, simeprevir, as a PI4KIIIα inhibitor In a PDAC setting. Simeprevir potently mislocalized KRAS from the PM, reduced the clonogenic potential of pancreatic cancer cell lines in vitro, and abrogated the growth of KRAS-dependent tumors in vivo with enhanced efficacy when combined with MAPK and PI3K inhibitors. We conclude that the cellular ER-to-PM PtdSer transport mechanism is essential for KRAS PM localization and oncogenesis and is accessible to therapeutic intervention.
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13
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Gora RJ, de Jong B, van Hage P, Rhiemus MA, van Steenis F, van Noort J, Schmidt T, Schaaf MJM. Analysis of the H-Ras mobility pattern in vivo shows cellular heterogeneity inside epidermal tissue. Dis Model Mech 2021; 15:274496. [PMID: 34927194 PMCID: PMC8891639 DOI: 10.1242/dmm.049099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 12/14/2021] [Indexed: 12/04/2022] Open
Abstract
Developments in single-molecule microscopy (SMM) have enabled imaging individual proteins in biological systems, focusing on the analysis of protein mobility patterns inside cultured cells. In the present study, SMM was applied in vivo, using the zebrafish embryo model. We studied dynamics of the membrane protein H-Ras, its membrane-anchoring domain, C10H-Ras, and mutants, using total internal reflection fluorescence microscopy. Our results consistently confirm the presence of fast- and slow-diffusing subpopulations of molecules, which confine to microdomains within the plasma membrane. The active mutant H-RasV12 exhibits higher diffusion rates and is confined to larger domains than the wild-type H-Ras and its inactive mutant H-RasN17. Subsequently, we demonstrate that the structure and composition of the plasma membrane have an imperative role in modulating H-Ras mobility patterns. Ultimately, we establish that differences between cells within the same embryo largely contribute to the overall data variability. Our findings agree with a model in which the cell architecture and the protein activation state determine protein mobility, underlining the importance of SMM imaging for studying factors influencing protein dynamics in an intact living organism. This article has an associated First Person interview with the first author of the paper. Summary: Single-molecule microscopy analysis of factors altering the in vivo dynamics of H-Ras proteins in epidermal cells in living zebrafish embryos revealed that cell architecture and protein activation state determine protein mobility.
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Affiliation(s)
- Radoslaw J Gora
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Babette de Jong
- Biological, Soft and Complex Systems, Leiden Institute of Physics, Leiden University, Bohrweg 2, 2333 CA, Leiden, the Netherlands
| | - Patrick van Hage
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Mary Ann Rhiemus
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Fjodor van Steenis
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - John van Noort
- Biological, Soft and Complex Systems, Leiden Institute of Physics, Leiden University, Bohrweg 2, 2333 CA, Leiden, the Netherlands
| | - Thomas Schmidt
- Biological, Soft and Complex Systems, Leiden Institute of Physics, Leiden University, Bohrweg 2, 2333 CA, Leiden, the Netherlands
| | - Marcel J M Schaaf
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
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14
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KRAS-G12C covalent inhibitors: A game changer in the scene of cancer therapies. Crit Rev Oncol Hematol 2021; 168:103524. [PMID: 34800654 DOI: 10.1016/j.critrevonc.2021.103524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/05/2021] [Accepted: 11/02/2021] [Indexed: 12/14/2022] Open
Abstract
RAS is the most frequently mutated oncogene in human cancer. Scientists attempted for decades to target this protein or its pathways, however, all the attempts failed and RAS was labeled as "undruggable". With KRAS-G12C covalent inhibitors entering clinical trials, the myth of this "undruggable" RAS is fading away. In 2021, the Food and Drug Administration (FDA) approved the use of Sotorasib (Lumakras) for the treatment of adult patients with KRAS-G12C mutated locally advanced or metastatic NSCLC, following at least one prior systemic therapy. However, and as every other drug, KRAS-G12C inhibitors are facing intrinsic and acquired resistances. In order to overcome these resistances, researchers are now working on combination strategies. Furthermore, studies are currently ongoing to better elucidate the status of KRAS-G12C as a predictive and prognostic tool and to strengthen its role in the field of personalized medicine.
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15
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Role of oncogenic KRAS in the prognosis, diagnosis and treatment of colorectal cancer. Mol Cancer 2021; 20:143. [PMID: 34742312 PMCID: PMC8571891 DOI: 10.1186/s12943-021-01441-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease at the cellular and molecular levels. Kirsten rat sarcoma (KRAS) is a commonly mutated oncogene in CRC, with mutations in approximately 40% of all CRC cases; its mutations result in constitutive activation of the KRAS protein, which acts as a molecular switch to persistently stimulate downstream signaling pathways, including cell proliferation and survival, thereby leading to tumorigenesis. Patients whose CRC harbors KRAS mutations have a dismal prognosis. Currently, KRAS mutation testing is a routine clinical practice before treating metastatic cases, and the approaches developed to detect KRAS mutations have exhibited favorable sensitivity and accuracy. Due to the presence of KRAS mutations, this group of CRC patients requires more precise therapies. However, KRAS was historically thought to be an undruggable target until the development of KRASG12C allele-specific inhibitors. These promising inhibitors may provide novel strategies to treat KRAS-mutant CRC. Here, we provide an overview of the role of KRAS in the prognosis, diagnosis and treatment of CRC.
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16
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Affiliation(s)
- John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
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17
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RAS Dimers: The Novice Couple at the RAS-ERK Pathway Ball. Genes (Basel) 2021; 12:genes12101556. [PMID: 34680951 PMCID: PMC8535645 DOI: 10.3390/genes12101556] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023] Open
Abstract
Signals conveyed through the RAS-ERK pathway constitute a pivotal regulatory element in cancer-related cellular processes. Recently, RAS dimerization has been proposed as a key step in the relay of RAS signals, critically contributing to RAF activation. RAS clustering at plasma membrane microdomains and endomembranes facilitates RAS dimerization in response to stimulation, promoting RAF dimerization and subsequent activation. Remarkably, inhibiting RAS dimerization forestalls tumorigenesis in cellular and animal models. Thus, the pharmacological disruption of RAS dimers has emerged as an additional target for cancer researchers in the quest for a means to curtail aberrant RAS activity.
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18
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Heinrich F, Van QN, Jean-Francois F, Stephen AG, Lösche M. Membrane-bound KRAS approximates an entropic ensemble of configurations. Biophys J 2021; 120:4055-4066. [PMID: 34384763 PMCID: PMC8510975 DOI: 10.1016/j.bpj.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/08/2021] [Accepted: 08/04/2021] [Indexed: 11/27/2022] Open
Abstract
KRAS4B is a membrane-anchored signaling protein and a primary target in cancer research. Predictions from molecular dynamics simulations that have previously shaped our mechanistic understanding of KRAS signaling disagree with recent experimental results from neutron reflectometry, NMR, and thermodynamic binding studies. To gain insight into these discrepancies, we compare this body of biophysical data to back-calculated experimental results from a series of molecular simulations that implement different subsets of molecular interactions. Our results show that KRAS4B approximates an entropic ensemble of configurations at model membranes containing 30% phosphatidylserine lipids, which is not significantly shaped by interactions between the globular G-domain of KRAS4B and the lipid membrane. These findings revise our understanding of KRAS signaling and promote a model in which the protein samples the accessible conformational space in a near-uniform manner while being available to bind to effector proteins.
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Affiliation(s)
- Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland.
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Frantz Jean-Francois
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
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19
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Oncogenic KRAS is dependent upon an EFR3A-PI4KA signaling axis for potent tumorigenic activity. Nat Commun 2021; 12:5248. [PMID: 34504076 PMCID: PMC8429657 DOI: 10.1038/s41467-021-25523-5] [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: 08/03/2020] [Accepted: 08/10/2021] [Indexed: 11/15/2022] Open
Abstract
The HRAS, NRAS, and KRAS genes are collectively mutated in a fifth of all human cancers. These mutations render RAS GTP-bound and active, constitutively binding effector proteins to promote signaling conducive to tumorigenic growth. To further elucidate how RAS oncoproteins signal, we mined RAS interactomes for potential vulnerabilities. Here we identify EFR3A, an adapter protein for the phosphatidylinositol kinase PI4KA, to preferentially bind oncogenic KRAS. Disrupting EFR3A or PI4KA reduces phosphatidylinositol-4-phosphate, phosphatidylserine, and KRAS levels at the plasma membrane, as well as oncogenic signaling and tumorigenesis, phenotypes rescued by tethering PI4KA to the plasma membrane. Finally, we show that a selective PI4KA inhibitor augments the antineoplastic activity of the KRASG12C inhibitor sotorasib, suggesting a clinical path to exploit this pathway. In sum, we have discovered a distinct KRAS signaling axis with actionable therapeutic potential for the treatment of KRAS-mutant cancers. The lipid composition of the plasma membrane defines the localisation of KRAS and its oncogenic function. Here the authors show that EFR3A binds to active KRAS to recruit PI4KA and alters the lipid composition of the plasma membrane to promote KRAS oncogenic signalling and tumorigenesis.
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20
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Ras Isoforms from Lab Benches to Lives-What Are We Missing and How Far Are We? Int J Mol Sci 2021; 22:ijms22126508. [PMID: 34204435 PMCID: PMC8233758 DOI: 10.3390/ijms22126508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/21/2022] Open
Abstract
The central protein in the oncogenic circuitry is the Ras GTPase that has been under intense scrutiny for the last four decades. From its discovery as a viral oncogene and its non-oncogenic contribution to crucial cellular functioning, an elaborate genetic, structural, and functional map of Ras is being created for its therapeutic targeting. Despite decades of research, there still exist lacunae in our understanding of Ras. The complexity of the Ras functioning is further exemplified by the fact that the three canonical Ras genes encode for four protein isoforms (H-Ras, K-Ras4A, K-Ras4B, and N-Ras). Contrary to the initial assessment that the H-, K-, and N-Ras isoforms are functionally similar, emerging data are uncovering crucial differences between them. These Ras isoforms exhibit not only cell-type and context-dependent functions but also activator and effector specificities on activation by the same receptor. Preferential localization of H-, K-, and N-Ras in different microdomains of the plasma membrane and cellular organelles like Golgi, endoplasmic reticulum, mitochondria, and endosome adds a new dimension to isoform-specific signaling and diverse functions. Herein, we review isoform-specific properties of Ras GTPase and highlight the importance of considering these towards generating effective isoform-specific therapies in the future.
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21
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Van QN, Prakash P, Shrestha R, Balius TE, Turbyville TJ, Stephen AG. RAS Nanoclusters: Dynamic Signaling Platforms Amenable to Therapeutic Intervention. Biomolecules 2021; 11:377. [PMID: 33802474 PMCID: PMC8000715 DOI: 10.3390/biom11030377] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 01/18/2023] Open
Abstract
RAS proteins are mutated in approximately 20% of all cancers and are generally associated with poor clinical outcomes. RAS proteins are localized to the plasma membrane and function as molecular switches, turned on by partners that receive extracellular mitogenic signals. In the on-state, they activate intracellular signal transduction cascades. Membrane-bound RAS molecules segregate into multimers, known as nanoclusters. These nanoclusters, held together through weak protein-protein and protein-lipid associations, are highly dynamic and respond to cellular input signals and fluctuations in the local lipid environment. Disruption of RAS nanoclusters results in downregulation of RAS-mediated mitogenic signaling. In this review, we discuss the propensity of RAS proteins to display clustering behavior and the interfaces that are associated with these assemblies. Strategies to therapeutically disrupt nanocluster formation or the stabilization of signaling incompetent RAS complexes are discussed.
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Affiliation(s)
| | | | | | | | | | - Andrew G. Stephen
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, National Cancer Institute RAS Initiative, Inc., Frederick, MD 21702, USA; (Q.N.V.); (P.P.); (R.S.); (T.E.B.); (T.J.T.)
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22
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Huang Z, Liu M, Li D, Tan Y, Zhang R, Xia Z, Wang P, Jiao B, Liu P, Ren R. PTPN2 regulates the activation of KRAS and plays a critical role in proliferation and survival of KRAS-driven cancer cells. J Biol Chem 2020; 295:18343-18354. [PMID: 33122197 PMCID: PMC7939389 DOI: 10.1074/jbc.ra119.011060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/12/2020] [Indexed: 12/30/2022] Open
Abstract
RAS genes are the most commonly mutated in human cancers and play critical roles in tumor initiation, progression, and drug resistance. Identification of targets that block RAS signaling is pivotal to develop therapies for RAS-related cancer. As RAS translocation to the plasma membrane (PM) is essential for its effective signal transduction, we devised a high-content screening assay to search for genes regulating KRAS membrane association. We found that the tyrosine phosphatase PTPN2 regulates the plasma membrane localization of KRAS. Knockdown of PTPN2 reduced the proliferation and promoted apoptosis in KRAS-dependent cancer cells, but not in KRAS-independent cells. Mechanistically, PTPN2 negatively regulates tyrosine phosphorylation of KRAS, which, in turn, affects the activation KRAS and its downstream signaling. Consistently, analysis of the TCGA database demonstrates that high expression of PTPN2 is significantly associated with poor prognosis of patients with KRAS-mutant pancreatic adenocarcinoma. These results indicate that PTPN2 is a key regulator of KRAS and may serve as a new target for therapy of KRAS-driven cancer.
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Affiliation(s)
- Zhangsen Huang
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingzhu Liu
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Donghe Li
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Tan
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruihong Zhang
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhizhou Xia
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peihong Wang
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Jiao
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Liu
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ruibao Ren
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Abankwa D, Gorfe AA. Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again. Biomolecules 2020; 10:E1522. [PMID: 33172116 PMCID: PMC7694788 DOI: 10.3390/biom10111522] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
Ras is the most frequently mutated oncogene and recent drug development efforts have spurred significant new research interest. Here we review progress toward understanding how Ras functions in nanoscale, proteo-lipid signaling complexes on the plasma membrane, called nanoclusters. We discuss how G-domain reorientation is plausibly linked to Ras-nanoclustering and -dimerization. We then look at how these mechanistic features could cooperate in the engagement and activation of RAF by Ras. Moreover, we show how this structural information can be integrated with microscopy data that provide nanoscale resolution in cell biological experiments. Synthesizing the available data, we propose to distinguish between two types of Ras nanoclusters, an active, immobile RAF-dependent type and an inactive/neutral membrane anchor-dependent. We conclude that it is possible that Ras reorientation enables dynamic Ras dimerization while the whole Ras/RAF complex transits into an active state. These transient di/oligomer interfaces of Ras may be amenable to pharmacological intervention. We close by highlighting a number of open questions including whether all effectors form active nanoclusters and whether there is an isoform specific composition of Ras nanocluster.
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Affiliation(s)
- Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA
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24
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Modulation and dynamics of cell membrane heterogeneities. Chem Phys Lipids 2020; 233:105006. [PMID: 33144069 DOI: 10.1016/j.chemphyslip.2020.105006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 01/02/2023]
Abstract
Numerous studies provide evidence that the lipid bilayer of the plasma membrane contains lateral nanodomains, and that these are functionally important regulators of transmembrane cell signaling. Depending on their chemical composition and the biophysical mechanism bringing the lipids together, multiple types of nanodomains exist in the inner and the outer leaflet of the plasma membrane bilayer. In intact cells, these domains are smaller than the optical resolution limit of light microscopy and also highly dynamic. Recently, advanced fluorescence methods have provided data to characterize many biophysical and thermodynamic aspects of these nanodomains. In this review, we summarize the physicochemical determinants of nanodomain formation, stability and extent. Then, we detail how these nanodomains play a structural role by anchoring nucleation sites for the membrane cytoskeleton on the lipid bilayer. Further, we review the existing literature on mechanisms that modulate the nanodomain size and stability, both acute and chronic events. We conclude that regulation of the nanodomains distribution in the lipid bilayer of the plasma membrane is important for modulation of transmembrane signaling. However, only very few modulators of nanodomain stability and size have been quantified in cells, suggesting interesting directions for future studies.
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25
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Beljan S, Herak Bosnar M, Ćetković H. Rho Family of Ras-Like GTPases in Early-Branching Animals. Cells 2020; 9:cells9102279. [PMID: 33066017 PMCID: PMC7600811 DOI: 10.3390/cells9102279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Non-bilaterian animals consist of four phyla; Porifera, Cnidaria, Ctenophora, and Placozoa. These early-diverging animals are crucial for understanding the evolution of the entire animal lineage. The Rho family of proteins make up a major branch of the Ras superfamily of small GTPases, which function as key molecular switches that play important roles in converting and amplifying external signals into cellular responses. This review represents a compilation of the current knowledge on Rho-family GTPases in non-bilaterian animals, the available experimental data about their biochemical characteristics and functions, as well as original bioinformatics analysis, in order to gain a general insight into the evolutionary history of Rho-family GTPases in simple animals.
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Affiliation(s)
- Silvestar Beljan
- Division of Molecular Biology, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
- Division of Molecular Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia
| | - Maja Herak Bosnar
- Division of Molecular Medicine, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
| | - Helena Ćetković
- Division of Molecular Biology, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
- Correspondence: ; Tel.: +385-1-456-1115
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García-Ibáñez Y, Riesco-Eizaguirre G, Santisteban P, Casar B, Crespo P. RAS Subcellular Localization Inversely Regulates Thyroid Tumor Growth and Dissemination. Cancers (Basel) 2020; 12:cancers12092588. [PMID: 32927904 PMCID: PMC7565207 DOI: 10.3390/cancers12092588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary RAS mutations occur frequently in thyroid tumors, but the extent to which they are associated to tumor aggressiveness is still uncertain. HRAS proteins occupy different subcellular localizations, from which they regulate distinct biochemical processes. Herein, we demonstrate that the capacity of HRAS-transformed thyroid cells to extravasate and invade distant organs is orchestrated by HRAS subcellular localization, by a mechanism dependent on VEGF-B secretion. Interestingly, aggressiveness inversely correlates with tumor size. Moreover, we have identified the acyl protein thioesterase APT-1, a regulator of HRAS sublocalization, as a determinant of thyroid tumor growth versus dissemination. As such, alterations in APT-1 expression levels can dramatically affect the behavior of thyroid tumors. In this respect, APT-1 levels could serve as a biomarker that may help in the stratification of HRAS mutant thyroid tumors based on their aggressiveness. Abstract RAS mutations are the second most common genetic alteration in thyroid tumors. However, the extent to which they are associated with the most aggressive phenotypes is still controversial. Regarding their malignancy, the majority of RAS mutant tumors are classified as undetermined, which complicates their clinical management and can lead to undesired under- or overtreatment. Using the chick embryo spontaneous metastasis model, we herein demonstrate that the aggressiveness of HRAS-transformed thyroid cells, as determined by the ability to extravasate and metastasize at distant organs, is orchestrated by HRAS subcellular localization. Remarkably, aggressiveness inversely correlates with tumor size. In this respect, we also show that RAS site-specific capacity to regulate tumor growth and dissemination is dependent on VEGF-B secretion. Furthermore, we have identified the acyl protein thioesterase APT-1 as a determinant of thyroid tumor growth versus dissemination. We show that alterations in APT-1 expression levels can dramatically affect the behavior of thyroid tumors, based on its role as a regulator of HRAS sublocalization at distinct plasma membrane microdomains. In agreement, APT-1 emerges in thyroid cancer clinical samples as a prognostic factor. As such, APT-1 levels could serve as a biomarker that could help in the stratification of HRAS mutant thyroid tumors based on their aggressiveness.
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Affiliation(s)
- Yaiza García-Ibáñez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria. Santander, E-39011 Cantabria, Spain; (Y.G.-I.); (B.C.)
| | - Garcilaso Riesco-Eizaguirre
- Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas -Universidad Autónoma de Madrid. E-28029 Madrid, Spain; (G.R.-E.); (P.S.)
- Departamento de Endocrinología y Nutrición, Hospital Universitario de Móstoles, E-28935 Madrid, Spain
- Departamento de Endocrinología Molecular, Universidad Francisco de Vitoria, E-28223 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas -Universidad Autónoma de Madrid. E-28029 Madrid, Spain; (G.R.-E.); (P.S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Berta Casar
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria. Santander, E-39011 Cantabria, Spain; (Y.G.-I.); (B.C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Piero Crespo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria. Santander, E-39011 Cantabria, Spain; (Y.G.-I.); (B.C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence:
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Kattan WE, Hancock JF. RAS Function in cancer cells: translating membrane biology and biochemistry into new therapeutics. Biochem J 2020; 477:2893-2919. [PMID: 32797215 PMCID: PMC7891675 DOI: 10.1042/bcj20190839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
Abstract
The three human RAS proteins are mutated and constitutively activated in ∼20% of cancers leading to cell growth and proliferation. For the past three decades, many attempts have been made to inhibit these proteins with little success. Recently; however, multiple methods have emerged to inhibit KRAS, the most prevalently mutated isoform. These methods and the underlying biology will be discussed in this review with a special focus on KRAS-plasma membrane interactions.
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Affiliation(s)
- Walaa E. Kattan
- Department of Integrative Biology and Pharmacology, McGovern Medical School University of Texas Health Science Center at Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, TX 77030, USA
| | - John F. Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School University of Texas Health Science Center at Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, TX 77030, USA
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Yurugi H, Zhuang Y, Siddiqui FA, Liang H, Rosigkeit S, Zeng Y, Abou-Hamdan H, Bockamp E, Zhou Y, Abankwa D, Zhao W, Désaubry L, Rajalingam K. A subset of flavaglines inhibits KRAS nanoclustering and activation. J Cell Sci 2020; 133:jcs244111. [PMID: 32501281 DOI: 10.1242/jcs.244111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/30/2020] [Indexed: 08/31/2023] Open
Abstract
The RAS oncogenes are frequently mutated in human cancers and among the three isoforms (KRAS, HRAS and NRAS), KRAS is the most frequently mutated oncogene. Here, we demonstrate that a subset of flavaglines, a class of natural anti-tumour drugs and chemical ligands of prohibitins, inhibit RAS GTP loading and oncogene activation in cells at nanomolar concentrations. Treatment with rocaglamide, the first discovered flavagline, inhibited the nanoclustering of KRAS, but not HRAS and NRAS, at specific phospholipid-enriched plasma membrane domains. We further demonstrate that plasma membrane-associated prohibitins directly interact with KRAS, phosphatidylserine and phosphatidic acid, and these interactions are disrupted by rocaglamide but not by the structurally related flavagline FL1. Depletion of prohibitin-1 phenocopied the rocaglamide-mediated effects on KRAS activation and stability. We also demonstrate that flavaglines inhibit the oncogenic growth of KRAS-mutated cells and that treatment with rocaglamide reduces non-small-cell lung carcinoma (NSCLC) tumour nodules in autochthonous KRAS-driven mouse models without severe side effects. Our data suggest that it will be promising to further develop flavagline derivatives as specific KRAS inhibitors for clinical applications.
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Affiliation(s)
- Hajime Yurugi
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Yinyin Zhuang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637457 Singapore
| | - Farid A Siddiqui
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, Mcgovern Medical School, UT Health, 6431 Fannin St. MSE R382, Houston, TX 77030, USA
| | - Sebastian Rosigkeit
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Yongpeng Zeng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637457 Singapore
| | - Hussein Abou-Hamdan
- Therapeutic Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, University of Strasbourg, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg, France
| | - Ernesto Bockamp
- Institute for Translational Immunology and Research Center for Immunotherapy, University Medical Center, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, Mcgovern Medical School, UT Health, 6431 Fannin St. MSE R382, Houston, TX 77030, USA
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
- Cancer Cell Biology and Drug Discovery Group, Life Sciences Research Unit University of Luxembourg, L 4362 Esch-sur-Alzette, Luxembourg
| | - Wenting Zhao
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637457 Singapore
| | - Laurent Désaubry
- Therapeutic Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, University of Strasbourg, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg, France
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
- University Cancer Center Mainz, University Medical Center Mainz, D 55131 Mainz, Germany
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Chen K, Shang Z, Dai AL, Dai PL. Novel PI3K/Akt/mTOR pathway inhibitors plus radiotherapy: Strategy for non-small cell lung cancer with mutant RAS gene. Life Sci 2020; 255:117816. [PMID: 32454155 DOI: 10.1016/j.lfs.2020.117816] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/07/2020] [Accepted: 05/16/2020] [Indexed: 02/07/2023]
Abstract
Non-small cell lung cancer (NSCLC) with RAS -mutant gene has been the most difficult obstacle to overcome. Over 25% of muted lung adenocarcinomas have RAS mutation. The prognosis of NSCLC patients with RAS-mutant genes is always poor because there is no effective drug to suppress RAS-mutant genes. NSCLC patients with RAS-mutant usually develop resistance to radiotherapy and chemotherapy, which in some cases leads to a 5-10% survival rate for non-small cell lung cancer (NSCLC). As little clinical symptom of NSCLC was presented at its early stages, thus it always brings in disappointing treatment outcome. Currently, NSCLC presents the highest morbidity and mortality all over the world. The combination of PI3K/AKT/mTOR pathway inhibitors with radiotherapy is a novel strategy to improve radiosensitivity and therapeutic outcome of NSCLC with a RAS-mutant gene. There have been many preclinical studies and clinical trials on the effect of PI3K/AKT/mTOR pathway inhibitors combined with radiotherapy in NSCLC with a RAS-mutant gene have been reported in the past years. This review provides current knowledge of the combination of PI3K/Akt/mTOR pathway inhibitors with radiotherapy, which prove to be a significant improvement for the treatment of NSCLC patients with RAS mutations and will benefit NSCLC patients with RAS mutations.
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Affiliation(s)
- Kai Chen
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Zhongjun Shang
- Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming 650118, China
| | - Ai-Lin Dai
- Kunming Medical University Haiyuan School, Kunming 650100, China; Maternal and Child Health and Family Planning Service Center of Wenshan state, 663000, China
| | - Pei-Ling Dai
- Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming 650118, China; Kunming Medical University, Kunming 650100, China.
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Palmitoylated Cysteines in Chikungunya Virus nsP1 Are Critical for Targeting to Cholesterol-Rich Plasma Membrane Microdomains with Functional Consequences for Viral Genome Replication. J Virol 2020; 94:JVI.02183-19. [PMID: 32132240 DOI: 10.1128/jvi.02183-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 02/28/2020] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, alphavirus replication complexes are anchored to the plasma membrane. This interaction with lipid bilayers is mediated through the viral methyl/guanylyltransferase nsP1 and reinforced by palmitoylation of cysteine residue(s) in the C-terminal region of this protein. Lipid content of membranes supporting nsP1 anchoring remains poorly studied. Here, we explore the membrane binding capacity of nsP1 with regard to cholesterol. Using the medically important chikungunya virus (CHIKV) as a model, we report that nsP1 cosegregates with cholesterol-rich detergent-resistant membrane microdomains (DRMs), also called lipid rafts. In search for the critical factor for cholesterol partitioning, we identify nsP1 palmitoylated cysteines as major players in this process. In cells infected with CHIKV or transfected with CHIKV trans-replicase plasmids, nsP1, together with the other nonstructural proteins, are detected in DRMs. While the functional importance of CHIKV nsP1 preference for cholesterol-rich membrane domains remains to be determined, we observed that U18666A- and imipramine-induced sequestration of cholesterol in late endosomes redirected nsP1 to these compartments and simultaneously dramatically decreased CHIKV genome replication. A parallel study of Sindbis virus (SINV) revealed that nsP1 from this divergent alphavirus displays a low affinity for cholesterol and only moderately segregates with DRMs. Behaviors of CHIKV and SINV with regard to cholesterol, therefore, match with the previously reported differences in the requirement for nsP1 palmitoylation, which is dispensable for SINV but strictly required for CHIKV replication. Altogether, this study highlights the functional importance of nsP1 segregation with DRMs and provides new insight into the functional role of nsP1 palmitoylated cysteines during alphavirus replication.IMPORTANCE Functional alphavirus replication complexes are anchored to the host cell membranes through the interaction of nsP1 with the lipid bilayers. In this work, we investigate the importance of cholesterol for such an association. We show that nsP1 has affinity for cholesterol-rich membrane microdomains formed at the plasma membrane and identify conserved palmitoylated cysteine(s) in nsP1 as the key determinant for cholesterol affinity. We demonstrate that drug-induced cholesterol sequestration in late endosomes not only redirects nsP1 to this compartment but also dramatically decreases genome replication, suggesting the functional importance of nsP1 targeting to cholesterol-rich plasma membrane microdomains. Finally, we show evidence that nsP1 from chikungunya and Sindbis viruses displays different sensitivity to cholesterol sequestering agents that parallel with their difference in the requirement for nsP1 palmitoylation for replication. This research, therefore, gives new insight into the functional role of palmitoylated cysteines in nsP1 for the assembly of functional alphavirus replication complexes in their mammalian host.
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Sheng SG, Wang YN, Wang SR, Zhao K, Wang YY, Xu XN, Wang QM, Tong L, Chen ZG. [Effects of farnesyltransferase silencing on the migration and invasion of tongue squamous cell carcinoma]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2020; 38:177-184. [PMID: 32314892 DOI: 10.7518/hxkq.2020.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
OBJECTIVE This study aimed to explore the effects of silencing farnesyltransferase (FTase) on the migration and invasion of tongue squamous cell carcinoma (TSCC) through RNA interference. METHODS TSCC cells (CAL27 and SCC-4) were cultured in vitro and then transfected with siRNA to silence FTase expression. The tested cells were categorized as follows: experimental group (three RNA interference groups), negative control group, and blank control group. mRNA expression of FTase and HRAS in each group was analyzed by quantitative real-time polymerase chain reaction. On the basis of FTase mRNA expression, the optimum interference group (highest silencing efficiency) was selected as the experimental group for further study. The protein expression of FTase, HRAS, p65, p-p65(S536), matrix metalloprotein-9 (MMP-9), hypoxia inducible factor-1α (HIF-1α), and vascular endothelial growth factor (VEGF) was analyzed by Western blot. The invasion and migration abilities of TSCC cells were determined by Transwell invasion assay and cell wound healing assay. RESULTS The mRNA and protein expression of FTase in the experimental group decreased compared with that in the negative control and blank control groups (P<0.05). The mRNA and protein expression of HRAS was not significantly different among the groups (P>0.05). In the experimental group, the protein expression of p-p65(S536), MMP-9, HIF-1α, and VEGF decreased (P<0.05), whereas that of p65 had no significant change (P>0.05). The migration and invasion abilities of the experimental group were inhibited significantly (P<0.05). CONCLUSIONS Silencing FTase in vitro could effectively downregulate its expression in TSCC cell lines and reduce the migration and invasion abilities to a certain extent. FTase could be a new gene therapy target of TSCC, and this research provided a new idea for the clinical treatment of TSCC.
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Affiliation(s)
- Shan-Gui Sheng
- School of Stomatology, Qingdao University, Qingdao 266003, China
| | - Ya-Nan Wang
- Dept. of Oral and Maxillofacial Surgery, Qingdao Stomatological Hospital, Qingdao 266000, China
| | - Shao-Ru Wang
- Medical Center of Stomatology, Qingdao Municipal Hospital, Qingdao 266071, China;Stomatology College, Dalian Medical University, Dalian 116044, China
| | - Kai Zhao
- School of Stomatology, Qingdao University, Qingdao 266003, China
| | - Yun-Ying Wang
- Central Laboratory of Qingdao Municipal Hospital, Qingdao 266000, China
| | - Xiao-Na Xu
- Central Laboratory of Qingdao Municipal Hospital, Qingdao 266000, China
| | - Qi-Min Wang
- Medical Center of Stomatology, Qingdao Municipal Hospital, Qingdao 266071, China
| | - Lei Tong
- Medical Center of Stomatology, Qingdao Municipal Hospital, Qingdao 266071, China
| | - Zheng-Gang Chen
- Medical Center of Stomatology, Qingdao Municipal Hospital, Qingdao 266071, China
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Kattan WE, Chen W, Ma X, Lan TH, van der Hoeven D, van der Hoeven R, Hancock JF. Targeting plasma membrane phosphatidylserine content to inhibit oncogenic KRAS function. Life Sci Alliance 2019; 2:e201900431. [PMID: 31451509 PMCID: PMC6709719 DOI: 10.26508/lsa.201900431] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 12/14/2022] Open
Abstract
The small GTPase KRAS, which is frequently mutated in human cancers, must be localized to the plasma membrane (PM) for biological activity. We recently showed that the KRAS C-terminal membrane anchor exhibits exquisite lipid-binding specificity for select species of phosphatidylserine (PtdSer). We, therefore, investigated whether reducing PM PtdSer content is sufficient to abrogate KRAS oncogenesis. Oxysterol-related binding proteins ORP5 and ORP8 exchange PtdSer synthesized in the ER for phosphatidyl-4-phosphate synthesized in the PM. We show that depletion of ORP5 or ORP8 reduced PM PtdSer levels, resulting in extensive mislocalization of KRAS from the PM. Concordantly, ORP5 or ORP8 depletion significantly reduced proliferation and anchorage-independent growth of multiple KRAS-dependent cancer cell lines, and attenuated KRAS signaling in vivo. Similarly, functionally inhibiting ORP5 and ORP8 by inhibiting PI4KIIIα-mediated synthesis of phosphatidyl-4-phosphate at the PM selectively inhibited the growth of KRAS-dependent cancer cell lines over normal cells. Inhibiting KRAS function through regulating PM lipid PtdSer content may represent a viable strategy for KRAS-driven cancers.
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Affiliation(s)
- Walaa E Kattan
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Wei Chen
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Xiaoping Ma
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Tien Hung Lan
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center, Houston, TX, USA
| | - Ransome van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center, Houston, TX, USA
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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Barklis E, Stephen AG, Staubus AO, Barklis RL, Alfadhli A. Organization of Farnesylated, Carboxymethylated KRAS4B on Membranes. J Mol Biol 2019; 431:3706-3717. [PMID: 31330153 PMCID: PMC6733658 DOI: 10.1016/j.jmb.2019.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 11/24/2022]
Abstract
Mutations of the Ras proteins HRAS, KRAS4A, KRAS4B, and NRAS are associated with a high percentage of all human cancers. The proteins are composed of highly homologous N-terminal catalytic or globular domains, plus C-terminal hypervariable regions (HVRs). Post-translational modifications of all RAS HVRs helps target RAS proteins to cellular membrane locations where they perform their signaling functions. For the predominant KRAS4 isoform, KRAS4B, post-translational farnesylation and carboxymethylation, along with a patch of HVR basic residues help foster membrane binding. Recent investigations implicate membrane-bound RAS dimers, oligomers, and nanoclusters as landing pads for effector proteins that relay RAS signals. The details of these RAS signaling platforms have not been elucidated completely, in part due to the difficulties in preparing modified proteins. We have employed properly farnesylated and carboxymethylated KRAS4B in lipid monolayer incubations to examine how the proteins assemble on membranes. Our results reveal novel insights into to how KRAS4B may organize on membranes.
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Affiliation(s)
- Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA.
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21072, USA
| | - August O Staubus
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA
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Klochkov SG, Neganova ME, Yarla NS, Parvathaneni M, Sharma B, Tarasov VV, Barreto G, Bachurin SO, Ashraf GM, Aliev G. Implications of farnesyltransferase and its inhibitors as a promising strategy for cancer therapy. Semin Cancer Biol 2019; 56:128-134. [DOI: 10.1016/j.semcancer.2017.10.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/14/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
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Indarte M, Puentes R, Maruggi M, Ihle NT, Grandjean G, Scott M, Ahmed Z, Meuillet EJ, Zang S, Lemos R, Du-Cuny L, Layng FIAL, Correa RG, Bankston LA, Liddington RC, Kirkpatrick L, Powis G. An Inhibitor of the Pleckstrin Homology Domain of CNK1 Selectively Blocks the Growth of Mutant KRAS Cells and Tumors. Cancer Res 2019; 79:3100-3111. [PMID: 31040156 DOI: 10.1158/0008-5472.can-18-2372] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/03/2018] [Accepted: 04/26/2019] [Indexed: 12/11/2022]
Abstract
Cnk1 (connector enhancer of kinase suppressor of Ras 1) is a pleckstrin homology (PH) domain-containing scaffold protein that increases the efficiency of Ras signaling pathways, imparting efficiency and specificity to the response of cell proliferation, survival, and migration. Mutated KRAS (mut-KRAS) is the most common proto-oncogenic event, occurring in approximately 25% of human cancers and has no effective treatment. In this study, we show that selective inhibition of Cnk1 blocks growth and Raf/Mek/Erk, Rho and RalA/B signaling in mut-KRAS lung and colon cancer cells with little effect on wild-type (wt)-KRAS cells. Cnk1 inhibition decreased anchorage-independent mut-KRas cell growth more so than growth on plastic, without the partial "addiction" to mut-KRAS seen on plastic. The PH domain of Cnk1 bound with greater affinity to PtdIns(4,5)P2 than PtdIns(3,4,5)P3, and Cnk1 localized to areas of the plasma membranes rich in PtdIns, suggesting a role for the PH domain in the biological activity of Cnk1. Through molecular modeling and structural modification, we identified a compound PHT-7.3 that bound selectively to the PH domain of Cnk1, preventing plasma membrane colocalization with mut-KRas. PHT-7.3 inhibited mut-KRas, but not wild-type KRas cancer cell and tumor growth and signaling. Thus, the PH domain of Cnk1 is a druggable target whose inhibition selectively blocks mutant KRas activation, making Cnk1 an attractive therapeutic target in patients with mut-KRAS-driven cancer. SIGNIFICANCE: These findings identify a therapeutic strategy to selectively block oncogenic KRas activity through the PH domain of Cnk1, which reduces its cell membrane binding, decreasing the efficiency of Ras signaling and tumor growth.
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Affiliation(s)
| | - Roisin Puentes
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, California
| | - Marco Maruggi
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, California
| | | | - Geoffrey Grandjean
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, California
| | | | | | | | | | - Robert Lemos
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, California
| | | | - Fabiana I A L Layng
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, California
| | - Ricardo G Correa
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, California
| | - Laurie A Bankston
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, California
| | - Robert C Liddington
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, California
| | | | - Garth Powis
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, California.
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Jung J, Cho KJ, Naji AK, Clemons KN, Wong CO, Villanueva M, Gregory S, Karagas NE, Tan L, Liang H, Rousseau MA, Tomasevich KM, Sikora AG, Levental I, van der Hoeven D, Zhou Y, Hancock JF, Venkatachalam K. HRAS-driven cancer cells are vulnerable to TRPML1 inhibition. EMBO Rep 2019; 20:e46685. [PMID: 30787043 PMCID: PMC6446245 DOI: 10.15252/embr.201846685] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/28/2019] [Accepted: 02/01/2019] [Indexed: 12/28/2022] Open
Abstract
By serving as intermediaries between cellular metabolism and the bioenergetic demands of proliferation, endolysosomes allow cancer cells to thrive under normally detrimental conditions. Here, we show that an endolysosomal TRP channel, TRPML1, is necessary for the proliferation of cancer cells that bear activating mutations in HRAS Expression of MCOLN1, which encodes TRPML1, is significantly elevated in HRAS-positive tumors and inversely correlated with patient prognosis. Concordantly, MCOLN1 knockdown or TRPML1 inhibition selectively reduces the proliferation of cancer cells that express oncogenic, but not wild-type, HRAS Mechanistically, TRPML1 maintains oncogenic HRAS in signaling-competent nanoclusters at the plasma membrane by mediating cholesterol de-esterification and transport. TRPML1 inhibition disrupts the distribution and levels of cholesterol and thereby attenuates HRAS nanoclustering and plasma membrane abundance, ERK phosphorylation, and cell proliferation. These findings reveal a selective vulnerability of HRAS-driven cancers to TRPML1 inhibition, which may be leveraged as an actionable therapeutic strategy.
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Affiliation(s)
- Jewon Jung
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| | - Ali K Naji
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center, Houston, TX, USA
| | - Kristen N Clemons
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Ching On Wong
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Mariana Villanueva
- Bobby R. Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA
- Patient Derived Xenografts and Advanced in vivo Models Core Facility, Baylor College of Medicine, Houston, TX, USA
| | - Steven Gregory
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Nicholas E Karagas
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Lingxiao Tan
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Morgan A Rousseau
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Kelly M Tomasevich
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Andrew G Sikora
- Bobby R. Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA
- Patient Derived Xenografts and Advanced in vivo Models Core Facility, Baylor College of Medicine, Houston, TX, USA
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center, Houston, TX, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Kartik Venkatachalam
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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37
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Oncogenic KRas mobility in the membrane and signaling response. Semin Cancer Biol 2019; 54:109-113. [DOI: 10.1016/j.semcancer.2018.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 12/12/2022]
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38
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Perspectives of RAS and RHEB GTPase Signaling Pathways in Regenerating Brain Neurons. Int J Mol Sci 2018; 19:ijms19124052. [PMID: 30558189 PMCID: PMC6321366 DOI: 10.3390/ijms19124052] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/29/2022] Open
Abstract
Cellular activation of RAS GTPases into the GTP-binding “ON” state is a key switch for regulating brain functions. Molecular protein structural elements of rat sarcoma (RAS) and RAS homolog protein enriched in brain (RHEB) GTPases involved in this switch are discussed including their subcellular membrane localization for triggering specific signaling pathways resulting in regulation of synaptic connectivity, axonal growth, differentiation, migration, cytoskeletal dynamics, neural protection, and apoptosis. A beneficial role of neuronal H-RAS activity is suggested from cellular and animal models of neurodegenerative diseases. Recent experiments on optogenetic regulation offer insights into the spatiotemporal aspects controlling RAS/mitogen activated protein kinase (MAPK) or phosphoinositide-3 kinase (PI3K) pathways. As optogenetic manipulation of cellular signaling in deep brain regions critically requires penetration of light through large distances of absorbing tissue, we discuss magnetic guidance of re-growing axons as a complementary approach. In Parkinson’s disease, dopaminergic neuronal cell bodies degenerate in the substantia nigra. Current human trials of stem cell-derived dopaminergic neurons must take into account the inability of neuronal axons navigating over a large distance from the grafted site into striatal target regions. Grafting dopaminergic precursor neurons directly into the degenerating substantia nigra is discussed as a novel concept aiming to guide axonal growth by activating GTPase signaling through protein-functionalized intracellular magnetic nanoparticles responding to external magnets.
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39
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Garrido E, Lázaro J, Jaumot M, Agell N, Rubio-Martinez J. Modeling and subtleties of K-Ras and Calmodulin interaction. PLoS Comput Biol 2018; 14:e1006552. [PMID: 30376570 PMCID: PMC6226203 DOI: 10.1371/journal.pcbi.1006552] [Citation(s) in RCA: 8] [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: 04/11/2018] [Revised: 11/09/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022] Open
Abstract
K-Ras, one of the most common small GTPases of the cell, still presents many riddles, despite the intense efforts to unveil its mysteries. Such is the case of its interaction with Calmodulin, a small acidic protein known for its role as a calcium ion sensor. Although the interaction between these two proteins and its biological implications have been widely studied, a model of their interaction has not been performed. In the present work we analyse this intriguing interaction by computational means. To do so, both conventional molecular dynamics and scaled molecular dynamics have been used. Our simulations suggest a model in which Calmodulin would interact with both the hypervariable region and the globular domain of K-Ras, using a lobe to interact with each of them. According to the presented model, the interface of helixes α4 and α5 of the globular domain of K-Ras would be relevant for the interaction with a lobe of Calmodulin. These results were also obtained when bringing the proteins together in a step wise manner with the umbrella sampling methodology. The computational results have been validated using SPR to determine the relevance of certain residues. Our results demonstrate that, when mutating residues of the α4-α5 interface described to be relevant for the interaction with Calmodulin, the interaction of the globular domain of K-Ras with Calmodulin diminishes. However, it is to be considered that our simulations indicate that the bulk of the interaction would fall on the hypervariable region of K-Ras, as many more interactions are identified in said region. All in all our simulations present a suitable model in which K-Ras could interact with Calmodulin at membrane level using both its globular domain and its hypervariable region to stablish an interaction that leads to an altered signalling. K-Ras is one of the most mutated oncogenes in human cancer. Although several studies validate K-Ras protein as good candidate for direct therapeutic targeting, pharmacologic targeting has not been successful. During the last years increasing evidences demonstrate that oncogenic K-Ras activity can be modulated in vivo by dimerization, nanoclustering at the plasma membrane or interaction with non-effector proteins, consequently opening new therapeutic strategies. We have previously demonstrated that Calmodulin, an ubiquitous Ca2+-binding protein, is one of this K-Ras interacting proteins and that it negatively modulates K-Ras signaling. Although experimental data were available showing the relevant regions for this interaction, a model of K-Ras and Calmodulin interaction was missing. In the present work by using different computational modeling techniques we obtained a model for this interaction that agrees with the experimental data. We believe the present model will help to better understand K-Ras regulation, and to design new inhibitors. For instance, base on our model, we can predict that the interaction can take place at the plasma membrane, and that since the surface of K-Ras that interact with Calmodulin is the same that it uses for dimerization, that Calmodulin could be inhibiting K-Ras dimerization.
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Affiliation(s)
- Eduardo Garrido
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Institut de Recerca en Química Teòrica i Computacional (IQTCUB), Barcelona, Spain
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Juan Lázaro
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Montserrat Jaumot
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Neus Agell
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
- * E-mail: (NA); (JRM)
| | - Jaime Rubio-Martinez
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Institut de Recerca en Química Teòrica i Computacional (IQTCUB), Barcelona, Spain
- * E-mail: (NA); (JRM)
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40
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Zhou Y, Prakash P, Gorfe AA, Hancock JF. Ras and the Plasma Membrane: A Complicated Relationship. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031831. [PMID: 29229665 DOI: 10.1101/cshperspect.a031831] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The primary site of Ras signal transduction is the plasma membrane (PM). On the PM, the ubiquitously expressed Ras isoforms, H-, N-, and K-Ras, spatially segregate to nonoverlapping nanometer-sized domains, called nanoclusters, with further lateral segregation into nonoverlapping guanosine triphosphate (GTP)-bound and guanosine diphosphate (GDP)-bound nanoclusters. Effector binding and activation is restricted to GTP nanoclusters, rendering the underlying assembly mechanism essential to Ras signaling. Ras nanoclusters have distinct lipid compositions as a result of lipid-sorting specificity encoded in each Ras carboxy-terminal membrane anchor. The role of the G-domain in regulating anchor-membrane interactions is becoming clearer. Ras G-domains undergo significant conformational orientation changes on guanine nucleotide switch, leading to differential direct contacts between the G-domain and reorganization of the membrane anchor. Ras G-domains also contain weak dimer interfaces, resulting in homodimerization, which is an obligate step of nanoclustering. Modulating the formation of Ras dimers, the lipid composition of the PM or lateral dynamics of key PM phospholipids represent novel mechanisms whereby the extent of Ras nanoclustering can be regulated to tune the gain in Ras signaling circuits.
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Affiliation(s)
- Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030
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41
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Casar B, Badrock AP, Jiménez I, Arozarena I, Colón-Bolea P, Lorenzo-Martín LF, Barinaga-Rementería I, Barriuso J, Cappitelli V, Donoghue DJ, Bustelo XR, Hurlstone A, Crespo P. RAS at the Golgi antagonizes malignant transformation through PTPRκ-mediated inhibition of ERK activation. Nat Commun 2018; 9:3595. [PMID: 30185827 PMCID: PMC6125387 DOI: 10.1038/s41467-018-05941-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 08/02/2018] [Indexed: 11/12/2022] Open
Abstract
RAS GTPases are frequently mutated in human cancer. H- and NRAS isoforms are distributed over both plasma-membrane and endomembranes, including the Golgi complex, but how this organizational context contributes to cellular transformation is unknown. Here we show that RAS at the Golgi is selectively activated by apoptogenic stimuli and antagonizes cell survival by suppressing ERK activity through the induction of PTPRκ, which targets CRAF for dephosphorylation. Consistently, in contrast to what occurs at the plasma-membrane, RAS at the Golgi cannot induce melanoma in zebrafish. Inactivation of PTPRκ, which occurs frequently in human melanoma, often coincident with TP53 inactivation, accelerates RAS-ERK pathway-driven melanomagenesis in zebrafish. Likewise, tp53 disruption in zebrafish facilitates oncogenesis driven by RAS from the Golgi complex. Thus, RAS oncogenic potential is strictly dependent on its sublocalization, with Golgi complex-located RAS antagonizing tumor development. RAS isoforms are associated with the plasma membrane and endomembranes, but how their localization contributes to tumorigenesis is unclear. Here, the authors show that RAS signals from Golgi complex antagonize tumour formation by inducing apoptosis via ERK inhibition.
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Affiliation(s)
- Berta Casar
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Andrew P Badrock
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Iñaki Jiménez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain
| | - Imanol Arozarena
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain.,Navarrabiomed-FMS IDISNA, Pamplona, Navarra, 31008, Spain
| | - Paula Colón-Bolea
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain
| | - L Francisco Lorenzo-Martín
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, 28029, Spain.,Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Salamanca, 37007, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Salamanca, 37007, Spain
| | - Irene Barinaga-Rementería
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Jorge Barriuso
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Vincenzo Cappitelli
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain
| | - Daniel J Donoghue
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA92093, USA
| | - Xosé R Bustelo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, 28029, Spain.,Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Salamanca, 37007, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Salamanca, 37007, Spain
| | - Adam Hurlstone
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK.
| | - Piero Crespo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, 39011, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, 28029, Spain.
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42
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Van Geel O, Hartsuiker R, Gadella TWJ. Increasing spatial resolution of photoregulated GTPases through immobilized peripheral membrane proteins. Small GTPases 2018; 11:441-450. [PMID: 30182785 PMCID: PMC7549704 DOI: 10.1080/21541248.2018.1507411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Light-induced dimerizing systems, e.g. iLID, are an increasingly utilized optogenetics tool to perturb cellular signaling. The major benefit of this technique is that it allows external spatiotemporal control over protein localization with sub-cellular specificity. However, when it comes to local recruitment of signaling components to the plasmamembrane, this precision in localization is easily lost due to rapid diffusion of the membrane anchor. In this study, we explore different approaches of countering the diffusion of peripheral membrane anchors, to the point where we detect immobilized fractions with iFRAP on a timescale of several minutes. One method involves simultaneous binding of the membrane anchor to a secondary structure, the microtubules. The other strategy utilizes clustering of the anchor into large immobile structures, which can also be interlinked by employing tandem recruitable domains. For both approaches, the anchors are peripheral membrane constructs, which also makes them suitable for in vitro use. Upon combining these slower diffusing anchors with recruitable guanine exchange factors (GEFs), we show that we can elicit much more localized morphological responses from Rac1 and Cdc42 as compared to a regular CAAX-box based membrane anchor in living cells. Thanks to these new slow diffusing anchors, more precisely defined membrane recruitment experiments are now possible.
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Affiliation(s)
- Orry Van Geel
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam , Amsterdam, The Netherlands
| | - Roland Hartsuiker
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam , Amsterdam, The Netherlands
| | - Theodorus W J Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam , Amsterdam, The Netherlands
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43
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Rac1 Nanoscale Organization on the Plasma Membrane Is Driven by Lipid Binding Specificity Encoded in the Membrane Anchor. Mol Cell Biol 2018; 38:MCB.00186-18. [PMID: 29967243 DOI: 10.1128/mcb.00186-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022] Open
Abstract
Rac1 is a small guanine nucleotide binding protein that cycles between an inactive GDP-bound and active GTP-bound state to regulate cell motility and migration. Rac1 signaling is initiated from the plasma membrane (PM). Here, we used high-resolution spatial mapping and manipulation of PM lipid composition to define Rac1 nanoscale organization. We found that Rac1 proteins in the GTP- and GDP-bound states assemble into nonoverlapping nanoclusters; thus, Rac1 proteins undergo nucleotide-dependent segregation. Rac1 also selectively interacts with phosphatidic acid (PA) and phosphoinositol (3,4,5)-trisphosphate (PIP3), resulting in nanoclusters enriched in these lipids. These lipids are structurally important because depleting the PM of PA or PIP3 impairs both Rac1 PM binding and Rac1 nanoclustering. Lipid binding specificity of Rac1 is encoded in the amino acid sequence of the polybasic domain (PBD) of the C-terminal membrane anchor. Point mutations within the PBD, including arginine-to-lysine substitutions, profoundly alter Rac1 lipid binding specificity without changing the electrostatics of the protein and result in impaired macropinocytosis and decreased cell spreading. We propose that Rac1 nanoclusters act as lipid-based signaling platforms emulating the spatiotemporal organization of Ras proteins and show that the Rac1 PBD-prenyl anchor has a biological function that extends beyond simple electrostatic engagement with the PM.
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44
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Parker JA, Mattos C. The K-Ras, N-Ras, and H-Ras Isoforms: Unique Conformational Preferences and Implications for Targeting Oncogenic Mutants. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031427. [PMID: 29038336 DOI: 10.1101/cshperspect.a031427] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ras controls a multitude of cellular signaling processes, including cell proliferation, differentiation, and apoptosis. Deregulation of Ras cycling often promotes tumorigenesis and various other developmental disorders, termed RASopothies. Although the structure of Ras has been known for many decades, it is still one of the most highly sought-after drug targets today, and is often referred to as "undruggable." At the center of this paradoxical protein is a lack of understanding of fundamental differences in the G domains between the highly similar Ras isoforms and common oncogenic mutations, despite the immense wealth of knowledge accumulated about this protein to date. A shift in the field during the past few years toward a high-resolution understanding of the structure confirms the hypothesis that each isoform and oncogenic mutation must be considered individually, and that not all Ras mutations are created equal. For the first time in Ras history, we have the ability to directly compare the structures of each wild-type isoform to construct a "base-line" understanding, which can then be used as a springboard for analyzing the effects of oncogenic mutations on the structure-function relationship in Ras. This is a fundamental and large step toward the goal of developing personalized therapies for patients with Ras-driven cancers and diseases.
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Affiliation(s)
- Jillian A Parker
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
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45
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Remorino A, De Beco S, Cayrac F, Di Federico F, Cornilleau G, Gautreau A, Parrini MC, Masson JB, Dahan M, Coppey M. Gradients of Rac1 Nanoclusters Support Spatial Patterns of Rac1 Signaling. Cell Rep 2018; 21:1922-1935. [PMID: 29141223 DOI: 10.1016/j.celrep.2017.10.069] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/18/2017] [Accepted: 10/18/2017] [Indexed: 01/03/2023] Open
Abstract
Rac1 is a small RhoGTPase switch that orchestrates actin branching in space and time and protrusion/retraction cycles of the lamellipodia at the cell front during mesenchymal migration. Biosensor imaging has revealed a graded concentration of active GTP-loaded Rac1 in protruding regions of the cell. Here, using single-molecule imaging and super-resolution microscopy, we show an additional supramolecular organization of Rac1. We find that Rac1 partitions and is immobilized into nanoclusters of 50-100 molecules each. These nanoclusters assemble because of the interaction of the polybasic tail of Rac1 with the phosphoinositide lipids PIP2 and PIP3. The additional interactions with GEFs and possibly GAPs, downstream effectors, and other partners are responsible for an enrichment of Rac1 nanoclusters in protruding regions of the cell. Our results show that subcellular patterns of Rac1 activity are supported by gradients of signaling nanodomains of heterogeneous molecular composition, which presumably act as discrete signaling platforms.
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Affiliation(s)
- Amanda Remorino
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Simon De Beco
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Fanny Cayrac
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Fahima Di Federico
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Gaetan Cornilleau
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Alexis Gautreau
- Ecole Polytechnique, Université Paris-Saclay, CNRS UMR7654, 91120 Palaiseau, France
| | - Maria Carla Parrini
- Institut Curie, Centre de Recherche, Paris Sciences Lettres, ART Group, Inserm U830, Paris 75005, France
| | - Jean-Baptiste Masson
- Decision and Bayesian Computation, Institut Pasteur, 25 Rue du Docteur Roux, Paris, 75015, France; Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | - Maxime Dahan
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France
| | - Mathieu Coppey
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Universite Pierre et Marie Curie-Paris 6, 75005 Paris, France.
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46
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Hastings JF, Skhinas JN, Fey D, Croucher DR, Cox TR. The extracellular matrix as a key regulator of intracellular signalling networks. Br J Pharmacol 2018; 176:82-92. [PMID: 29510460 DOI: 10.1111/bph.14195] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/06/2018] [Accepted: 02/13/2018] [Indexed: 12/11/2022] Open
Abstract
The extracellular matrix (ECM) is a salient feature of all solid tissues within the body. This complex, acellular entity is composed of hundreds of individual molecules whose assembly, architecture and biomechanical properties are critical to controlling the behaviour and phenotype of the different cell types residing within tissues. Cells are the basic unit of life and the core building block of tissues and organs. At their simplest, they follow a set of rules, governed by their genetic code and effected through the complex protein signalling networks that these genes encode. These signalling networks assimilate and process the information received by the cell to control cellular decisions that govern cell fate. The ECM is the biggest provider of external stimuli to cells and as such is responsible for influencing intracellular signalling dynamics. In this review, we discuss the inclusion of ECM as a central regulatory signalling sub-network in computational models of cellular decision making, with a focus on its role in diseases such as cancer. LINKED ARTICLES: This article is part of a themed section on Translating the Matrix. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.1/issuetoc.
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Affiliation(s)
- Jordan F Hastings
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Darlinghurst, NSW, 2010, Australia
| | - Joanna N Skhinas
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Darlinghurst, NSW, 2010, Australia
| | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - David R Croucher
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Kensington, NSW, 2010, Australia.,School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Thomas R Cox
- The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Kensington, NSW, 2010, Australia
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Han CW, Jeong MS, Jang SB. Structure, signaling and the drug discovery of the Ras oncogene protein. BMB Rep 2018; 50:355-360. [PMID: 28571593 PMCID: PMC5584742 DOI: 10.5483/bmbrep.2017.50.7.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 01/04/2023] Open
Abstract
Mutations in Ras GTPase are among the most common genetic alterations in human cancers. Despite extensive research investigating Ras proteins, their functions still remain a challenge over a long period of time. The currently available data suggests that solving the outstanding issues regarding Ras could lead to development of effective drugs that could have a significant impact on cancer treatment. Developing a better understanding of their biochemical properties or modes of action, along with improvements in their pharmacologic profiles, clinical design and scheduling will enable the development of more effective therapies.
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Affiliation(s)
- Chang Woo Han
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Mi Suk Jeong
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
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48
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Jin W, Simsek MF, Pralle A. Quantifying spatial and temporal variations of the cell membrane ultra-structure by bimFCS. Methods 2018. [PMID: 29530504 DOI: 10.1016/j.ymeth.2018.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
It has been long recognized that the cell membrane is heterogeneous on scales ranging from a couple of molecules to micrometers in size and hence diffusion of receptors is length scale dependent. This heterogeneity modulates many cell-membrane-associated processes requiring transient spatiotemporal separation of components. The transient increase in local concentration of interacting signal components enables robust signaling in an otherwise thermally noisy system. Understanding how lipids and proteins self-organize and interact with the cell cortex requires quantifying the motion of the components. Multi-length scale diffusion measurements by single particle tracking, fluorescence correlation spectroscopy (FCS) or related techniques are able to identify components being transiently trapped in nanodomains, from freely moving one and from ones with reduced long-scale diffusion due to interaction with the cell cortex. One particular implementation of multi-length scale diffusion measurements is the combination of FCS with a spatially resolved detector, such as a camera and two-dimensional extended excitation profile. The main advantages of this approach are that all length scales are interrogated simultaneously, uniquely permits quantifying changes to the membrane structure caused by extrenal or internal perturbations. Here, we review how combining total internal reflection microscopy (TIRF) with FC resolves the membrane organization in living cells. We show how to implement the method, which requires only a few seconds of data acquisition to quantify membrane nanodomains, or the spacing of membrane fences caused by the actin cortex. The choice of diffusing fluorescent probe determines which membrane heterogeneity is detected. We review the instrument, sample preparation, experimental and computational requirements to perform such measurements, and discuss the potential and limitations. The discussion includes examples of spatial and temporal comparisons of the membrane structure in response to perturbations demonstrating the complex cell physiology.
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Affiliation(s)
- Weixiang Jin
- Dept. of Physics, 239 Fronczak Hall, University at Buffalo, SUNY, Buffalo, NY 14260-1500, United States
| | - M Fethullah Simsek
- Dept. of Physics, 239 Fronczak Hall, University at Buffalo, SUNY, Buffalo, NY 14260-1500, United States
| | - Arnd Pralle
- Dept. of Physics, 239 Fronczak Hall, University at Buffalo, SUNY, Buffalo, NY 14260-1500, United States.
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49
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Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland. .,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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50
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Nussinov R, Tsai CJ, Jang H. Oncogenic Ras Isoforms Signaling Specificity at the Membrane. Cancer Res 2018; 78:593-602. [PMID: 29273632 PMCID: PMC5811325 DOI: 10.1158/0008-5472.can-17-2727] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 01/21/2023]
Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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