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Tateno K, Ando T, Tabata M, Sugasawa H, Hayashi T, Yu S, Pm S, Inomata K, Mikawa T, Ito Y, Ikeya T. Different molecular recognition by three domains of the full-length GRB2 to SOS1 proline-rich motifs and EGFR phosphorylated sites. Chem Sci 2024:d4sc02656j. [PMID: 39282643 PMCID: PMC11391413 DOI: 10.1039/d4sc02656j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 08/02/2024] [Indexed: 09/19/2024] Open
Abstract
The adaptor protein human GRB2 plays crucial roles in mediating signal transduction from cell membrane receptors to RAS and its downstream proteins by recruiting SOS1. Recent studies have revealed that GRB2 also serves as a scaffold for liquid-liquid phase separation (LLPS) with SOS1 and transmembrane receptors, which is thought to regulate the magnitude of cell signalling pathways. In this study, we employed solution NMR spectroscopy to investigate the interactions of the full-length GRB2 with proline-rich motifs (PRMs) derived from ten potential GRB2-binding sites in SOS1, as well as a peptide from a phosphorylation site of EGFR. Our findings indicate that the binding affinity of the two SH3 domains of GRB2 for PRMs differs by a factor of ten to twenty, with the N-terminal SH3 domain (NSH3) exhibiting a markedly higher affinity. The interactions of PRMs with the SH3 domains affected not only the regions surrounding the PRM binding sites on the SH3 domains but also the linker area connecting the three domains and parts of the SH2 domain. Analysis of the interaction between the phosphorylated EGFR binding site and the SH2 domain revealed chemical shift perturbations in regions distal from the known binding site of SH2. Moreover, we observed that the inter-domain interactions of the two SH3 domains with the SH2 domain of GRB2 are asymmetric. These findings suggest that the local binding of PRMs and phosphorylated EGFR to GRB2 impacts the overall structure of the GRB2 molecule, including domain orientation and dimerisation, which may contribute to LLPS formation.
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Affiliation(s)
- Keita Tateno
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
| | - Takami Ando
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
| | - Maako Tabata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
| | - Haruka Sugasawa
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
| | - Toshifumi Hayashi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
| | - Sangya Yu
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
| | - Sayeesh Pm
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
| | - Kohsuke Inomata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
| | - Tsutomu Mikawa
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN 1-7-22 Suehiro-Cho, Tsurumi-Ku Yokohama 230-0045 Japan
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
| | - Teppei Ikeya
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University 1-1 Minamiosawa Hachioji Tokyo 192-0397 Japan
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2
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Lilja J, Kaivola J, Conway JRW, Vuorio J, Parkkola H, Roivas P, Dibus M, Chastney MR, Varila T, Jacquemet G, Peuhu E, Wang E, Pentikäinen U, Martinez D Posada I, Hamidi H, Najumudeen AK, Sansom OJ, Barsukov IL, Abankwa D, Vattulainen I, Salmi M, Ivaska J. SHANK3 depletion leads to ERK signalling overdose and cell death in KRAS-mutant cancers. Nat Commun 2024; 15:8002. [PMID: 39266533 PMCID: PMC11393128 DOI: 10.1038/s41467-024-52326-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 09/03/2024] [Indexed: 09/14/2024] Open
Abstract
The KRAS oncogene drives many common and highly fatal malignancies. These include pancreatic, lung, and colorectal cancer, where various activating KRAS mutations have made the development of KRAS inhibitors difficult. Here we identify the scaffold protein SH3 and multiple ankyrin repeat domain 3 (SHANK3) as a RAS interactor that binds active KRAS, including mutant forms, competes with RAF and limits oncogenic KRAS downstream signalling, maintaining mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) activity at an optimal level. SHANK3 depletion breaches this threshold, triggering MAPK/ERK signalling hyperactivation and MAPK/ERK-dependent cell death in KRAS-mutant cancers. Targeting this vulnerability through RNA interference or nanobody-mediated disruption of the SHANK3-KRAS interaction constrains tumour growth in vivo in female mice. Thus, inhibition of SHANK3-KRAS interaction represents an alternative strategy for selective killing of KRAS-mutant cancer cells through excessive signalling.
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Affiliation(s)
- Johanna Lilja
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Jasmin Kaivola
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - James R W Conway
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Joni Vuorio
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Hanna Parkkola
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Pekka Roivas
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland
| | - Michal Dibus
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Megan R Chastney
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Taru Varila
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, FI-20520, Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, FI-20520, Turku, Finland
| | - Emilia Peuhu
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Institute of Biomedicine, Cancer Research Laboratory FICAN West, University of Turku, FI-20520, Turku, Finland
| | - Emily Wang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Ulla Pentikäinen
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland
| | | | - Hellyeh Hamidi
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
| | - Arafath K Najumudeen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- CRUK Scotland Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Owen J Sansom
- CRUK Scotland Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Igor L Barsukov
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel Abankwa
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland
- Department of Life Sciences and Medicine, University of Luxembourg, 4365, Esch- sur-Alzette, Luxembourg
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Marko Salmi
- Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland
- MediCity Research Laboratory, University of Turku, FI-20520, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20520, Turku, Finland
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku, FI-20520, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, FI-20520, Turku, Finland.
- Department of Life Technologies, University of Turku, Turku, Finland.
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, FI-00014, Helsinki, Finland.
- Western Finnish Cancer Center, University of Turku, Turku, FI-20520, Finland.
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3
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Ghadrdoost Nakhchi B, Kosuru R, Chrzanowska M. Towards Targeting Endothelial Rap1B to Overcome Vascular Immunosuppression in Cancer. Int J Mol Sci 2024; 25:9853. [PMID: 39337337 PMCID: PMC11432579 DOI: 10.3390/ijms25189853] [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: 07/31/2024] [Revised: 08/23/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
The vascular endothelium, a specialized monolayer of endothelial cells (ECs), is crucial for maintaining vascular homeostasis by controlling the passage of substances and cells. In the tumor microenvironment, Vascular Endothelial Growth Factor A (VEGF-A) drives tumor angiogenesis, leading to endothelial anergy and vascular immunosuppression-a state where ECs resist cytotoxic CD8+ T cell infiltration, hindering immune surveillance. Immunotherapies have shown clinical promise. However, their effectiveness is significantly reduced by tumor EC anergy. Anti-angiogenic treatments aim to normalize tumor vessels and improve immune cell infiltration. Despite their potential, these therapies often cause significant systemic toxicities, necessitating new treatments. The small GTPase Rap1B emerges as a critical regulator of Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) signaling in ECs. Our studies using EC-specific Rap1B knockout mice show that the absence of Rap1B impairs tumor growth, alters vessel morphology, and increases CD8+ T cell infiltration and activation. This indicates that Rap1B mediates VEGF-A's immunosuppressive effects, making it a promising target for overcoming vascular immunosuppression in cancer. Rap1B shares structural and functional similarities with RAS oncogenes. We propose that targeting Rap1B could enhance therapies' efficacy while minimizing adverse effects by reversing endothelial anergy. We briefly discuss strategies successfully developed for targeting RAS as a model for developing anti-Rap1 therapies.
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Affiliation(s)
| | - Ramoji Kosuru
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
| | - Magdalena Chrzanowska
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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4
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Chour A, Toffart AC, Berton E, Duruisseaux M. Mechanisms of resistance to KRASG12C inhibitors in KRASG12C-mutated non-small cell lung cancer. Front Oncol 2024; 14:1328728. [PMID: 39301544 PMCID: PMC11410594 DOI: 10.3389/fonc.2024.1328728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 07/25/2024] [Indexed: 09/22/2024] Open
Abstract
The KRAS protein, a product of the KRAS gene (V-ki-ras2 Kirsten rat sarcoma viral oncogene homolog), functions as a small GTPase that alternates between an active GTP-bound state (KRAS(ON)) and an inactive GDP-bound state (KRAS(OFF)). The KRASG12C mutation results in the accumulation of KRASG12C(OFF), promoting cell cycle survival and proliferation primarily through the canonical MAPK and PI3K pathways. The KRASG12C mutation is found in 13% of lung adenocarcinomas. Previously considered undruggable, sotorasib and adagrasib are the first available OFF-state KRASG12C inhibitors, but treatment resistance is frequent. In this review, after briefly summarizing the KRAS pathway and the mechanism of action of OFF-state KRASG12C inhibitors, we discuss primary and acquired resistance mechanisms. Acquired resistance is the most frequent, with "on-target" mechanisms such as a new KRAS mutation preventing inhibitor binding; and "off-target" mechanisms leading to bypass of KRAS through gain-of-function mutations in other oncogenes such as NRAS, BRAF, and RET; or loss-of-function mutations in tumor suppressor genes such as PTEN. Other "off-target" mechanisms described include epithelial-to-mesenchymal transition and histological transformation. Multiple co-existing mechanisms can be found in patients, but few cases have been published. We highlight the lack of data on non-genomic resistance and the need for comprehensive clinical studies exploring histological, genomic, and non-genomic changes at resistance. This knowledge could help foster new treatment initiatives in this challenging context.
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Affiliation(s)
- Ali Chour
- Respiratory Department and Early Phase (EPSILYON), Louis Pradel Hospital, Hospices Civils de Lyon Cancer Institute, Lyon, France
- Oncopharmacology Laboratory, Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Lyon, France
- Université Claude Bernard, Université de Lyon, Lyon, France
| | - Anne-Claire Toffart
- Service de Pneumologie et Physiologie, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
- Institute for Advanced Biosciences, UGA/INSERM U1209/CNRS 5309, Université Grenoble Alpes, Grenoble, France
| | - Elodie Berton
- Service de Pneumologie et Physiologie, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Michael Duruisseaux
- Respiratory Department and Early Phase (EPSILYON), Louis Pradel Hospital, Hospices Civils de Lyon Cancer Institute, Lyon, France
- Oncopharmacology Laboratory, Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Lyon, France
- Université Claude Bernard, Université de Lyon, Lyon, France
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5
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Choi DH, Jang HL, Lim SH, Kim ST, Hong JY, Park SH, Park JO, Kim DG, Kim KM, Lee J. Prevalence of KRAS amplification in patients with metastatic cancer: Real-world next-generation sequencing analysis. Pathol Res Pract 2024; 261:155473. [PMID: 39106591 DOI: 10.1016/j.prp.2024.155473] [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: 04/10/2024] [Accepted: 07/15/2024] [Indexed: 08/09/2024]
Abstract
BACKGROUND The Kirsten rat sarcoma virus (KRAS) is a prominent proto-oncogene. Several treatments for KRAS mutations have been developed. However, KRAS amplification, a KRAS alteration, is poorly understood, and there is currently no appropriate treatment other than conventional chemotherapy. This study aimed to elucidate the role of KRAS amplification in different types of cancers. METHODS From October 2019 to June 2023, we performed next-generation sequencing using Trusight Oncology 500 on 3895 patients with 37 different cancer types at the Samsung Medical Center. We analyzed the distribution of KRAS amplification according to cancer type and its correlation with tumor mutation burden (TMB). Concomitant KRAS mutations were also identified. RESULTS Of the total 3895 patients, 99 (2.5 %) had KRAS amplification. The highest frequency of KRAS amplification was detected in 2 % (27/1350) of patients with colorectal cancer, followed by 3.48 % (32/920) of patients with gastric cancer and 3.88 % (9/232) patients with of pancreatic cancer. MSI-High was not detected in patients with KRAS amplification. There was no correlation between KRAS copy number variation and TMB status. Among patients with KRAS amplification, 27.3 % (27/99) had a concomitant KRAS mutation. More than 50 % of patients had G12D or G12V mutations. In gastric cancer, patients with both KRAS amplification and mutation were extremely rare at 3.1 % (1/32); however, in colorectal cancer, more than half of the patients had KRAS amplification and mutation (51.9 %, 14/27). KRAS amplification and mutations are associated with mutations in tumor suppressor genes TP53, BRCA2, ARID1B, and PTCH1. CONCLUSIONS Of the 3895 patients with metastatic solid tumors, 99 (2.5 %) had KRAS amplification, and next-generation sequencing analysis provided a deeper understanding of KRAS amplification.
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Affiliation(s)
- Dae-Ho Choi
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hye-Lim Jang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea; Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul, South Korea
| | - Sung Hee Lim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jung Yong Hong
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Se Hoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Joon Oh Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Deok Geun Kim
- Department of Clinical Genomic Center, Samsung Medical Center, Seoul 06351, South Korea; Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul 06351, South Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, South Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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6
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Jungholm O, Trkulja C, Moche M, Srinivasa SP, Christakopoulou MN, Davidson M, Reymer A, Jardemark K, Fogaça RL, Ashok A, Jeffries G, Ampah-Korsah H, Strandback E, Andréll J, Nyman T, Nouairia G, Orwar O. Novel druggable space in human KRAS G13D discovered using structural bioinformatics and a P-loop targeting monoclonal antibody. Sci Rep 2024; 14:19656. [PMID: 39179604 PMCID: PMC11344056 DOI: 10.1038/s41598-024-70217-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024] Open
Abstract
KRAS belongs to a family of small GTPases that act as binary switches upstream of several signalling cascades, controlling proliferation and survival of cells. Mutations in KRAS drive oncogenesis, especially in pancreatic, lung, and colorectal cancers (CRC). Although historic attempts at targeting mutant KRAS with small molecule inhibitors have proven challenging, there are recent successes with the G12C, and G12D mutations. However, clinically important RAS mutations such as G12V, G13D, Q61L, and A146T, remain elusive drug targets, and insights to their structural landscape is of critical importance to develop novel, and effective therapeutic concepts. We present a fully open, P-loop exposing conformer of KRAS G13D by X-ray crystallography at 1.4-2.4 Å resolution in Mg2+-free phosphate and malonate buffers. The G13D conformer has the switch-I region displaced in an upright position leaving the catalytic core fully exposed. To prove that this state is druggable, we developed a P-loop-targeting monoclonal antibody (mAb). The mAb displayed high-affinity binding to G13D and was shown using high resolution fluorescence microscopy to be spontaneously taken up by G13D-mutated HCT 116 cells (human CRC derived) by macropinocytosis. The mAb inhibited KRAS signalling in phosphoproteomic and genomic studies. Taken together, the data propose novel druggable space of G13D that is reachable in the cellular context. It is our hope that these findings will stimulate attempts to drug this fully open state G13D conformer using mAbs or other modalities.
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Affiliation(s)
- Oscar Jungholm
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Carolina Trkulja
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden
- Fluicell AB, Flöjelbergsgatan 8C, 431 37, Mölndal, Sweden
| | - Martin Moche
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Sreesha P Srinivasa
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | | | - Max Davidson
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden
| | - Anna Reymer
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Kent Jardemark
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | | | | | - Gavin Jeffries
- Fluicell AB, Flöjelbergsgatan 8C, 431 37, Mölndal, Sweden
| | - Henry Ampah-Korsah
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Emilia Strandback
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Juni Andréll
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Tomas Nyman
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Ghada Nouairia
- Department of Medicine Huddinge, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Owe Orwar
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden.
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.
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7
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Ngo VA. Insight into molecular basis and dynamics of full-length CRaf kinase in cellular signaling mechanisms. Biophys J 2024; 123:2623-2637. [PMID: 38946141 PMCID: PMC11365224 DOI: 10.1016/j.bpj.2024.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/15/2024] [Accepted: 06/28/2024] [Indexed: 07/02/2024] Open
Abstract
Raf kinases play key roles in signal transduction in cells for regulating proliferation, differentiation, and survival. Despite decades of research into functions and dynamics of Raf kinases with respect to other cytosolic proteins, understanding Raf kinases is limited by the lack of their full-length structures at the atomic resolution. Here, we present the first model of the full-length CRaf kinase obtained from artificial intelligence/machine learning algorithms with a converging ensemble of structures simulated by large-scale temperature replica exchange simulations. Our model is validated by comparing simulated structures with the latest cryo-EM structure detailing close contacts among three key domains and regions of the CRaf. Our simulations identify potentially new epitopes of intramolecule interactions within the CRaf and reveal a dynamical nature of CRaf kinases, in which the three domains can move back and forth relative to each other for regulatory dynamics. The dynamic conformations are then used in a docking algorithm to shed insight into the paradoxical effect caused by vemurafenib in comparison with a paradox breaker PLX7904. We propose a model of Raf-heterodimer/KRas-dimer as a signalosome based on the dynamics of the full-length CRaf.
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Affiliation(s)
- Van A Ngo
- Advanced Computing for Life Sciences and Engineering, Science Engagement Section, Computing and Computational Sciences, National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
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8
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Zhang JZ, Ong SE, Baker D, Maly DJ. Single-cell sensor analyses reveal signaling programs enabling Ras-G12C drug resistance. Nat Chem Biol 2024:10.1038/s41589-024-01684-4. [PMID: 39103633 DOI: 10.1038/s41589-024-01684-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 06/23/2024] [Indexed: 08/07/2024]
Abstract
Clinical resistance to rat sarcoma virus (Ras)-G12C inhibitors is a challenge. A subpopulation of cancer cells has been shown to undergo genomic and transcriptional alterations to facilitate drug resistance but the immediate adaptive effects on Ras signaling in response to these drugs at the single-cell level is not well understood. Here, we used Ras biosensors to profile the activity and signaling environment of endogenous Ras at the single-cell level. We found that a subpopulation of KRas-G12C cells treated with Ras-G12C-guanosine-diphosphate inhibitors underwent adaptive signaling and metabolic changes driven by wild-type Ras at the Golgi and mutant KRas at the mitochondria, respectively. Our Ras biosensors identified major vault protein as a mediator of Ras activation through its scaffolding of Ras signaling pathway components and metabolite channels. Overall, methods including ours that facilitate direct analysis on the single-cell level can report the adaptations that subpopulations of cells adopt in response to cancer therapies, thus providing insight into drug resistance.
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Affiliation(s)
- Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Dustin J Maly
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Chemistry, University of Washington, Seattle, WA, USA
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9
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Fink JC, Landry D, Webb LJ. Probing the Electrostatic Effects of H-Ras Tyrosine 32 Mutations on Intrinsic GTP Hydrolysis Using Vibrational Stark Effect Spectroscopy of a Thiocyanate Probe. Biochemistry 2024; 63:1752-1760. [PMID: 38967549 DOI: 10.1021/acs.biochem.4c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The wildtype H-Ras protein functions as a molecular switch in a variety of cell signaling pathways, and mutations to key residues result in a constitutively active oncoprotein. However, there is some debate regarding the mechanism of the intrinsic GTPase activity of H-Ras. It has been hypothesized that ordered water molecules are coordinated at the active site by Q61, a highly transforming amino acid site, and Y32, a position that has not previously been investigated. Here, we examine the electrostatic contribution of the Y32 position to GTP hydrolysis by comparing the rate of GTP hydrolysis of Y32X mutants to the vibrational energy shift of each mutation measured by a nearby thiocyanate vibrational probe to estimate changes in the electrostatic environment caused by changes at the Y32 position. We further compared vibrational energy shifts for each mutation to the hydration potential of the respective side chain and demonstrated that Y32 is less critical for recruiting water molecules into the active site to promote hydrolysis than Q61. Our results show a clear interplay between a steric contribution from Y32 and an electrostatic contribution from Q61 that are both critical for intrinsic GTP hydrolysis.
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Affiliation(s)
- Jackson C Fink
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Danielle Landry
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
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10
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Alsharoh H, Chiroi P, Isachesku E, Tanasa RA, Pop OL, Pirlog R, Berindan-Neagoe I. Personalizing Therapy Outcomes through Mitogen-Activated Protein Kinase Pathway Inhibition in Non-Small Cell Lung Cancer. Biomedicines 2024; 12:1489. [PMID: 39062063 PMCID: PMC11275062 DOI: 10.3390/biomedicines12071489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/18/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Lung cancer (LC) is a highly invasive malignancy and the leading cause of cancer-related deaths, with non-small cell lung cancer (NSCLC) as its most prevalent histological subtype. Despite all breakthroughs achieved in drug development, the prognosis of NSCLC remains poor. The mitogen-activated protein kinase signaling cascade (MAPKC) is a complex network of interacting molecules that can drive oncogenesis, cancer progression, and drug resistance when dysregulated. Over the past decades, MAPKC components have been used to design MAPKC inhibitors (MAPKCIs), which have shown varying efficacy in treating NSCLC. Thus, recent studies support the potential clinical use of MAPKCIs, especially in combination with other therapeutic approaches. This article provides an overview of the MAPKC and its inhibitors in the clinical management of NSCLC. It addresses the gaps in the current literature on different combinations of selective inhibitors while suggesting two particular therapy approaches to be researched in NSCLC: parallel and aggregate targeting of the MAPKC. This work also provides suggestions that could serve as a potential guideline to aid future research in MAPKCIs to optimize clinical outcomes in NSCLC.
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Affiliation(s)
- Hasan Alsharoh
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (H.A.); (P.C.); (E.I.); (I.B.-N.)
| | - Paul Chiroi
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (H.A.); (P.C.); (E.I.); (I.B.-N.)
| | - Ekaterina Isachesku
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (H.A.); (P.C.); (E.I.); (I.B.-N.)
| | | | - Ovidiu-Laurean Pop
- Department of Morphology Sciences, University of Oradea, 410087 Oradea, Romania;
| | - Radu Pirlog
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (H.A.); (P.C.); (E.I.); (I.B.-N.)
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (H.A.); (P.C.); (E.I.); (I.B.-N.)
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11
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Haertle L, Munawar U, Hernández HNC, Arroyo-Barea A, Heckel T, Cuenca I, Martin L, Höschle C, Müller N, Vogt C, Bischler T, Del Campo PL, Han S, Buenache N, Zhou X, Bassermann F, Waldschmidt J, Steinbrunn T, Rasche L, Stühmer T, Martinez-Lopez J, Martin Kortüm K, Barrio S. Clonal competition assays identify fitness signatures in cancer progression and resistance in multiple myeloma. Hemasphere 2024; 8:e110. [PMID: 38993727 PMCID: PMC11237348 DOI: 10.1002/hem3.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 04/15/2024] [Accepted: 05/09/2024] [Indexed: 07/13/2024] Open
Abstract
Multiple myeloma (MM) is a genetically heterogeneous disease and the management of relapses is one of the biggest clinical challenges. TP53 alterations are established high-risk markers and are included in the current disease staging criteria. KRAS is the most frequently mutated gene affecting around 20% of MM patients. Applying Clonal Competition Assays (CCA) by co-culturing color-labeled genetically modified cell models, we recently showed that mono- and biallelic alterations in TP53 transmit a fitness advantage to the cells. Here, we report a similar dynamic for two mutations in KRAS (G12A and A146T), providing a biological rationale for the high frequency of KRAS and TP53 alterations at MM relapse. Resistance mutations, on the other hand, did not endow MM cells with a general fitness advantage but rather presented a disadvantage compared to the wild-type. CUL4B KO and IKZF1 A152T transmit resistance against immunomodulatory agents, PSMB5 A20T to proteasome inhibition. However, MM cells harboring such lesions only outcompete the culture in the presence of the respective drug. To better prevent the selection of clones with the potential of inducing relapse, these results argue in favor of treatment-free breaks or a switch of the drug class given as maintenance therapy. In summary, the fitness benefit of TP53 and KRAS mutations was not treatment-related, unlike patient-derived drug resistance alterations that may only induce an advantage under treatment. CCAs are suitable models for the study of clonal evolution and competitive (dis)advantages conveyed by a specific genetic lesion of interest, and their dependence on external factors such as the treatment.
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Affiliation(s)
- Larissa Haertle
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
- Department of Medicine III, Klinikum rechts der Isar Technical University of Munich Munich Germany
| | - Umair Munawar
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Hipólito N C Hernández
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Andres Arroyo-Barea
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
- Department of Biochemistry and Molecular Biology, Pharmacy School Complutense University Madrid Madrid Spain
| | - Tobias Heckel
- Core Unit Systems Medicine University of Würzburg Würzburg Germany
| | - Isabel Cuenca
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Lucia Martin
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Carlotta Höschle
- TranslaTUM, Center for Translational Cancer Research Technical University of Munich Munich Germany
| | - Nicole Müller
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Cornelia Vogt
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | | | - Paula L Del Campo
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Seungbin Han
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Natalia Buenache
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Xiang Zhou
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Florian Bassermann
- Department of Medicine III, Klinikum rechts der Isar Technical University of Munich Munich Germany
- TranslaTUM, Center for Translational Cancer Research Technical University of Munich Munich Germany
| | - Johannes Waldschmidt
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Torsten Steinbrunn
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
- Department of Medical Oncology Dana-Farber Cancer Institute, Harvard Medical School Boston Massachusetts USA
| | - Leo Rasche
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Thorsten Stühmer
- Comprehensive Cancer Center Mainfranken University Hospital Würzburg Würzburg Germany
| | - Joaquin Martinez-Lopez
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - K Martin Kortüm
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Santiago Barrio
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
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12
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Rasche R, Apken LH, Michalke E, Kümmel D, Oeckinghaus A. κB-Ras proteins are fast-exchanging GTPases and function via nucleotide-independent binding of Ral GTPase-activating protein complexes. FEBS Lett 2024; 598:1769-1782. [PMID: 38604989 DOI: 10.1002/1873-3468.14860] [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: 09/26/2023] [Revised: 01/29/2024] [Accepted: 02/27/2024] [Indexed: 04/13/2024]
Abstract
κB-Ras (NF-κB inhibitor-interacting Ras-like protein) GTPases are small Ras-like GTPases but harbor interesting differences in important sequence motifs. They act in a tumor-suppressive manner as negative regulators of Ral (Ras-like) GTPase and NF-κB signaling, but little is known about their mode of function. Here, we demonstrate that, in contrast to predictions based on primary structure, κB-Ras GTPases possess hydrolytic activity. Combined with low nucleotide affinity, this renders them fast-cycling GTPases that are predominantly GTP-bound in cells. We characterize the impact of κB-Ras mutations occurring in tumors and demonstrate that nucleotide binding affects κB-Ras stability but is not strictly required for RalGAP (Ral GTPase-activating protein) binding. This demonstrates that κB-Ras control of RalGAP/Ral signaling occurs in a nucleotide-binding- and switch-independent fashion.
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Affiliation(s)
- René Rasche
- Institute of Biochemistry, University Münster, Germany
| | | | - Esther Michalke
- Institute of Molecular Tumor Biology, University Münster, Germany
| | - Daniel Kümmel
- Institute of Biochemistry, University Münster, Germany
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13
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Matsuda A, Masuzawa R, Takahashi K, Takano K, Endo T. MEK inhibitors and DA-Raf, a dominant-negative antagonist of the Ras-ERK pathway, prevent the migration and invasion of KRAS-mutant cancer cells. Cytoskeleton (Hoboken) 2024. [PMID: 38872577 DOI: 10.1002/cm.21881] [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: 04/05/2024] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
The Ras-induced ERK pathway (Raf-MEK-ERK signaling cascade) regulates a variety of cellular responses including cell proliferation, survival, and migration. Activating mutations in RAS genes, particularly in the KRAS gene, constitutively activate the ERK pathway, resulting in tumorigenesis, cancer cell invasion, and metastasis. DA-Raf1 (DA-Raf) is a splicing isoform of A-Raf and contains the Ras-binding domain but lacks the kinase domain. Consequently, DA-Raf antagonizes the Ras-ERK pathway in a dominant-negative manner and can serve as a tumor suppressor that targets mutant Ras protein-induced tumorigenesis. We show here that MEK inhibitors and DA-Raf interfere with the in vitro collective cell migration and invasion of human KRAS-mutant carcinoma cell lines, the lung adenocarcinoma A549, colorectal carcinoma HCT116, and pancreatic carcinoma MIA PaCa-2 cells. DA-Raf expression was silenced in these cancer cell lines. All these cell lines had high collective migration abilities and invasion properties in Matrigel, compared with nontumor cells. Their migration and invasion abilities were impaired by suppressing the ERK pathway with the MEK inhibitors U0126 and trametinib, an approved anticancer drug. Expression of DA-Raf in MIA PaCa-2 cells reduced the ERK activity and hindered the migration and invasion abilities. Therefore, DA-Raf may function as an invasion suppressor protein in the KRAS-mutant cancer cells by blocking the Ras-ERK pathway when DA-Raf expression is induced in invasive cancer cells.
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Affiliation(s)
- Aoi Matsuda
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Chiba, Japan
| | - Ryuichi Masuzawa
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Chiba, Japan
| | - Kazuya Takahashi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Chiba, Japan
| | - Kazunori Takano
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Chiba, Japan
| | - Takeshi Endo
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Chiba, Japan
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14
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Abudereheman M, Lian Z, Ainitu B. Weighted gene co-expression network analysis and whole genome sequencing identify potential lung cancer biomarkers. Front Oncol 2024; 14:1355527. [PMID: 38854719 PMCID: PMC11157001 DOI: 10.3389/fonc.2024.1355527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/08/2024] [Indexed: 06/11/2024] Open
Abstract
Background Tuberculosis (TB) leads to an increased risk of lung cancer (LC). However, the carcinogenetic mechanism of TB remains unclear. We constructed gene co-expression networks and carried out whole-exome sequencing (WES) to identify key modules, hub genes, and the most recurrently mutated genes involved in the pathogenesis of TB-associated LC. Methods The data used in this study were obtained from the Gene Expression Omnibus (GEO) and WES. First, we screened LC-related genes in GSE43458 and TB-related genes in GSE83456 by weighted gene co-expression network analysis (WGCNA). Subsequently, we screened differentially expressed genes related to LC and TB in GSE42834. We also performed WES of 15 patients (TB, n = 5; LC, n = 5; TB+LC, n = 5), constructed mutational profiles, and identified differences in the profiles of the three groups for further investigation. Results We identified 278 hub genes associated with tumorigenesis of pulmonary TB. Moreover, WES identified 112 somatic mutations in 25 genes in the 15 patients. Finally, four common genes (EGFR, HSPA2, CECR2, and LAMA3) were confirmed in a Venn diagram of the 278 hub genes and the mutated genes from WES. KEGG analysis revealed various pathway changes. The PI3K-AKT signaling pathway was the most enriched pathway, and all four genes are included in this pathway. Thus, these four genes and the PI3K-AKT signaling pathway may play important roles in LC. Conclusion Several potential genes and pathways related to TB-associated LC were identified, including EGFR and three target genes not found in previous studies. These genes are related to cell proliferation, colony formation, migration, and invasion, and provide a direction for future research into the mechanisms of LC co-occurring with TB. The PI3K-AKT signaling pathway was also identified as a potential key pathway involved in LC development.
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Affiliation(s)
| | | | - Baidurula Ainitu
- Oncology Department, The Eighth Affiliated Hospital of XinJiang Medical University, Urumqi, China
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15
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Torres-Jiménez J, Espinar JB, de Cabo HB, Berjaga MZ, Esteban-Villarrubia J, Fraile JZ, Paz-Ares L. Targeting KRAS G12C in Non-Small-Cell Lung Cancer: Current Standards and Developments. Drugs 2024; 84:527-548. [PMID: 38625662 DOI: 10.1007/s40265-024-02030-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/17/2024]
Abstract
Among the most common molecular alterations detected in non-small-cell lung cancer (NSCLC) are mutations in Kristen Rat Sarcoma viral oncogene homolog (KRAS). KRAS mutant NSCLC is a heterogenous group of diseases, different from other oncogene-driven tumors in terms of biology and response to therapies. Despite efforts to develop drugs aimed at inhibiting KRAS or its signaling pathways, KRAS had remained undruggable for decades. The discovery of a small pocket in the binding switch II region of KRASG12C has revolutionized the treatment of KRASG12C-mutated NSCLC patients. Sotorasib and adagrasib, direct KRASG12C inhibitors, have been approved by the US Food and Drug Administration (FDA) and other regulatory agencies for patients with previously treated KRASG12C-mutated NSCLC, and these advances have become practice changing. However, first-line treatment in KRASG12C-mutated NSCLC does not differ from NSCLC without actionable driver genomic alterations. Treatment with KRASG12C inhibitors is not curative and patients develop progressive disease, so understanding associated mechanisms of drug resistance is key. New KRASG12C inhibitors and several combination therapy strategies, including with immune checkpoint inhibitors, are being studied in clinical trials. The aim of this review is to explore the clinical impact of KRAS, and outline different treatment approaches, focusing on the novel treatment of KRASG12C-mutated NSCLC.
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Affiliation(s)
- Javier Torres-Jiménez
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain.
| | - Javier Baena Espinar
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
| | - Helena Bote de Cabo
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
| | - María Zurera Berjaga
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
| | - Jorge Esteban-Villarrubia
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
| | - Jon Zugazagoitia Fraile
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
- Lung Cancer Group, Clinical Research Program, CNIO (Centro Nacional de Investigaciones Oncológicas) and Instituto de Investigación i+12, Madrid, Spain
| | - Luis Paz-Ares
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
- Lung Cancer Group, Clinical Research Program, CNIO (Centro Nacional de Investigaciones Oncológicas) and Instituto de Investigación i+12, Madrid, Spain
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16
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Ajmal A, Danial M, Zulfat M, Numan M, Zakir S, Hayat C, Alabbosh KF, Zaki MEA, Ali A, Wei D. In Silico Prediction of New Inhibitors for Kirsten Rat Sarcoma G12D Cancer Drug Target Using Machine Learning-Based Virtual Screening, Molecular Docking, and Molecular Dynamic Simulation Approaches. Pharmaceuticals (Basel) 2024; 17:551. [PMID: 38794122 PMCID: PMC11124053 DOI: 10.3390/ph17050551] [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: 02/28/2024] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 05/26/2024] Open
Abstract
Single-point mutations in the Kirsten rat sarcoma (KRAS) viral proto-oncogene are the most common cause of human cancer. In humans, oncogenic KRAS mutations are responsible for about 30% of lung, pancreatic, and colon cancers. One of the predominant mutant KRAS G12D variants is responsible for pancreatic cancer and is an attractive drug target. At the time of writing, no Food and Drug Administration (FDA) approved drugs are available for the KRAS G12D mutant. So, there is a need to develop an effective drug for KRAS G12D. The process of finding new drugs is expensive and time-consuming. On the other hand, in silico drug designing methodologies are cost-effective and less time-consuming. Herein, we employed machine learning algorithms such as K-nearest neighbor (KNN), support vector machine (SVM), and random forest (RF) for the identification of new inhibitors against the KRAS G12D mutant. A total of 82 hits were predicted as active against the KRAS G12D mutant. The active hits were docked into the active site of the KRAS G12D mutant. Furthermore, to evaluate the stability of the compounds with a good docking score, the top two complexes and the standard complex (MRTX-1133) were subjected to 200 ns MD simulation. The top two hits revealed high stability as compared to the standard compound. The binding energy of the top two hits was good as compared to the standard compound. Our identified hits have the potential to inhibit the KRAS G12D mutation and can help combat cancer. To the best of our knowledge, this is the first study in which machine-learning-based virtual screening, molecular docking, and molecular dynamics simulation were carried out for the identification of new promising inhibitors for the KRAS G12D mutant.
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Affiliation(s)
- Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Muhammad Danial
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Maryam Zulfat
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Muhammad Numan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Sidra Zakir
- Department of Chemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Chandni Hayat
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | | | - Magdi E. A. Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Arif Ali
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongqing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang 473006, China
- Henan Biological Industry Group, 41 Nongye East Rd., Jinshui, Zhengzhou 450008, China
- Peng Cheng National Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China
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17
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Karachaliou A, Kotteas E, Fiste O, Syrigos K. Emerging Therapies in Kirsten Rat Sarcoma Virus (+) Non-Small-Cell Lung Cancer. Cancers (Basel) 2024; 16:1447. [PMID: 38672529 PMCID: PMC11048139 DOI: 10.3390/cancers16081447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/31/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
Kirsten rat sarcoma virus (KRAS) is the most frequently found oncogene in human cancers, including non-small-cell lung cancer (NSCLC). For many years, KRAS was considered "undruggable" due to its structure and difficult targeting. However, the discovery of the switch II region in the KRAS-G12C-mutated protein has changed the therapeutic landscape with the design and development of novel direct KRAS-G12C inhibitors. Sotorasib and adagrasib are FDA-approved targeted agents for pre-treated patients with KRAS-G12C-mutated NSCLC. Despite promising results, the efficacy of these novel inhibitors is limited by mechanisms of resistance. Ongoing studies are evaluating combination strategies for overcoming resistance. In this review, we summarize the biology of the KRAS protein and the characteristics of KRAS mutations. We then present current and emerging therapeutic approaches for targeting KRAS mutation subtypes intending to provide individualized treatment for lung cancer harboring this challenging driver mutation.
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Affiliation(s)
- Anastasia Karachaliou
- Oncology Unit, Third Department of Internal Medicine and Laboratory, Medical School, National and Kapodistrian University of Athens, “Sotiria” General Hospital, 11527 Athens, Greece; (E.K.); (O.F.); (K.S.)
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18
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Aspenström P. Miro GTPases at the Crossroads of Cytoskeletal Dynamics and Mitochondrial Trafficking. Cells 2024; 13:647. [PMID: 38607086 PMCID: PMC11012113 DOI: 10.3390/cells13070647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Miro GTPases are key components in the machinery responsible for transporting mitochondria and peroxisomes along microtubules, and also play important roles in regulating calcium homeostasis and organizing contact sites between mitochondria and the endoplasmic reticulum. Moreover, Miro GTPases have been shown to interact with proteins that actively regulate cytoskeletal organization and dynamics, suggesting that these GTPases participate in organizing cytoskeletal functions and organelle transport. Derailed mitochondrial transport is associated with neuropathological conditions such as Parkinson's and Alzheimer's diseases. This review explores our recent understanding of the diverse roles of Miro GTPases under cytoskeletal control, both under normal conditions and during the course of human diseases such as neuropathological disorders.
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Affiliation(s)
- Pontus Aspenström
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology (IGP), Uppsala University, SE 751 85 Uppsala, Sweden
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19
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Pagba CV, Gupta AK, Dilsha K, Sadrpour P, Jakubec J, Prakash P, van der Hoeven D, Cho KJ, Gilbertson S, Gorfe AA. Biophysical and Biochemical Characterization of Structurally Diverse Small Molecule Hits for KRAS Inhibition. Chembiochem 2024; 25:e202300827. [PMID: 38349283 DOI: 10.1002/cbic.202300827] [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: 12/12/2023] [Revised: 02/12/2024] [Indexed: 03/08/2024]
Abstract
We describe six compounds as early hits for the development of direct inhibitors of KRAS, an important anticancer drug target. We show that these compounds bind to KRAS with affinities in the low micromolar range and exert different effects on its interactions with binding partners. Some of the compounds exhibit selective binding to the activated form of KRAS and inhibit signal transduction through both the MAPK or the phosphatidylinositide 3-kinase PI3K-protein kinase B (AKT) pathway in cells expressing mutant KRAS. Most inhibit intrinsic and/or SOS-mediated KRAS activation while others inhibit RAS-effector interaction. We propose these compounds as starting points for the development of non-covalent allosteric KRAS inhibitors.
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Affiliation(s)
- Cynthia V Pagba
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Amit K Gupta
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Kasuni Dilsha
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Parisa Sadrpour
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Jacob Jakubec
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge St., Houston, Texas, 77030, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Scott Gilbertson
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
- Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, UTHealth MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, 6431 Fannin St., Houston, Texas, 77030, USA
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20
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Wu J, Li X, Wu C, Wang Y, Zhang J. Current advances and development strategies of targeting son of sevenless 1 (SOS1) in drug discovery. Eur J Med Chem 2024; 268:116282. [PMID: 38430853 DOI: 10.1016/j.ejmech.2024.116282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
The Son of Sevenless 1 (SOS1) guanine nucleotide exchange factor, prevalent across eukaryotic species, plays a pivotal role in facilitating the attachment of RAS protein to GTP, thereby regulating the activation of intracellular RAS proteins. This regulation is part of a feedback mechanism involving SOS1, which allows both activators and inhibitors of SOS1 to exert control over downstream signaling pathways, demonstrating potential anti-tumor effects. Predominantly, small molecule modulators that target SOS1 focus on a hydrophobic pocket within the CDC25 protein domain. The effectiveness of these modulators largely depends on their ability to interact with specific amino acids, notably Phe890 and Tyr884. This interaction is crucial for influencing the protein-protein interaction (PPI) between RAS and the catalytic domain of SOS1. Currently, most small molecule modulators targeting SOS1 are in the preclinical research phase, with a few advancing to clinical trials. This progression raises safety concerns, making the assurance of drug safety a primary consideration alongside the enhancement of efficacy in the development of SOS1 modulators. This review encapsulates recent advancements in the chemical categorization of SOS1 inhibitors and activators. It delves into the evolution of small molecule modulation targeting SOS1 and offers perspectives on the design of future generations of selective SOS1 small molecule modulators.
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Affiliation(s)
- Jialin Wu
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiaoxue Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chengyong Wu
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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21
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Dedden D, Nitsche J, Schneider EV, Thomsen M, Schwarz D, Leuthner B, Grädler U. Cryo-EM Structures of CRAF 2/14-3-3 2 and CRAF 2/14-3-3 2/MEK1 2 Complexes. J Mol Biol 2024; 436:168483. [PMID: 38331211 DOI: 10.1016/j.jmb.2024.168483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/22/2023] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
RAF protein kinases are essential effectors in the MAPK pathway and are important cancer drug targets. Structural understanding of RAF activation is so far based on cryo-electron microscopy (cryo-EM) and X-ray structures of BRAF in different conformational states as inactive or active complexes with KRAS, 14-3-3 and MEK1. In this study, we have solved the first cryo-EM structures of CRAF2/14-3-32 at 3.4 Å resolution and CRAF2/14-3-32/MEK12 at 4.2 Å resolution using CRAF kinase domain expressed as constitutively active Y340D/Y341D mutant in insect cells. The overall architecture of our CRAF2/14-3-32 and CRAF2/14-3-32/MEK12 cryo-EM structures is highly similar to corresponding BRAF structures in complex with 14-3-3 or 14-3-3/MEK1 and represent the activated dimeric RAF conformation. Our CRAF cryo-EM structures provide additional insights into structural understanding of the activated CRAF2/14-3-32/MEK12 complex.
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Affiliation(s)
- Dirk Dedden
- Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | - Julius Nitsche
- Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | | | - Maren Thomsen
- Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | - Daniel Schwarz
- The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Birgitta Leuthner
- The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Ulrich Grädler
- The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany.
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22
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Shang Y, Fu S, Hao Q, Ying H, Wang J, Shen T. Multiple medicinal chemistry strategies of targeting KRAS: State-of-the art and future directions. Bioorg Chem 2024; 144:107092. [PMID: 38271825 DOI: 10.1016/j.bioorg.2023.107092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/27/2024]
Abstract
KRAS is the most frequently mutated oncogene and drives the development and progression of malignancies, most notably non-small cell lung cancer (NSCLS), pancreatic ductal adenocarcinoma (PDAC) and colorectal cancer (CRC). However, KRAS proteins have maintained the reputation of being "undruggable" due to the lack of suitable deep pockets on its surface. One major milestone for KRAS inhibition was the discovery of the covalent inhibitors bond to the allosteric switch-II pocket of the KRASG12C protein. To date, the FDA has approved two KRASG12C inhibitors, sotorasib and adagrasib, for the treatment of patients with KRASG12C-driven cancers. Researchers have paid close attention to the development of inhibitors for other KRAS mutations and upstream regulatory factors. The KRAS targeted drug discovery has entered a state of rapid development. This article has aimed to present the current state of the art of drug development in the KRAS field. We systematically summarize recent advances in the discovery and optimization processes of direct KRAS inhibitors (including KRASG12C, KRASG12D, KRASG12A and KRASG12R inhibitors), indirect KRAS inhibitors (SOS1 and SHP2 inhibitors), pan-KRAS inhibitors, as well as proteolysis-targetingchimeras degrades and molecular chaperone modulators from the perspective of medicinal chemistry. We also discuss the current challenges and opportunities of KRAS inhibition and hope to shed light on future KRAS drug discovery.
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Affiliation(s)
- Yanguo Shang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Shengnan Fu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qingjing Hao
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Jinxin Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Tao Shen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.
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23
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Whitley MJ, Tran TH, Rigby M, Yi M, Dharmaiah S, Waybright TJ, Ramakrishnan N, Perkins S, Taylor T, Messing S, Esposito D, Nissley DV, McCormick F, Stephen AG, Turbyville T, Cornilescu G, Simanshu DK. Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties. SCIENCE ADVANCES 2024; 10:eadj4137. [PMID: 38354232 DOI: 10.1126/sciadv.adj4137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
KRAS, the most frequently mutated oncogene in human cancer, produces two isoforms, KRAS4a and KRAS4b, through alternative splicing. These isoforms differ in exon 4, which encodes the final 15 residues of the G-domain and hypervariable regions (HVRs), vital for trafficking and membrane localization. While KRAS4b has been extensively studied, KRAS4a has been largely overlooked. Our multidisciplinary study compared the structural and functional characteristics of KRAS4a and KRAS4b, revealing distinct structural properties and thermal stability. Position 151 influences KRAS4a's thermal stability, while position 153 affects binding to RAF1 CRD protein. Nuclear magnetic resonance analysis identified localized structural differences near sequence variations and provided a solution-state conformational ensemble. Notably, KRAS4a exhibits substantial transcript abundance in bile ducts, liver, and stomach, with transcript levels approaching KRAS4b in the colon and rectum. Functional disparities were observed in full-length KRAS variants, highlighting the impact of HVR variations on interaction with trafficking proteins and downstream effectors like RAF and PI3K within cells.
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Affiliation(s)
- Matthew J Whitley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Megan Rigby
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ming Yi
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Timothy J Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nitya Ramakrishnan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shelley Perkins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thomas Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gabriel Cornilescu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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24
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Chen R, Yang D, Liu Y, Wang B, Xu H. Case report outcome of cetuximab treatment in a metastatic colorectal cancer patient with novel KRAS P34R. Anticancer Drugs 2024; 35:195-198. [PMID: 38018809 DOI: 10.1097/cad.0000000000001493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Cetuximab [the epidermal growth factor receptor (EGFR)-targeting mAb] improves clinical outcomes when added to standard chemotherapy used in the treatment of metastatic colorectal cancer. Patients with hotspot mutations in Kirsten rat sarcoma viral oncogene ( KRAS ) mutation in exon 2 were not recommended to be treated with cetuximab. However, there is still a lack of clinical data for those unreported non-hotspot KRAS mutations in exon 2 and their response to cetuximab. In this study, we reported a 35-year-old woman who was diagnosed with stage IVA CRC with liver metastases. An exceptionally uncommon KRASP34R mutation in KRAS exon 2 was detected in tumor specimens by next-generation sequencing. This patient obtained limited benefit from first-line chemotherapy and did not respond to cetuximab in the second-line course. In the third-line course, the patient also did not respond to the combination treatment of furaquitinib and cindilimab. The patient died 8 months after treatment initiation. In this study, we found amplification of the rare oncogenic KRASP34R was not only associated with an aggressive phenotype, but also supported cancer resistance to cetuximab, chemotherapy, and immunotherapy.
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Affiliation(s)
- Ruizhi Chen
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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25
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Zhang JZ, Nguyen WH, Greenwood N, Rose JC, Ong SE, Maly DJ, Baker D. Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution. Nat Biotechnol 2024:10.1038/s41587-023-02107-w. [PMID: 38273065 DOI: 10.1038/s41587-023-02107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
The utility of genetically encoded biosensors for sensing the activity of signaling proteins has been hampered by a lack of strategies for matching sensor sensitivity to the physiological concentration range of the target. Here we used computational protein design to generate intracellular sensors of Ras activity (LOCKR-based Sensor for Ras activity (Ras-LOCKR-S)) and proximity labelers of the Ras signaling environment (LOCKR-based, Ras activity-dependent Proximity Labeler (Ras-LOCKR-PL)). These tools allow the detection of endogenous Ras activity and labeling of the surrounding environment at subcellular resolution. Using these sensors in human cancer cell lines, we identified Ras-interacting proteins in oncogenic EML4-Alk granules and found that Src-Associated in Mitosis 68-kDa (SAM68) protein specifically enhances Ras activity in the granules. The ability to subcellularly localize endogenous Ras activity should deepen our understanding of Ras function in health and disease and may suggest potential therapeutic strategies.
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Affiliation(s)
- Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - William H Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Greenwood
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John C Rose
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Dustin J Maly
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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26
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Tariq M, Ikeya T, Togashi N, Fairall L, Kamei S, Mayooramurugan S, Abbott LR, Hasan A, Bueno-Alejo C, Sukegawa S, Romartinez-Alonso B, Muro Campillo MA, Hudson AJ, Ito Y, Schwabe JW, Dominguez C, Tanaka K. Structural insights into the complex of oncogenic KRas4B G12V and Rgl2, a RalA/B activator. Life Sci Alliance 2024; 7:e202302080. [PMID: 37833074 PMCID: PMC10576006 DOI: 10.26508/lsa.202302080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
About a quarter of total human cancers carry mutations in Ras isoforms. Accumulating evidence suggests that small GTPases, RalA, and RalB, and their activators, Ral guanine nucleotide exchange factors (RalGEFs), play an essential role in oncogenic Ras-induced signalling. We studied the interaction between human KRas4B and the Ras association (RA) domain of Rgl2 (Rgl2RA), one of the RA-containing RalGEFs. We show that the G12V oncogenic KRas4B mutation changes the interaction kinetics with Rgl2RA The crystal structure of the KRas4BG12V: Rgl2RA complex shows a 2:2 heterotetramer where the switch I and switch II regions of each KRasG12V interact with both Rgl2RA molecules. This structural arrangement is highly similar to the HRasE31K:RALGDSRA crystal structure and is distinct from the well-characterised Ras:Raf complex. Interestingly, the G12V mutation was found at the dimer interface of KRas4BG12V with its partner. Our study reveals a potentially distinct mode of Ras:effector complex formation by RalGEFs and offers a possible mechanistic explanation for how the oncogenic KRas4BG12V hyperactivates the RalA/B pathway.
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Affiliation(s)
- Mishal Tariq
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Teppei Ikeya
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Naoyuki Togashi
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Louise Fairall
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Shun Kamei
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Sannojah Mayooramurugan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Lauren R Abbott
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Anab Hasan
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Carlos Bueno-Alejo
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Sakura Sukegawa
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Beatriz Romartinez-Alonso
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Miguel Angel Muro Campillo
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Andrew J Hudson
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Department of Chemistry, University of Leicester, Leicester, UK
| | - Yutaka Ito
- https://ror.org/00ws30h19 Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - John Wr Schwabe
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Cyril Dominguez
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- https://ror.org/04h699437 Leicester Institute of Structure and Chemical Biology, University of Leicester, Leicester, UK
| | - Kayoko Tanaka
- https://ror.org/04h699437 Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
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27
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Larsen EK, Abreu-Blanco M, Rabara D, Stephen AG. KRAS4b:RAF-1 Homogenous Time-Resolved Fluorescence Resonance Energy Transfer Assay for Drug Discovery. Methods Mol Biol 2024; 2797:159-175. [PMID: 38570459 DOI: 10.1007/978-1-0716-3822-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Homogenous time-resolved FRET (HTRF) assays have become one of the most popular tools for pharmaceutical drug screening efforts over the last two decades. Large Stokes shifts and long fluorescent lifetimes of lanthanide chelates lead to robust signal to noise, as well as decreased false positive rates compared to traditional assay techniques. In this chapter, we describe an HTRF protein-protein interaction (PPI) assay for the KRAS4b G-domain in the GppNHp-bound state and the RAF-1-RBD currently used for drug screens. Application of this assay contributes to the identification of lead compounds targeting the GTP-bound active state of K-RAS.
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Affiliation(s)
- Erik K Larsen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Maria Abreu-Blanco
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dana Rabara
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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28
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Zeng L, Wang J, Zhu H, Huang Y, Deng Y, Wei P, Nie J, Tang B, Chen A, Zhu S. The RRAS2 pathogenic variant (c.67G>T; p. Gly23Cys) produces Noonan syndrome with embryonal rhabdomyosarcoma. Mol Genet Genomic Med 2024; 12:e2313. [PMID: 37942564 PMCID: PMC10767593 DOI: 10.1002/mgg3.2313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/01/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Noonan syndrome (NS) due to the RRAS2 gene, the pathogenic variant is an extremely rare RASopathies. Our objective was to identify the potential site of RRAS2, combined with the literature review, to find the correlation between clinical phenotype and genotype. De novo missense mutations affect different aspects of the RRAS2 function, leading to hyperactivation of the RAS-MAPK signaling cascade. METHODS Conventional G-banding was used to analyze the chromosome karyotype of the patient. Copy number variation sequencing (CNV-seq) was used to detect the chromosomal gene microstructure of the patient and her parents. The exomes of the patient and her parents were sequenced using trio-based whole exome sequencing (trio-WES) technology. The candidate variant was verified by Sanger sequencing. The pathogenicity of the variant was predicted with a variety of bioinformatics tools. RESULTS Chromosome analysis of the proband revealed 46, XX, and no abnormality was found by CNV-seq. After sequencing and bioinformatics filtering, the variant of RRAS2(c.67G>T; p. Gly23Cys) was found in the proband, while the mutation was absent in her parents. To the best of our knowledge, our patient was with the typical Noonan syndrome, such as short stature, facial dysmorphism, and developmental delay. Furthermore, our study is the first case of NS with embryonal rhabdomyosarcoma (ERMS) caused by the RRAS2 gene mutation reported in China. CONCLUSIONS Our investigations suggested that the heterozygous missense of RRAS2 may be a potential causal variant in a rare cause of Noonan syndrome, expanding our understanding of the causally relevant mutations for this disorder.
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Affiliation(s)
- Lan Zeng
- Department of Medical Genetics and Prenatal DiagnosisSichuan Provincial Maternity and Child Health Care HospitalChengduChina
| | - Jin Wang
- Department of Medical Genetics and Prenatal DiagnosisSichuan Provincial Maternity and Child Health Care HospitalChengduChina
| | - Hui Zhu
- Department of PediatricsSichuan Provincial Maternity and Child Health Care HospitalChengduChina
| | - Yu Huang
- Department of PediatricsSichuan Provincial Maternity and Child Health Care HospitalChengduChina
| | - Yi Deng
- Department of Medical Genetics and Prenatal DiagnosisSichuan Provincial Maternity and Child Health Care HospitalChengduChina
| | - Ping Wei
- Department of Medical Genetics and Prenatal DiagnosisSichuan Provincial Maternity and Child Health Care HospitalChengduChina
| | - Jing Nie
- Department of Children's Health CareSichuan Provincial Maternity and Child Health Care HospitalChengduChina
| | - Bei Tang
- Department of UltrasoundSichuan Provincial Maternity and Child Health Care HospitalChengduChina
| | - Ai Chen
- Department of PediatricsSichuan Provincial Maternity and Child Health Care HospitalChengduChina
| | - Shuyao Zhu
- Department of PediatricsSichuan Provincial Maternity and Child Health Care HospitalChengduChina
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29
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Schaefer A, Hodge RG, Zhang H, Hobbs GA, Dilly J, Huynh M, Goodwin CM, Zhang F, Diehl JN, Pierobon M, Baldelli E, Javaid S, Guthrie K, Rashid NU, Petricoin EF, Cox AD, Hahn WC, Aguirre AJ, Bass AJ, Der CJ. RHOA L57V drives the development of diffuse gastric cancer through IGF1R-PAK1-YAP1 signaling. Sci Signal 2023; 16:eadg5289. [PMID: 38113333 PMCID: PMC10791543 DOI: 10.1126/scisignal.adg5289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 11/03/2023] [Indexed: 12/21/2023]
Abstract
Cancer-associated mutations in the guanosine triphosphatase (GTPase) RHOA are found at different locations from the mutational hotspots in the structurally and biochemically related RAS. Tyr42-to-Cys (Y42C) and Leu57-to-Val (L57V) substitutions are the two most prevalent RHOA mutations in diffuse gastric cancer (DGC). RHOAY42C exhibits a gain-of-function phenotype and is an oncogenic driver in DGC. Here, we determined how RHOAL57V promotes DGC growth. In mouse gastric organoids with deletion of Cdh1, which encodes the cell adhesion protein E-cadherin, the expression of RHOAL57V, but not of wild-type RHOA, induced an abnormal morphology similar to that of patient-derived DGC organoids. RHOAL57V also exhibited a gain-of-function phenotype and promoted F-actin stress fiber formation and cell migration. RHOAL57V retained interaction with effectors but exhibited impaired RHOA-intrinsic and GAP-catalyzed GTP hydrolysis, which favored formation of the active GTP-bound state. Introduction of missense mutations at KRAS residues analogous to Tyr42 and Leu57 in RHOA did not activate KRAS oncogenic potential, indicating distinct functional effects in otherwise highly related GTPases. Both RHOA mutants stimulated the transcriptional co-activator YAP1 through actin dynamics to promote DGC progression; however, RHOAL57V additionally did so by activating the kinases IGF1R and PAK1, distinct from the FAK-mediated mechanism induced by RHOAY42C. Our results reveal that RHOAL57V and RHOAY42C drive the development of DGC through distinct biochemical and signaling mechanisms.
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Affiliation(s)
- Antje Schaefer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Richard G. Hodge
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Haisheng Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - G. Aaron Hobbs
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julien Dilly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Minh Huynh
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Feifei Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Sehrish Javaid
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karson Guthrie
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Naim U. Rashid
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Adrienne D. Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew J. Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adam J. Bass
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Herbert Irving Comprehensive Cancer Center at Columbia University, New York, NY 10032, USA
| | - Channing J. Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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30
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Bahar ME, Kim HJ, Kim DR. Targeting the RAS/RAF/MAPK pathway for cancer therapy: from mechanism to clinical studies. Signal Transduct Target Ther 2023; 8:455. [PMID: 38105263 PMCID: PMC10725898 DOI: 10.1038/s41392-023-01705-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/03/2023] [Accepted: 11/12/2023] [Indexed: 12/19/2023] Open
Abstract
Metastatic dissemination of solid tumors, a leading cause of cancer-related mortality, underscores the urgent need for enhanced insights into the molecular and cellular mechanisms underlying metastasis, chemoresistance, and the mechanistic backgrounds of individuals whose cancers are prone to migration. The most prevalent signaling cascade governed by multi-kinase inhibitors is the mitogen-activated protein kinase (MAPK) pathway, encompassing the RAS-RAF-MAPK kinase (MEK)-extracellular signal-related kinase (ERK) pathway. RAF kinase is a primary mediator of the MAPK pathway, responsible for the sequential activation of downstream targets, such as MEK and the transcription factor ERK, which control numerous cellular and physiological processes, including organism development, cell cycle control, cell proliferation and differentiation, cell survival, and death. Defects in this signaling cascade are associated with diseases such as cancer. RAF inhibitors (RAFi) combined with MEK blockers represent an FDA-approved therapeutic strategy for numerous RAF-mutant cancers, including melanoma, non-small cell lung carcinoma, and thyroid cancer. However, the development of therapy resistance by cancer cells remains an important barrier. Autophagy, an intracellular lysosome-dependent catabolic recycling process, plays a critical role in the development of RAFi resistance in cancer. Thus, targeting RAF and autophagy could be novel treatment strategies for RAF-mutant cancers. In this review, we delve deeper into the mechanistic insights surrounding RAF kinase signaling in tumorigenesis and RAFi-resistance. Furthermore, we explore and discuss the ongoing development of next-generation RAF inhibitors with enhanced therapeutic profiles. Additionally, this review sheds light on the functional interplay between RAF-targeted therapies and autophagy in cancer.
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Affiliation(s)
- Md Entaz Bahar
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Hyun Joon Kim
- Department of Anatomy and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea.
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31
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Liang X, Jung SY, Fong LW, Bildik G, Gray JP, Mao W, Zhang S, Millward SW, Gorfe AA, Zhou Y, Lu Z, Bast RC. Membrane anchoring of the DIRAS3 N-terminal extension permits tumor suppressor function. iScience 2023; 26:108151. [PMID: 37915607 PMCID: PMC10616557 DOI: 10.1016/j.isci.2023.108151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/16/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023] Open
Abstract
DIRAS3 is an imprinted tumor suppressor gene encoding a GTPase that has a distinctive N-terminal extension (NTE) not found in other RAS proteins. This NTE and the prenylated C-terminus are required for DIRAS3-mediated inhibition of RAS/MAP signaling and PI3K activity at the plasma membrane. In this study, we applied biochemical, biophysical, and computational methods to characterize the structure and function of the NTE. The NTE peptide recognizes phosphoinositides PI(3,4,5)P3 and PI(4,5)P2 with rapid kinetics and strong affinity. Lipid binding induces NTE structural change from disorder to amphipathic helix. Mass spectrometry identified N-myristoylation of DIRAS3. All-atom molecular dynamic simulations predict DIRAS3 could adhere to the membrane through both termini, suggesting the NTE is involved in targeting and stabilizing DIRAS3 on the membrane by double anchoring. Overall, our results are consistent with DIRAS3's function as a tumor suppressor, whereby the membrane-bound DIRAS3 can effectively target PI3K and KRAS at the membrane.
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Affiliation(s)
- Xiaowen Liang
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Sung Yun Jung
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lon Wolf Fong
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Gamze Bildik
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Joshua P. Gray
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Weiqun Mao
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Shuxing Zhang
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Steven W. Millward
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Zhen Lu
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Robert C. Bast
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
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32
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Araya MK, Gorfe AA. Conformational ensemble-dependent lipid recognition and segregation by prenylated intrinsically disordered regions in small GTPases. Commun Biol 2023; 6:1111. [PMID: 37919400 PMCID: PMC10622456 DOI: 10.1038/s42003-023-05487-6] [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: 05/15/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023] Open
Abstract
We studied diverse prenylated intrinsically disordered regions (PIDRs) of Ras and Rho family small GTPases using long timescale atomistic molecular dynamics simulations in an asymmetric model membrane of phosphatidylcholine (PC) and phosphatidylserine (PS) lipids. Here we show that conformational plasticity is a key determinant of lipid sorting by polybasic PIDRs and provide evidence for lipid sorting based on both headgroup and acyl chain structures. We further show that conformational ensemble-based lipid recognition is generalizable to all polybasic PIDRs, and that the sequence outside the polybasic domain (PBD) modulates the conformational plasticity, bilayer adsorption, and interactions of PIDRs with membrane lipids. Specifically, we find that palmitoylation, the ratio of basic to acidic residues, and the hydrophobic content of the sequence outside the PBD significantly impact the diversity of conformational substates and hence the extent of conformation-dependent lipid interactions. We thus propose that the PBD is required but not sufficient for the full realization of lipid sorting by prenylated PBD-containing membrane anchors, and that the membrane anchor is not only responsible for high affinity membrane binding but also directs the protein to the right target membrane where it participates in lipid sorting.
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Affiliation(s)
- Mussie K Araya
- McGovern Medical School, University of Texas Health Science Center at Houston, Department of Integrative Biology and Pharmacology, 6431 Fannin St., Houston, TX, 77030, USA
| | - Alemayehu A Gorfe
- McGovern Medical School, University of Texas Health Science Center at Houston, Department of Integrative Biology and Pharmacology, 6431 Fannin St., Houston, TX, 77030, USA.
- Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, UTHealth MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, 6431 Fannin St., TX, 77030, USA.
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33
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Zhang J, Darman L, Hassan MS, Von Holzen U, Awasthi N. Targeting KRAS for the potential treatment of pancreatic ductal adenocarcinoma: Recent advancements provide hope (Review). Oncol Rep 2023; 50:206. [PMID: 37800636 PMCID: PMC10570661 DOI: 10.3892/or.2023.8643] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 10/07/2023] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRAS) is one of the most frequently mutated oncogenes in solid tumors. More than 90% of pancreatic ductal adenocarcinoma (PDAC) are driven by mutations in the KRAS gene, suggesting the importance of targeting this oncogene in PDAC. Initial efforts to target KRAS have been unsuccessful due to its small size, high affinity for guanosine triphosphate/guanosine diphosphate, and lack of distinct drug‑binding pockets. Therefore, much of the focus has been directed at inhibiting the activation of major signaling pathways downstream of KRAS, most notably the PI3K/AKT and RAF/MAPK pathways, using tyrosine kinase inhibitors and monoclonal antibodies. While preclinical studies showed promising results, clinical data using the inhibitors alone and in combination with other standard therapies have shown limited practicality, largely due to the lack of efficacy and dose‑limiting toxicities. Recent therapeutic approaches for KRAS‑driven tumors focus on mutation‑specific drugs such as selective KRASG12C inhibitors and son of sevenless 1 pan‑KRAS inhibitors. While KRASG12C inhibitors showed great promise against patients with non‑small cell lung cancer (NSCLC) harboring KRASG12C mutations, they were not efficacious in PDAC largely because the major KRAS mutant isoforms in PDAC are G12D, G12V, and G12R. As a result, KRASG12D and pan‑KRAS inhibitors are currently under investigation as potential therapeutic options for PDAC. The present review summarized the importance of KRAS oncogenic signaling, challenges in its targeting, and preclinical and clinical targeted agents including recent direct KRAS inhibitors for blocking KRAS signaling in PDAC.
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Affiliation(s)
- Joshua Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Lily Darman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Md Sazzad Hassan
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Surgery, Indiana University School of Medicine, South Bend, IN 46617, USA
| | - Urs Von Holzen
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Surgery, Indiana University School of Medicine, South Bend, IN 46617, USA
- Goshen Center for Cancer Care, Goshen, IN 46526, USA
- University of Basel School of Medicine, 4056 Basel, Switzerland
| | - Niranjan Awasthi
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Surgery, Indiana University School of Medicine, South Bend, IN 46617, USA
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Zhang JZ, Ong SE, Baker D, Maly DJ. Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560617. [PMID: 37873412 PMCID: PMC10592919 DOI: 10.1101/2023.10.02.560617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Recently developed covalent inhibitors for RasG12C provide the first pharmacological tools to target mutant Ras-driven cancers. However, the rapid development of resistance to current clinical Ras G12C inhibitors is common. Presumably, a subpopulation of RasG12C-expressing cells adapt their signaling to evade these inhibitors and the mechanisms for this phenomenon are unclear due to the lack of tools that can measure signaling with single-cell resolution. Here, we utilized recently developed Ras sensors to profile the environment of active Ras and to measure the activity of endogenous Ras in order to pair structure (Ras signalosome) to function (Ras activity), respectively, at a single-cell level. With this approach, we identified a subpopulation of KRasG12C cells treated with RasG12C-GDP inhibitors underwent oncogenic signaling and metabolic changes driven by WT Ras at the golgi and mutant Ras at the mitochondria, respectively. Our Ras sensors identified Major Vault Protein (MVP) as a mediator of Ras activation at both compartments by scaffolding Ras signaling pathway components and metabolite channels. We found that recently developed RasG12C-GTP inhibitors also led to MVP-mediated WT Ras signaling at the golgi, demonstrating that this a general mechanism RasG12C inhibitor resistance. Overall, single-cell analysis of structure-function relationships enabled the discovery of a RasG12C inhibitor-resistant subpopulation driven by MVP, providing insight into the complex and heterogenous rewiring occurring during drug resistance in cancer.
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Affiliation(s)
- Jason Z. Zhang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Dustin J. Maly
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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35
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Ajmal A, Ali Y, Khan A, Wadood A, Rehman AU. Identification of novel peptide inhibitors for the KRas-G12C variant to prevent oncogenic signaling. J Biomol Struct Dyn 2023; 41:8866-8875. [PMID: 36300526 DOI: 10.1080/07391102.2022.2138550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/15/2022] [Indexed: 10/31/2022]
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRas) activating mutations are common in solid tumors, accounting for 90%, 45%, and 35% of pancreatic, colorectal, and lung cancers (LC), respectively. Each year, nearly 150k new cases (both men and women) of KRas-mutated malignancies are reported in the United States. NSCLC (non-small cell lung cancer) accounts for 80% of all LC cases. KRas mutations are found in 15% to 25% of NSCLC patients. The main cause of NSCLC is the KRas-G12C mutation. The drugs Sotorasib and Adagrasib were recently developed to treat advanced NSCLC caused by the KRas-G12C mutation. Most patients do not respond to KRas-G12C inhibitors due to cellular, molecular, and genetic resistance. Because of their safety, efficacy, and selectivity, peptide inhibitors have the potential to treat newly developing KRas mutations. Based on the KRas mutations, peptide inhibitors that are highly selective and specific to individual lung cancers can be rationally designed. The current study uses an alanine and residue scanning approach to design peptide inhibitors for KRas-G12C based on the known peptide. Our findings show that substitution of F3K, G11T, L8C, T14C, K13D, G11S, and G11P considerably enhances the binding affinity of the novel peptides, whereas F3K, G11T, L8C, and T14C peptides have higher stability and favorable binding to the altered peptides. Overall, our study paves the road for the development of potential therapeutic peptidomimetics that target the KRas-G12C complex and may inhibit the KRas and SOS complex from interacting.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
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36
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Wu L, Wang F, Moncman CL, Pandey M, Clarke HA, Frazier HN, Young LE, Gentry MS, Cai W, Thibault O, Sun RC, Andres DA. RIT1 regulation of CNS lipids RIT1 deficiency Alters cerebral lipid metabolism and reduces white matter tract oligodendrocytes and conduction velocities. Heliyon 2023; 9:e20384. [PMID: 37780758 PMCID: PMC10539968 DOI: 10.1016/j.heliyon.2023.e20384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 07/21/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023] Open
Abstract
Oligodendrocytes (OLs) generate lipid-rich myelin membranes that wrap axons to enable efficient transmission of electrical impulses. Using a RIT1 knockout mouse model and in situ high-resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) coupled with MS-based lipidomic analysis to determine the contribution of RIT1 to lipid homeostasis. Here, we report that RIT1 loss is associated with altered lipid levels in the central nervous system (CNS), including myelin-associated lipids within the corpus callosum (CC). Perturbed lipid metabolism was correlated with reduced numbers of OLs, but increased numbers of GFAP+ glia, in the CC, but not in grey matter. This was accompanied by reduced myelin protein expression and axonal conduction deficits. Behavioral analyses revealed significant changes in voluntary locomotor activity and anxiety-like behavior in RIT1KO mice. Together, these data reveal an unexpected role for RIT1 in the regulation of cerebral lipid metabolism, which coincide with altered white matter tract oligodendrocyte levels, reduced axonal conduction velocity, and behavioral abnormalities in the CNS.
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Affiliation(s)
- Lei Wu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
| | - Fang Wang
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
| | - Carole L. Moncman
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
| | - Mritunjay Pandey
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
| | - Harrison A. Clarke
- Department of Neuroscience, College of Medicine, University of Kentucky, KY 40536, USA
| | - Hilaree N. Frazier
- Department of Pharmacological and Nutritional Sciences, College of Medicine, University of Kentucky, KY 40536, USA
| | - Lyndsay E.A. Young
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
- Markey Cancer Center, Lexington, KY 40536, USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
- Markey Cancer Center, Lexington, KY 40536, USA
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL 32611, USA
- Center for Advanced Spatial Biomolecule Research, University of Florida, College of Medicine, Gainesville, FL 32611, USA
| | - Weikang Cai
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, NY 11568, USA
| | - Olivier Thibault
- Department of Pharmacological and Nutritional Sciences, College of Medicine, University of Kentucky, KY 40536, USA
| | - Ramon C. Sun
- Department of Neuroscience, College of Medicine, University of Kentucky, KY 40536, USA
- Markey Cancer Center, Lexington, KY 40536, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL 32611, USA
- Center for Advanced Spatial Biomolecule Research, University of Florida, College of Medicine, Gainesville, FL 32611, USA
| | - Douglas A. Andres
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
- Markey Cancer Center, Lexington, KY 40536, USA
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, KY 40536, USA
- Gill Heart and Vascular Institute, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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37
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Palacio-Castañeda V, van de Crommert B, Verploegen E, Overeem M, van Oostrum J, Verdurmen WP. Potent and selective eradication of tumor cells by an EpCAM-targeted Ras-degrading enzyme. Mol Ther Oncolytics 2023; 30:16-26. [PMID: 37485031 PMCID: PMC10362089 DOI: 10.1016/j.omto.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/22/2023] [Indexed: 07/25/2023] Open
Abstract
Despite decades of efforts, an urgent need remains to develop tumor cell-selective rat sarcoma (Ras)-targeting therapies that can treat patients with Ras-driven tumors. Here we report modular engineered proteins that degrade Ras selectively in tumor cells that overexpress the tumor cell marker epithelial cell adhesion molecule (EpCAM) by fusing the Ras degrader Ras-Rap1-specific endopeptidase with the translocation domain of the Pseudomonas aeruginosa exotoxin A (ETA) or diphtheria toxin (DT). Redirection to EpCAM is achieved by a designed ankyrin repeat protein. In two-dimensional tumor cell cultures, complete degradation of Ras proteins after 24 h was observed with EpCAM-targeted Ras degraders fused to ETA or DT in EpCAM-overexpressing MCF7 and HCT116 cells, with median inhibition concentration values at sub-nanomolar levels. The viability of EpCAM-low non-cancerous fibroblasts remained unaffected. In a three-dimensional (3D) tumor-on-a-chip system that mimics the natural tumor microenvironment, effective Ras degradation and selective toxicity toward tumor cells, particularly with the ETA-fused constructs, was determined on-chip. To conclude, we demonstrate the potential of modular engineered proteins to kill tumor cells highly selectively by simultaneously exploiting EpCAM as a tumor-specific cell surface molecule as well as Ras as an intracellular oncotarget in a 3D system mimicking the natural tumor microenvironment.
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Affiliation(s)
- Valentina Palacio-Castañeda
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands
| | - Bas van de Crommert
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands
| | - Elke Verploegen
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands
| | - Mike Overeem
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands
| | - Jenny van Oostrum
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands
| | - Wouter P.R. Verdurmen
- Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands
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38
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Araya MK, Gorfe AA. Conformational ensemble dependent lipid recognition and segregation by prenylated intrinsically disordered regions in small GTPases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553039. [PMID: 37609330 PMCID: PMC10441427 DOI: 10.1101/2023.08.11.553039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
We studied diverse prenylated intrinsically disordered regions (PIDRs) of Ras and Rho family small GTPases using long timescale atomistic molecular dynamics simulations in an asymmetric model membrane of phosphatidylcholine (PC) and phosphatidylserine (PS) lipids. We show that conformational plasticity is a key determinant of lipid sorting by polybasic PIDRs and provide evidence for lipid sorting based on both headgroup and acyl chain structures. We further show that conformational ensemble-based lipid recognition is generalizable to all polybasic PIDRs, and that the sequence outside the polybasic domain (PBD) modulates the conformational plasticity, bilayer adsorption, and interactions of PIDRs with membrane lipids. Specifically, we found that palmitoylation, the ratio of basic to acidic residues, and the hydrophobic content of the sequence outside the PBD significantly impact the diversity of conformational substates and hence the extent of conformation-dependent lipid interactions. We thus propose that the PBD is required but not sufficient for the full realization of lipid sorting by prenylated PBD-containing membrane anchors, and that the membrane anchor is not only responsible for high affinity membrane binding but also directs the protein to the right target membrane where it participates in lipid sorting.
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39
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Simão S, Agostinho RR, Martínez-Ruiz A, Araújo IM. Regulation of Ras Signaling by S-Nitrosylation. Antioxidants (Basel) 2023; 12:1562. [PMID: 37627556 PMCID: PMC10451275 DOI: 10.3390/antiox12081562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Ras are a family of small GTPases that function as signal transduction mediators and are involved in cell proliferation, migration, differentiation and survival. The significance of Ras is further evidenced by the fact that Ras genes are among the most mutated oncogenes in different types of cancers. After translation, Ras proteins can be targets of post-translational modifications (PTM), which can alter the intracellular dynamics of the protein. In this review, we will focus on how S-nitrosylation of Ras affects the way these proteins interact with membranes, its cellular localization, and its activity. S-Nitrosylation occurs when a nitrosyl moiety of nitric oxide (NO) is covalently attached to a thiol group of a cysteine residue in a target protein. In Ras, the conserved Cys118 is the most surface-exposed Cys and the preferable residue for NO action, leading to the initiation of transduction events. Ras transduces the mitogen-activated protein kinases (MAPK), the phosphoinositide-3 kinase (PI3K) and the RalGEF cellular pathways. S-Nitrosylation of elements of the RalGEF cascade remains to be identified. On the contrary, it is well established that several components of the MAPK and PI3K pathways, as well as different proteins associated with these cascades, can be modified by S-nitrosylation. Overall, this review presents a better understanding of Ras S-nitrosylation, increasing the knowledge on the dynamics of these proteins in the presence of NO and the underlying implications in cellular signaling.
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Affiliation(s)
- Sónia Simão
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139 Faro, Portugal;
- Faculty of Medicine and Biomedical Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Rafaela Ribeiro Agostinho
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139 Faro, Portugal;
- Faculty of Medicine and Biomedical Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Antonio Martínez-Ruiz
- Unidad de Investigación, Hospital Universitario Santa Cristina, Instituto de Investigación Sanitaria Princesa, 28009 Madrid, Spain;
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Inês Maria Araújo
- Algarve Biomedical Center Research Institute (ABC-RI), University of Algarve, 8005-139 Faro, Portugal;
- Faculty of Medicine and Biomedical Sciences, University of Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, 1400-038 Lisbon, Portugal
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Oyedele AQK, Ogunlana AT, Boyenle ID, Ibrahim NO, Gbadebo IO, Owolabi NA, Ayoola AM, Francis AC, Eyinade OH, Adelusi TI. Pharmacophoric analogs of sotorasib-entrapped KRAS G12C in its inactive GDP-bound conformation: covalent docking and molecular dynamics investigations. Mol Divers 2023; 27:1795-1807. [PMID: 36271195 DOI: 10.1007/s11030-022-10534-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022]
Abstract
For decades, KRAS G12C was considered an undruggable target. However, in recent times, a covalent inhibitor known as sotorasib was discovered and approved for the treatment of patients with KRAS G12C-driven cancers. Ever since the discovery of this drug, several preclinical efforts have focused on identifying novel therapeutic candidates that could act as covalent binders of KRAS G12C. Despite these intensive efforts, only a few KRAS G12C inhibitors have entered clinical trials. Hence, this highlights the need to develop effective drug candidates that could be used in the treatment of KRAS G12C-driven cancers. Herein, we embarked on a virtual screening campaign that involves the identification of pharmacophores of sotorasib that could act as covalent arsenals against the KRAS G12C target. To our knowledge, this is the first computational study that involves the compilation of sotorasib pharmacophores from an online chemical database against KRAS G12C. After this library of chemical entities was compiled, we conducted a covalent docking-based virtual screening that revealed three promising drug candidates (CID_146235944, CID_160070181, and CID_140956845) binding covalently to the crucial nucleophilic side chain of Cys12 and interact with the residues that form the cryptic allosteric pocket of KRAS G12C in its inactive GDP-bound conformation. Subsequently, ADMET profiling portrayed the covalent inhibitors as lead-like candidates, while 100 ns molecular dynamics was used to substantiate their stability. Although our overall computational study has shown the promising potential of the lead-like candidates in impeding oncogenic RAS signaling, more experimental efforts are needed to validate and establish their preclinical relevance. Implication of KRAS G12C in cancer and computational approach towards impeding the KRAS G12C RAS signaling.
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Affiliation(s)
- Abdul-Quddus Kehinde Oyedele
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
- Department of Chemistry, University of New Haven, West Haven, CT, USA
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Abdeen Tunde Ogunlana
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Ibrahim Damilare Boyenle
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
- Department of Chemistry and Biochemistry, University of Maryland, Maryland, USA
- College of Health Sciences, Crescent University, Abeokuta, Nigeria
| | | | | | | | - Ashiru Mojeed Ayoola
- Biochemistry Unit, Department of Chemical Sciences, College of Natural and Applied Science, Fountain University, Osogbo, Nigeria
| | - Ann Christopher Francis
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Olajumoke Habeebah Eyinade
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Temitope Isaac Adelusi
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria.
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Tomazini A, Shifman JM. Targeting Ras with protein engineering. Oncotarget 2023; 14:672-687. [PMID: 37395750 DOI: 10.18632/oncotarget.28469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Ras proteins are small GTPases that regulate cell growth and division. Mutations in Ras genes are associated with many types of cancer, making them attractive targets for cancer therapy. Despite extensive efforts, targeting Ras proteins with small molecules has been extremely challenging due to Ras's mostly flat surface and lack of small molecule-binding cavities. These challenges were recently overcome by the development of the first covalent small-molecule anti-Ras drug, sotorasib, highlighting the efficacy of Ras inhibition as a therapeutic strategy. However, this drug exclusively inhibits the Ras G12C mutant, which is not a prevalent mutation in most cancer types. Unlike the G12C variant, other Ras oncogenic mutants lack reactive cysteines, rendering them unsuitable for targeting via the same strategy. Protein engineering has emerged as a promising method to target Ras, as engineered proteins have the ability to recognize various surfaces with high affinity and specificity. Over the past few years, scientists have engineered antibodies, natural Ras effectors, and novel binding domains to bind to Ras and counteract its carcinogenic activities via a variety of strategies. These include inhibiting Ras-effector interactions, disrupting Ras dimerization, interrupting Ras nucleotide exchange, stimulating Ras interaction with tumor suppressor genes, and promoting Ras degradation. In parallel, significant advancements have been made in intracellular protein delivery, enabling the delivery of the engineered anti-Ras agents into the cellular cytoplasm. These advances offer a promising path for targeting Ras proteins and other challenging drug targets, opening up new opportunities for drug discovery and development.
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Affiliation(s)
- Atilio Tomazini
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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Jang G, Kweon J, Kim Y. CRISPR prime editing for unconstrained correction of oncogenic KRAS variants. Commun Biol 2023; 6:681. [PMID: 37391511 PMCID: PMC10313713 DOI: 10.1038/s42003-023-05052-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/16/2023] [Indexed: 07/02/2023] Open
Abstract
KRAS is the most commonly mutated RAS family gene and is a primary cause of the occurrence of several types of cancer. However, KRAS mutations have several unique and diverse molecular identities, making it difficult to find specific treatments. Here, we developed universal pegRNAs which can correct all types of G12 and G13 oncogenic KRAS mutations with CRISPR-mediated prime editors (PEs). The universal pegRNA successfully corrected 12 types of KRAS mutations, accounting for 94% of all known KRAS mutations, by up to 54.8% correction frequency in HEK293T/17 cells. We also applied the universal pegRNA to correct endogenous KRAS mutations in human cancer cells and found that G13D KRAS mutation was successfully corrected to wild-type KRAS sequences with up to 40.6% correction frequency without indel mutations. We propose prime editing with the universal pegRNA as a 'one-to-many' potential therapeutic strategy for KRAS oncogene variants.
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Affiliation(s)
- Gayoung Jang
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jiyeon Kweon
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yongsub Kim
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Dandekar B, Ahalawat N, Sinha S, Mondal J. Markov State Models Reconcile Conformational Plasticity of GTPase with Its Substrate Binding Event. JACS AU 2023; 3:1728-1741. [PMID: 37388689 PMCID: PMC10302740 DOI: 10.1021/jacsau.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 07/01/2023]
Abstract
Ras GTPase is an enzyme that catalyzes the hydrolysis of guanosine triphosphate (GTP) and plays an important role in controlling crucial cellular signaling pathways. However, this enzyme has always been believed to be undruggable due to its strong binding affinity with its native substrate GTP. To understand the potential origin of high GTPase/GTP recognition, here we reconstruct the complete process of GTP binding to Ras GTPase via building Markov state models (MSMs) using a 0.1 ms long all-atom molecular dynamics (MD) simulation. The kinetic network model, derived from the MSM, identifies multiple pathways of GTP en route to its binding pocket. While the substrate stalls onto a set of non-native metastable GTPase/GTP encounter complexes, the MSM accurately discovers the native pose of GTP at its designated catalytic site in crystallographic precision. However, the series of events exhibit signatures of conformational plasticity in which the protein remains trapped in multiple non-native conformations even when GTP has already located itself in its native binding site. The investigation demonstrates mechanistic relays pertaining to simultaneous fluctuations of switch 1 and switch 2 residues which remain most instrumental in maneuvering the GTP-binding process. Scanning of the crystallographic database reveals close resemblance between observed non-native GTP binding poses and precedent crystal structures of substrate-bound GTPase, suggesting potential roles of these binding-competent intermediates in allosteric regulation of the recognition process.
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Affiliation(s)
| | - Navjeet Ahalawat
- Department
of Bioinformatics and Computational Biology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004 Haryana, India
| | - Suman Sinha
- Institute
of Pharmaceutical Research, GLA University, Mathura, 281406 Uttar Pradesh, India
| | - Jagannath Mondal
- Tata
Institute of Fundamental Research, Hyderabad, Telangana 500046, India
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Ikari M, Yagi H, Kasai T, Inomata K, Ito M, Higuchi K, Matsuda N, Ito Y, Kigawa T. Direct Observation of Membrane-Associated H-Ras in the Native Cellular Environment by In-Cell 19F-NMR Spectroscopy. JACS AU 2023; 3:1658-1669. [PMID: 37388687 PMCID: PMC10302746 DOI: 10.1021/jacsau.3c00108] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 07/01/2023]
Abstract
Ras acts as a molecular switch to control intracellular signaling on the plasma membrane (PM). Elucidating how Ras associates with PM in the native cellular environment is crucial for understanding its control mechanism. Here, we used in-cell nuclear magnetic resonance (NMR) spectroscopy combined with site-specific 19F-labeling to explore the membrane-associated states of H-Ras in living cells. The site-specific incorporation of p-trifluoromethoxyphenylalanine (OCF3Phe) at three different sites of H-Ras, i.e., Tyr32 in switch I, Tyr96 interacting with switch II, and Tyr157 on helix α5, allowed the characterization of their conformational states depending on the nucleotide-bound states and an oncogenic mutational state. Exogenously delivered 19F-labeled H-Ras protein containing a C-terminal hypervariable region was assimilated via endogenous membrane-trafficking, enabling proper association with the cell membrane compartments. Despite poor sensitivity of the in-cell NMR spectra of membrane-associated H-Ras, the Bayesian spectral deconvolution identified distinct signal components on three 19F-labeled sites, thus offering the conformational multiplicity of H-Ras on the PM. Our study may be helpful in elucidating the atomic-scale picture of membrane-associated proteins in living cells.
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Affiliation(s)
- Masaomi Ikari
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Hiromasa Yagi
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Takuma Kasai
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
- PRESTO/Japan
Science and Technology Agency, Saitama 332-0012, Japan
| | - Kohsuke Inomata
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
- PRESTO/Japan
Science and Technology Agency, Saitama 332-0012, Japan
| | - Masahiro Ito
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Kae Higuchi
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Natsuko Matsuda
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
- SI Innovation
Center, Taiyo Nippon Sanso Corporation, Tokyo 206-0001, Japan
| | - Yutaka Ito
- Department
of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Takanori Kigawa
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
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Tripathi K, Maurya N, Goel A, Singhai A, Garg M. Immunohistochemical expressions of EMT markers in pan-RAS-pERK1/2-positive tumors improve diagnosis and prognosis assessment of non-muscle invasive bladder cancer and muscle invasive bladder cancer patients. Mol Cell Biochem 2023; 478:1169-1190. [PMID: 36239855 DOI: 10.1007/s11010-022-04579-x] [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: 05/21/2022] [Accepted: 09/26/2022] [Indexed: 10/17/2022]
Abstract
Mutation or overexpression renders pan-RAS (rat sarcoma) proteins insensitive to inactivation. Activated pan-RAS communicates signal from the cell surface receptor to activate RAS-MAPK/ERK (RAS-mitogen-activated protein kinases/extracellular signal regulated kinases) signaling and orchestrates epithelial-to-mesenchymal transition-activating transcription factors (EMT-ATFs) reprogramming to induce EMT. Owing to limited studies available in bladder cancer, the present study is taken up to examine the expressions of the EMT-associated markers in pan-RAS-pERK1/2 (pan-RAS-phosphoERK1/2)-positive well-characterized cohort of forty-two non-muscle invasive bladder cancer (NMIBC) and forty-five muscle invasive bladder cancer (MIBC) patients. Immunohistochemical staining was performed on paraffin embedded tissue sections to determine the immunolevels and cellular localization of marker proteins. Semi-quantitative expressions of pan-RAS, pERK1/2, and EMT markers (E-cadherin, Vimentin, N-cadherin, Snail, Slug Twist, and Zeb1) were statistically examined with clinicohistopathological profile of the patients using SPSS, version 20.0 software. The study documents the diagnostic relevance of immunohistochemical expressions of pan-RAS-pERK1/2/EMT-associated markers in order to stratify NMIBC and MIBC patients. Follow-up studies supported the role of altered EMT phenotype in pan-RAS-pERK1/2-activated positive tumors with disease aggressiveness. To the best of our knowledge, our study is the first concluding the impact of altered EMT phenotype via pan-RAS-pERK1/2 axis on the short survival outcome [short overall survival (OS) (p = 0.04), short progression-free survival (PFS) (p = 0.02) and short cancer-specific survival (CSS) (p = 0.03)] of muscle invasive bladder cancer patients.
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Affiliation(s)
- Kiran Tripathi
- Department of Biochemistry, University of Lucknow, Lucknow, 226007, India
| | - Niharika Maurya
- Department of Biochemistry, University of Lucknow, Lucknow, 226007, India
| | - Apul Goel
- Department of Urology, King George's Medical University, Lucknow, 226003, India
| | - Atin Singhai
- Department of Pathology, King George's Medical University, Lucknow, 226003, India
| | - Minal Garg
- Department of Biochemistry, University of Lucknow, Lucknow, 226007, India.
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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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Yin G, Huang J, Petela J, Jiang H, Zhang Y, Gong S, Wu J, Liu B, Shi J, Gao Y. Targeting small GTPases: emerging grasps on previously untamable targets, pioneered by KRAS. Signal Transduct Target Ther 2023; 8:212. [PMID: 37221195 DOI: 10.1038/s41392-023-01441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 05/25/2023] Open
Abstract
Small GTPases including Ras, Rho, Rab, Arf, and Ran are omnipresent molecular switches in regulating key cellular functions. Their dysregulation is a therapeutic target for tumors, neurodegeneration, cardiomyopathies, and infection. However, small GTPases have been historically recognized as "undruggable". Targeting KRAS, one of the most frequently mutated oncogenes, has only come into reality in the last decade due to the development of breakthrough strategies such as fragment-based screening, covalent ligands, macromolecule inhibitors, and PROTACs. Two KRASG12C covalent inhibitors have obtained accelerated approval for treating KRASG12C mutant lung cancer, and allele-specific hotspot mutations on G12D/S/R have been demonstrated as viable targets. New methods of targeting KRAS are quickly evolving, including transcription, immunogenic neoepitopes, and combinatory targeting with immunotherapy. Nevertheless, the vast majority of small GTPases and hotspot mutations remain elusive, and clinical resistance to G12C inhibitors poses new challenges. In this article, we summarize diversified biological functions, shared structural properties, and complex regulatory mechanisms of small GTPases and their relationships with human diseases. Furthermore, we review the status of drug discovery for targeting small GTPases and the most recent strategic progress focused on targeting KRAS. The discovery of new regulatory mechanisms and development of targeting approaches will together promote drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Jing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Johnny Petela
- Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuetong Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Siqi Gong
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jiaxin Wu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Bei Liu
- National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, 100871, China
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, 610072, China.
| | - Yijun Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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Zhen DB, Safyan RA, Konick EQ, Nguyen R, Prichard CC, Chiorean EG. The role of molecular testing in pancreatic cancer. Therap Adv Gastroenterol 2023; 16:17562848231171456. [PMID: 37197396 PMCID: PMC10184226 DOI: 10.1177/17562848231171456] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/06/2023] [Indexed: 05/19/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) is highly aggressive and has few treatment options. To personalize therapy, it is critical to delineate molecular subtypes and understand inter- and intra-tumoral heterogeneity. Germline testing for hereditary genetic abnormalities is recommended for all patients with PDA and somatic molecular testing is recommended for all patients with locally advanced or metastatic disease. KRAS mutations are present in 90% of PDA, while 10% are KRAS wild type and are potentially targetable with epidermal growth factor receptor blockade. KRASG12C inhibitors have shown activity in G12C-mutated cancers, and novel G12D and pan-RAS inhibitors are in clinical trials. DNA damage repair abnormalities, germline or somatic, occur in 5-10% of patients and are likely to benefit from DNA damaging agents and maintenance therapy with poly-ADP ribose polymerase inhibitors. Fewer than 1% of PDA harbor microsatellite instability high status and are susceptible to immune checkpoint blockade. Albeit very rare, occurring in <1% of patients with KRAS wild-type PDAs, BRAF V600E mutations, RET and NTRK fusions are targetable with cancer agnostic Food and Drug Administration-approved therapies. Genetic, epigenetic, and tumor microenvironment targets continue to be identified at an unprecedented pace, enabling PDA patients to be matched to targeted and immune therapeutics, including antibody-drug conjugates, and genetically engineered chimeric antigen receptor or T-cell receptor - T-cell therapies. In this review, we highlight clinically relevant molecular alterations and focus on targeted strategies that can improve patient outcomes through precision medicine.
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Affiliation(s)
- David B. Zhen
- University of Washington School of Medicine, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Rachael A. Safyan
- University of Washington School of Medicine, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Eric Q. Konick
- University of Washington, School of Medicine Seattle, WA, USA
| | - Ryan Nguyen
- University of Washington, School of Medicine Seattle, WA, USA
| | | | - E. Gabriela Chiorean
- University of Washington School of Medicine, Fred Hutchinson Cancer Center, 825 Eastlake Avenue East, LG-465, Seattle, WA 98109, USA Fred Hutchinson
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Cheng CA, Chiang LC, Chu YS. Integrated pipeline for ultrasensitive protein detection in cancer nanomedicine. RSC Adv 2023; 13:14685-14697. [PMID: 37197682 PMCID: PMC10183811 DOI: 10.1039/d3ra02092d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/07/2023] [Indexed: 05/19/2023] Open
Abstract
Although nanotechnologies have attractive attributes in cancer therapy, their full potential has yet to be realized due to challenges in their translation to clinical settings. The evaluation of cancer nanomedicine efficacy in preclinical in vivo studies is limited to tumor size and animal survival metrics, which do not provide adequate understanding of the nanomedicine's mechanism of action. To address this, we have developed an integrated pipeline called nanoSimoa that combines an ultrasensitive protein detection technique (Simoa) with cancer nanomedicine. As a proof-of concept, we assessed the therapeutic efficacy of an ultrasound-responsive mesoporous silica nanoparticle (MSN) drug delivery system on OVCAR-3 ovarian cancer cells using CCK-8 assays to evaluate cell viability and Simoa assays to measure IL-6 protein levels. The results demonstrated significant reductions in both IL-6 levels and cell viability following nanomedicine treatment. In addition, a Ras Simoa assay (limit of detection: 0.12 pM) was developed to detect and quantify Ras protein levels in OVCAR-3 cells, which are undetectable by commercial enzyme-linked immunosorbent assays (ELISA). These results suggest that nanoSimoa has the potential to guide the development of cancer nanomedicines and predict their behavior in vivo, making it a valuable tool for preclinical testing and accelerating the development of precision medicine if its generalizability is confirmed.
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Affiliation(s)
- Chi-An Cheng
- School of Pharmacy, College of Medicine, National Taiwan University Taipei 10050 Taiwan
| | - Li-Chiao Chiang
- School of Pharmacy, College of Medicine, National Taiwan University Taipei 10050 Taiwan
| | - Yu-Syuan Chu
- School of Pharmacy, College of Medicine, National Taiwan University Taipei 10050 Taiwan
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García-España A, Philips MR. Origin and Evolution of RAS Membrane Targeting. Oncogene 2023; 42:1741-1750. [PMID: 37031342 PMCID: PMC10413328 DOI: 10.1038/s41388-023-02672-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 04/10/2023]
Abstract
KRAS, HRAS and NRAS proto-oncogenes belong to a family of 40 highly homologous genes, which in turn are a subset of a superfamily of >160 genes encoding small GTPases. RAS proteins consist of a globular G-domain (aa1-166) and a 22-23 aa unstructured hypervariable region (HVR) that mediates membrane targeting. The evolutionary origins of the RAS isoforms, their HVRs and alternative splicing of the KRAS locus has not been explored. We found that KRAS is basal to the RAS proto-oncogene family and its duplication generated HRAS in the common ancestor of vertebrates. In a second round of duplication HRAS generated NRAS and KRAS generated an additional RAS gene we have designated KRASBL, absent in mammals and birds. KRAS4A arose through a duplication and insertion of the 4th exon of NRAS into the 3rd intron of KRAS. We found evolutionary conservation of a short polybasic region (PBR1) in HRAS, NRAS and KRAS4A, a second polybasic region (PBR2) in KRAS4A, two neutralized basic residues (NB) and a serine in KRAS4B and KRASBL, and a modification of the CaaX motif in vertebrates with farnesyl rather than geranylgeranyl polyisoprene lipids, suggesting that a less hydrophobic membrane anchor is critical to RAS protein function. The persistence of four RAS isoforms through >400 million years of evolution argues strongly for differential function.
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Affiliation(s)
| | - Mark R Philips
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA.
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