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Méant A, Moussa O, Lebeau B, Gonçalves C, Richard VR, Cai F, Prabhu SA, Langke M, Guettler EM, Su J, Gagnon N, Zahedi RP, Borchers CH, Miller WH, Del Rincón SV, Witcher M. Combined inhibition of MNK signaling and BET proteins reveals TGM2 as a novel vulnerability in melanoma. J Invest Dermatol 2024:S0022-202X(24)02160-2. [PMID: 39357785 DOI: 10.1016/j.jid.2024.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 07/08/2024] [Accepted: 07/25/2024] [Indexed: 10/04/2024]
Affiliation(s)
- Antoine Méant
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Omar Moussa
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Benjamin Lebeau
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | | | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Feiyang Cai
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Sathyen A Prabhu
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Marios Langke
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | | | - Jie Su
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
| | - Natascha Gagnon
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
| | - Rene P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Wilson H Miller
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Sonia V Del Rincón
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada.
| | - Michael Witcher
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada; Department of Oncology, McGill University, Montréal, Québec, Canada.
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2
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Soler-Sáez I, Karz A, Hidalgo MR, Gómez-Cabañes B, López-Cerdán A, Català-Senent JF, Prutisto-Chang K, Eskow NM, Izar B, Redmer T, Kumar S, Davies MA, de la Iglesia-Vayá M, Hernando E, García-García F. Unveiling common transcriptomic features between melanoma brain metastases and neurodegenerative diseases. J Invest Dermatol 2024:S0022-202X(24)02149-3. [PMID: 39326662 DOI: 10.1016/j.jid.2024.09.005] [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: 05/07/2024] [Revised: 08/14/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024]
Abstract
Melanoma represents a critical clinical challenge due to its unfavorable outcomes. This type of skin cancer exhibits unique adaptability to the brain microenvironment, but its underlying molecular mechanisms are poorly understood. Recent findings have suggested that melanoma brain metastases (MBM) may share biological processes similar to those found in various neurodegenerative diseases. To further characterize MBM development, we explore the relationship between the transcriptional profiles of MBM and the neurodegenerative diseases Alzheimer's disease, Parkinson's disease, and multiple sclerosis. We take an in silico approach to unveil a neurodegenerative signature of MBM when compared to melanoma non-brain metastasis (53 dysregulated genes enriched in 11 functional terms, such as associated terms to the extracellular matrix and development) and to non tumor-bearing brain controls (195 dysregulated genes, mostly involved in development and cell differentiation, chromatin remodeling and nucleosome organization, and translation). Two genes, ITGA10 and DNAJC6, emerged as key potential markers being dysregulated in both scenarios. Lastly, we developed an open source, user-friendly web tool (https://bioinfo.cipf.es/metafun-mbm/) that allows interactive exploration of the complete results.
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Affiliation(s)
- Irene Soler-Sáez
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Alcida Karz
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, US
| | - Marta R Hidalgo
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Borja Gómez-Cabañes
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Adolfo López-Cerdán
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain; Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - José F Català-Senent
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Kylie Prutisto-Chang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, US
| | - Nicole M Eskow
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, US
| | - Benjamin Izar
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA; Columbia Center for Translational Immunology, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Torben Redmer
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Swaminathan Kumar
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Michael A Davies
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - María de la Iglesia-Vayá
- Biomedical Imaging Unit FISABIO-CIPF, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, 46012, Valencia, Spain
| | - Eva Hernando
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, US.
| | - Francisco García-García
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain.
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3
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Han D, Li A, Zhu L, Zhuang C, Zhao Q, Zou Y. Peptide inhibitors targeting Ras and Ras-associated protein-protein interactions. Eur J Med Chem 2024; 279:116878. [PMID: 39326269 DOI: 10.1016/j.ejmech.2024.116878] [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: 08/14/2024] [Revised: 09/04/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024]
Abstract
Peptides represent attractive molecules for targeting protein-protein interactions, and peptide drug development has made great progress during the last decades. Ras protein, the most promising target in cancer therapy, is one of the major growth drivers in various cancers. Although many small molecule inhibitors have been reported to effectively target Ras protein and some inhibitors (such as MRTX849 and AMG 510) have been translated into clinical application, just a few peptide inhibitors have been reported. Here we summarize different types of peptide inhibitors, including monocyclic peptides, bicyclic peptides, stapled peptides, and proteomimetic inhibitors, developed in recent years; emphasize the limits and achievements; and discuss the outlook and challenges associated with future research in peptide inhibitors. This review aims to provide a reference for the discovery of Ras peptide inhibitors.
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Affiliation(s)
- Dan Han
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China; School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, PR China
| | - Anpeng Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China; 92805 Military Hospital, Qingdao, PR China
| | - Lie Zhu
- Department of Burn Plastic Surgery, The Second Affiliated Hospital of Second Military Medical University, Shanghai, 200003, PR China
| | - Chunlin Zhuang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China.
| | - Qingjie Zhao
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China.
| | - Yan Zou
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, PR China.
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4
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Hashem O, Shahin AI, Al Hindawi MA, Fageeri MF, Al-Sbbagh SA, Tarazi H, El-Gamal MI. An overview of RAF kinases and their inhibitors (2019-2023). Eur J Med Chem 2024; 275:116631. [PMID: 38954961 DOI: 10.1016/j.ejmech.2024.116631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
Protein kinases (PKs) including RAF, perform a principal role in regulating countless cellular events such as cell growth, differentiation, and angiogenesis. Overexpression and mutation of RAF kinases are significant contributors to the development and spread of cancer. Therefore, RAF kinase inhibitors show promising outcomes as anti-cancer small molecules by suppressing the expression of RAF protein, blocking RAS/RAF interaction, or inhibiting RAF enzymes. Currently, there are insufficient reports about approving drugs with minimal degree of toxicity. Therefore, it is an urgent need to develop new RAF kinase inhibitors correlated with increased anticancer activity and lower cytotoxicity. This review outlines reported RAF kinase inhibitors for cancer treatment in patents and literature from 2019 to 2023. It highlights the available inhibitors by shedding light on their chemical structures, biochemical profiles, and current status. Additionally, we highlighted the hinge region-binding moiety of the reported compounds by showing the hydrogen bond patterns of representative inhibitors with the hinge region for each class. In recent years, RAF kinase inhibitors have gained considerable attention in cancer research and drug development due to their potential to be studied under clinical trials and their demonstration of various degrees of efficacy and safety profiles across different cancer types. However, addressing challenges related to drug resistance and safety represents a major avenue for the optimization and enhancement of RAF kinase inhibitors. Strategies to overcome such obstacles were discussed such as developing novel pan-RAF inhibitors, RAF dimer inhibitors, and combination treatments.
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Affiliation(s)
- Omar Hashem
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Afnan I Shahin
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Manar A Al Hindawi
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Mohamed F Fageeri
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Saif A Al-Sbbagh
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hamadeh Tarazi
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Mohammed I El-Gamal
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
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5
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Yaeger R, McKean MA, Haq R, Beck JT, Taylor MH, Cohen JE, Bowles DW, Gadgeel SM, Mihalcioiu C, Papadopoulos KP, Diamond EL, Sturtz KB, Feng G, Drescher SK, Reddy MB, Sengupta B, Maity AK, Brown SA, Singh A, Brown EN, Baer BR, Wong J, Mou TC, Wu WI, Kahn DR, Gadal S, Rosen N, Gaudino JJ, Lee PA, Hartley DP, Rothenberg SM. A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation. Cancer Discov 2024; 14:1599-1611. [PMID: 38691346 PMCID: PMC11372368 DOI: 10.1158/2159-8290.cd-24-0024] [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: 01/18/2024] [Revised: 03/21/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
RAF inhibitors have transformed treatment for patients with BRAFV600-mutant cancers, but clinical benefit is limited by adaptive induction of ERK signaling, genetic alterations that induce BRAFV600 dimerization, and poor brain penetration. Next-generation pan-RAF dimer inhibitors are limited by a narrow therapeutic index. PF-07799933 (ARRY-440) is a brain-penetrant, selective, pan-mutant BRAF inhibitor. PF-07799933 inhibited signaling in vitro, disrupted endogenous mutant-BRAF:wild-type-CRAF dimers, and spared wild-type ERK signaling. PF-07799933 ± binimetinib inhibited growth of mouse xenograft tumors driven by mutant BRAF that functions as dimers and by BRAFV600E with acquired resistance to current RAF inhibitors. We treated patients with treatment-refractory BRAF-mutant solid tumors in a first-in-human clinical trial (NCT05355701) that utilized a novel, flexible, pharmacokinetics-informed dose escalation design that allowed rapid achievement of PF-07799933 efficacious concentrations. PF-07799933 ± binimetinib was well-tolerated and resulted in multiple confirmed responses, systemically and in the brain, in patients with BRAF-mutant cancer who were refractory to approved RAF inhibitors. Significance: PF-07799933 treatment was associated with antitumor activity against BRAFV600- and non-V600-mutant cancers preclinically and in treatment-refractory patients, and PF-07799933 could be safely combined with a MEK inhibitor. The novel, rapid pharmacokinetics (PK)-informed dose escalation design provides a new paradigm for accelerating the testing of next-generation targeted therapies early in clinical development.
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Affiliation(s)
- Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, New York.
| | | | - Rizwan Haq
- Dana Farber Cancer Institute, Boston, Massachusetts.
| | | | - Matthew H. Taylor
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon.
| | | | | | | | | | | | - Eli L. Diamond
- Memorial Sloan Kettering Cancer Center, New York, New York.
| | | | - Gang Feng
- Pfizer Early Clinical Development, Cambridge, Massachusetts.
| | | | | | | | - Arnab K. Maity
- Pfizer Early Clinical Development, Cambridge, Massachusetts.
| | - Suzy A. Brown
- Pfizer Boulder Research and Development, Boulder, Colorado.
| | - Anurag Singh
- Pfizer Boulder Research and Development, Boulder, Colorado.
| | - Eric N. Brown
- Pfizer Boulder Research and Development, Boulder, Colorado.
| | - Brian R. Baer
- Pfizer Boulder Research and Development, Boulder, Colorado.
| | - Jim Wong
- Pfizer Boulder Research and Development, Boulder, Colorado.
| | - Tung-Chung Mou
- Pfizer Boulder Research and Development, Boulder, Colorado.
| | - Wen-I Wu
- Pfizer Boulder Research and Development, Boulder, Colorado.
| | - Dean R. Kahn
- Pfizer Boulder Research and Development, Boulder, Colorado.
| | - Sunyana Gadal
- Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Neal Rosen
- Memorial Sloan Kettering Cancer Center, New York, New York.
| | | | - Patrice A. Lee
- Pfizer Boulder Research and Development, Boulder, Colorado.
| | | | - S. Michael Rothenberg
- Pfizer Boulder Research and Development, Boulder, Colorado.
- Pfizer Oncology Research and Development, La Jolla, California.
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6
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Goetz A, Shanahan F, Brooks L, Lin E, Mroue R, Dela Cruz D, Hunsaker T, Czech B, Dixit P, Segal U, Martin S, Foster SA, Gerosa L. Computational Modeling of Drug Response Identifies Mutant-Specific Constraints for Dosing panRAF and MEK Inhibitors in Melanoma. Cancers (Basel) 2024; 16:2914. [PMID: 39199684 PMCID: PMC11353013 DOI: 10.3390/cancers16162914] [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: 06/05/2024] [Revised: 08/06/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
PURPOSE This study explores the potential of pre-clinical in vitro cell line response data and computational modeling in identifying the optimal dosage requirements of pan-RAF (Belvarafenib) and MEK (Cobimetinib) inhibitors in melanoma treatment. Our research is motivated by the critical role of drug combinations in enhancing anti-cancer responses and the need to close the knowledge gap around selecting effective dosing strategies to maximize their potential. RESULTS In a drug combination screen of 43 melanoma cell lines, we identified specific dosage landscapes of panRAF and MEK inhibitors for NRAS vs. BRAF mutant melanomas. Both experienced benefits, but with a notably more synergistic and narrow dosage range for NRAS mutant melanoma (mean Bliss score of 0.27 in NRAS vs. 0.1 in BRAF mutants). Computational modeling and follow-up molecular experiments attributed the difference to a mechanism of adaptive resistance by negative feedback. We validated the in vivo translatability of in vitro dose-response maps by predicting tumor growth in xenografts with high accuracy in capturing cytostatic and cytotoxic responses. We analyzed the pharmacokinetic and tumor growth data from Phase 1 clinical trials of Belvarafenib with Cobimetinib to show that the synergy requirement imposes stricter precision dose constraints in NRAS mutant melanoma patients. CONCLUSION Leveraging pre-clinical data and computational modeling, our approach proposes dosage strategies that can optimize synergy in drug combinations, while also bringing forth the real-world challenges of staying within a precise dose range. Overall, this work presents a framework to aid dose selection in drug combinations.
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Affiliation(s)
- Andrew Goetz
- gRED Computational Sciences, Genentech, South San Francisco, CA 94080, USA;
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA;
| | - Frances Shanahan
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA; (F.S.); (R.M.); (S.A.F.)
| | - Logan Brooks
- Department of Modeling and Simulation Clinical Pharmacology, Genentech, South San Francisco, CA 94080, USA;
| | - Eva Lin
- Department of Functional Genomics, Genentech, South San Francisco, CA 94080, USA; (E.L.); (S.M.)
| | - Rana Mroue
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA; (F.S.); (R.M.); (S.A.F.)
| | - Darlene Dela Cruz
- Department of Translational Oncology, Genentech, South San Francisco, CA 94080, USA; (D.D.C.); (T.H.); (U.S.)
| | - Thomas Hunsaker
- Department of Translational Oncology, Genentech, South San Francisco, CA 94080, USA; (D.D.C.); (T.H.); (U.S.)
| | - Bartosz Czech
- Roche Global IT Solution Centre, Roche, 02-672 Warsaw, Poland;
| | - Purushottam Dixit
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA;
| | - Udi Segal
- Department of Translational Oncology, Genentech, South San Francisco, CA 94080, USA; (D.D.C.); (T.H.); (U.S.)
| | - Scott Martin
- Department of Functional Genomics, Genentech, South San Francisco, CA 94080, USA; (E.L.); (S.M.)
| | - Scott A. Foster
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA; (F.S.); (R.M.); (S.A.F.)
| | - Luca Gerosa
- gRED Computational Sciences, Genentech, South San Francisco, CA 94080, USA;
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA; (F.S.); (R.M.); (S.A.F.)
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7
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Goetz A, Shanahan F, Brooks L, Lin E, Mroue R, Cruz DD, Hunsaker T, Czech B, Dixit P, Segal U, Martin S, Foster SA, Gerosa L. Computational modeling of drug response identifies mutant-specific constraints for dosing panRAF and MEK inhibitors in melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606432. [PMID: 39149377 PMCID: PMC11326189 DOI: 10.1101/2024.08.02.606432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Purpose This study explores the potential of preclinical in vitro cell line response data and computational modeling in identifying optimal dosage requirements of pan-RAF (Belvarafenib) and MEK (Cobimetinib) inhibitors in melanoma treatment. Our research is motivated by the critical role of drug combinations in enhancing anti-cancer responses and the need to close the knowledge gap around selecting effective dosing strategies to maximize their potential. Results In a drug combination screen of 43 melanoma cell lines, we identified unique dosage landscapes of panRAF and MEK inhibitors for NRAS vs BRAF mutant melanomas. Both experienced benefits, but with a notably more synergistic and narrow dosage range for NRAS mutant melanoma. Computational modeling and molecular experiments attributed the difference to a mechanism of adaptive resistance by negative feedback. We validated in vivo translatability of in vitro dose-response maps by accurately predicting tumor growth in xenografts. Then, we analyzed pharmacokinetic and tumor growth data from Phase 1 clinical trials of Belvarafenib with Cobimetinib to show that the synergy requirement imposes stricter precision dose constraints in NRAS mutant melanoma patients. Conclusion Leveraging pre-clinical data and computational modeling, our approach proposes dosage strategies that can optimize synergy in drug combinations, while also bringing forth the real-world challenges of staying within a precise dose range.
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Affiliation(s)
- Andrew Goetz
- gRED Computational Sciences, Genentech, South San Francisco, CA, US
- Department of Biomedical Engineering, Yale University, New Haven, CT, US
| | - Frances Shanahan
- Department of Discovery Oncology, Genentech, South San Francisco, CA, US
| | - Logan Brooks
- Department of Modeling and Simulation Clinical Pharmacology, Genentech, South San Francisco, CA, US
| | - Eva Lin
- Department of Functional Genomics, Genentech, South San Francisco, CA, US
| | - Rana Mroue
- Department of Discovery Oncology, Genentech, South San Francisco, CA, US
| | - Darlene Dela Cruz
- Department of Translational Oncology, Genentech, South San Francisco, CA, US
| | - Thomas Hunsaker
- Department of Translational Oncology, Genentech, South San Francisco, CA, US
| | | | - Purushottam Dixit
- Department of Biomedical Engineering, Yale University, New Haven, CT, US
| | - Udi Segal
- Department of Translational Oncology, Genentech, South San Francisco, CA, US
| | - Scott Martin
- Department of Functional Genomics, Genentech, South San Francisco, CA, US
| | - Scott A. Foster
- Department of Discovery Oncology, Genentech, South San Francisco, CA, US
| | - Luca Gerosa
- gRED Computational Sciences, Genentech, South San Francisco, CA, US
- Department of Discovery Oncology, Genentech, South San Francisco, CA, US
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Ryan MB, Quade B, Schenk N, Fang Z, Zingg M, Cohen SE, Swalm BM, Li C, Özen A, Ye C, Ritorto MS, Huang X, Dar AC, Han Y, Hoeflich KP, Hale M, Hagel M. The Pan-RAF-MEK Nondegrading Molecular Glue NST-628 Is a Potent and Brain-Penetrant Inhibitor of the RAS-MAPK Pathway with Activity across Diverse RAS- and RAF-Driven Cancers. Cancer Discov 2024; 14:1190-1205. [PMID: 38588399 PMCID: PMC11215411 DOI: 10.1158/2159-8290.cd-24-0139] [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: 01/26/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024]
Abstract
Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and are a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents the phosphorylation and activation of MEK by RAF, overcoming the limitations of traditional RAS-MAPK inhibitors and leading to deep durable inhibition of the pathway. Cellular, biochemical, and structural analyses of RAF-MEK complexes show that NST-628 engages all isoforms of RAF and prevents the formation of BRAF-CRAF heterodimers, a differentiated mechanism from all current RAF inhibitors. With a potent and durable inhibition of the RAF-MEK signaling complex as well as high intrinsic permeability into the brain, NST-628 demonstrates broad efficacy in cellular and patient-derived tumor models harboring diverse MAPK pathway alterations, including orthotopic intracranial models. Given its functional and pharmacokinetic mechanisms that are differentiated from previous therapies, NST-628 is positioned to make an impact clinically in areas of unmet patient need. Significance: This study introduces NST-628, a molecular glue having differentiated mechanism and drug-like properties. NST-628 treatment leads to broad efficacy with high tolerability and central nervous system activity across multiple RAS- and RAF-driven tumor models. NST-628 has the potential to provide transformative clinical benefits as both monotherapy and vertical combination anchor.
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Affiliation(s)
| | | | | | - Zhong Fang
- Nested Therapeutics, Cambridge, Massachusetts.
| | | | | | | | - Chun Li
- Nested Therapeutics, Cambridge, Massachusetts.
| | | | - Chaoyang Ye
- Nested Therapeutics, Cambridge, Massachusetts.
| | | | - Xin Huang
- Nested Therapeutics, Cambridge, Massachusetts.
| | - Arvin C. Dar
- Program in Chemical Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Yongxin Han
- Nested Therapeutics, Cambridge, Massachusetts.
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Bonsor DA, Simanshu DK. RAS and SHOC2 Roles in RAF Activation and Therapeutic Considerations. ANNUAL REVIEW OF CANCER BIOLOGY 2024; 8:97-113. [PMID: 38882927 PMCID: PMC11178279 DOI: 10.1146/annurev-cancerbio-062822-030450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Mutations in RAS proteins play a pivotal role in the development of human cancers, driving persistent RAF activation and deregulating the Mitogen-Activated Protein Kinase (MAPK) signaling pathway. While progress has been made in targeting specific oncogenic RAS proteins, effective drug-based therapies for the majority of RAS mutations remain limited. Recent investigations on RAS-RAF complexes and the SHOC2-MRAS-PP1C holoenzyme complex have provided crucial insights into the structural and functional aspects of RAF activation within the MAPK signaling pathway. Moreover, these studies have also unveiled new blueprints for developing inhibitors allowing us to think beyond the current RAS and MEK inhibitors. In this review, we explore the roles of RAS and SHOC2 in activating RAF and discuss potential therapeutic strategies to target these proteins. A comprehensive understanding of the molecular interactions involved in RAF activation and their therapeutic implications holds the potential to drive innovative approaches in combating RAS/RAF-driven cancers.
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Affiliation(s)
- Daniel A. Bonsor
- 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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10
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Konopleva MY, Dail M, Daver NG, Garcia JS, Jonas BA, Yee KWL, Kelly KR, Vey N, Assouline S, Roboz GJ, Paolini S, Pollyea DA, Tafuri A, Brandwein JM, Pigneux A, Powell BL, Fenaux P, Olin RL, Visani G, Martinelli G, Onishi M, Wang J, Huang W, Dunshee DR, Hamidi H, Ott MG, Hong WJ, Andreeff M. Venetoclax and Cobimetinib in Relapsed/Refractory AML: A Phase 1b Trial. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2024; 24:364-374. [PMID: 38378362 DOI: 10.1016/j.clml.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Therapies for relapsed/refractory acute myeloid leukemia remain limited and outcomes poor, especially amongst patients who are ineligible for cytotoxic chemotherapy or targeted therapies. PATIENTS AND METHODS This phase 1b trial evaluated venetoclax, a B-cell lymphoma-2 (BCL-2) inhibitor, plus cobimetinib, a MEK1/2 inhibitor, in patients with relapsed/refractory acute myeloid leukemia, ineligible for cytotoxic chemotherapy. Two-dimensional dose-escalation was performed for venetoclax dosed daily, and for cobimetinib dosed on days 1-21 of each 28-day cycle. RESULTS Thirty patients (median [range] age: 71.5 years [60-84]) received venetoclax-cobimetinib. The most common adverse events (AEs; in ≥40.0% of patients) were diarrhea (80.0%), nausea (60.0%), vomiting (40.0%), febrile neutropenia (40.0%), and fatigue (40.0%). Overall, 66.7% and 23.3% of patients experienced AEs leading to dose modification/interruption or treatment withdrawal, respectively. The composite complete remission (CRc) rate (complete remission [CR] + CR with incomplete blood count recovery + CR with incomplete platelet recovery) was 15.6%; antileukemic response rate (CRc + morphologic leukemia-free state/partial remission) was 18.8%. For the recommended phase 2 dose (venetoclax: 600 mg; cobimetinib: 40 mg), CRc and antileukemic response rates were both 12.5%. Failure to achieve an antileukemic response was associated with elevated baseline phosphorylated ERK and MCL-1 levels, but not BCL-xL. Baseline mutations in ≥1 signaling gene or TP53 were noted in nonresponders and emerged on treatment. Pharmacodynamic biomarkers revealed inconsistent, transient inhibition of the mitogen-activated protein kinase (MAPK) pathway. CONCLUSION Venetoclax-cobimetinib showed limited preliminary efficacy similar to single-agent venetoclax, but with added toxicity. Our findings will inform future trials of BCL-2/MAPK pathway inhibitor combinations.
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Affiliation(s)
| | | | - Naval G Daver
- University of Texas, MD Anderson Cancer Center, Houston, TX
| | | | - Brian A Jonas
- University of California Davis Comprehensive Cancer Center, Sacramento, CA
| | - Karen W L Yee
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Norbert Vey
- Hematologie Clinique, Institut Paoli Calmettes, Marseille, France
| | | | - Gail J Roboz
- Weill-Cornell Medical College, New York Presbyterian, New York, NY
| | - Stefania Paolini
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | | | - Agostino Tafuri
- Department of Clinical and Molecular Medicine, University Hospital Sant'Andrea-Sapienza, Rome, Italy
| | | | - Arnaud Pigneux
- Bordeaux Haut-Leveque University Hospital, Pessac, France
| | - Bayard L Powell
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC
| | - Pierre Fenaux
- Hôpital Saint-Louis, Université Paris Diderot, Paris, France
| | - Rebecca L Olin
- University of California San Francisco, San Francisco, CA
| | | | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | | | - Jue Wang
- Genentech, Inc., South San Francisco, CA
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11
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Scardaci R, Berlinska E, Scaparone P, Vietti Michelina S, Garbo E, Novello S, Santamaria D, Ambrogio C. Novel RAF-directed approaches to overcome current clinical limits and block the RAS/RAF node. Mol Oncol 2024; 18:1355-1377. [PMID: 38362705 PMCID: PMC11161739 DOI: 10.1002/1878-0261.13605] [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: 07/24/2023] [Revised: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Mutations in the RAS-RAF-MEK-ERK pathway are frequent alterations in cancer and RASopathies, and while RAS oncogene activation alone affects 19% of all patients and accounts for approximately 3.4 million new cases every year, less frequent alterations in the cascade's downstream effectors are also involved in cancer etiology. RAS proteins initiate the signaling cascade by promoting the dimerization of RAF kinases, which can act as oncoproteins as well: BRAFV600E is the most common oncogenic driver, mutated in the 8% of all malignancies. Research in this field led to the development of drugs that target the BRAFV600-like mutations (Class I), which are now utilized in clinics, but cause paradoxical activation of the pathway and resistance development. Furthermore, they are ineffective against non-BRAFV600E malignancies that dimerize and could be either RTK/RAS independent or dependent (Class II and III, respectively), which are still lacking an effective treatment. This review discusses the recent advances in anti-RAF therapies, including paradox breakers, dimer-inhibitors, immunotherapies, and other novel approaches, critically evaluating their efficacy in overcoming the therapeutic limitations, and their putative role in blocking the RAS pathway.
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Affiliation(s)
- Rossella Scardaci
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Ewa Berlinska
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Pietro Scaparone
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Sandra Vietti Michelina
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Edoardo Garbo
- Department of OncologyUniversity of Torino, San Luigi HospitalOrbassanoItaly
| | - Silvia Novello
- Department of OncologyUniversity of Torino, San Luigi HospitalOrbassanoItaly
| | - David Santamaria
- Centro de Investigación del CáncerCSIC‐Universidad de SalamancaSpain
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology CenterUniversity of TorinoItaly
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12
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Rasmussen DM, Semonis MM, Greene JT, Muretta JM, Thompson AR, Toledo Ramos S, Thomas DD, Pomerantz WCK, Freedman TS, Levinson NM. Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors. eLife 2024; 13:RP95481. [PMID: 38742856 PMCID: PMC11093583 DOI: 10.7554/elife.95481] [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] [Indexed: 05/16/2024] Open
Abstract
The type II class of RAF inhibitors currently in clinical trials paradoxically activate BRAF at subsaturating concentrations. Activation is mediated by induction of BRAF dimers, but why activation rather than inhibition occurs remains unclear. Using biophysical methods tracking BRAF dimerization and conformation, we built an allosteric model of inhibitor-induced dimerization that resolves the allosteric contributions of inhibitor binding to the two active sites of the dimer, revealing key differences between type I and type II RAF inhibitors. For type II inhibitors the allosteric coupling between inhibitor binding and BRAF dimerization is distributed asymmetrically across the two dimer binding sites, with binding to the first site dominating the allostery. This asymmetry results in efficient and selective induction of dimers with one inhibited and one catalytically active subunit. Our allosteric models quantitatively account for paradoxical activation data measured for 11 RAF inhibitors. Unlike type II inhibitors, type I inhibitors lack allosteric asymmetry and do not activate BRAF homodimers. Finally, NMR data reveal that BRAF homodimers are dynamically asymmetric with only one of the subunits locked in the active αC-in state. This provides a structural mechanism for how binding of only a single αC-in inhibitor molecule can induce potent BRAF dimerization and activation.
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Affiliation(s)
- Damien M Rasmussen
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Manny M Semonis
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
| | - Joseph T Greene
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
| | - Joseph M Muretta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Andrew R Thompson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | | | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | | | - Tanya S Freedman
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
- Center for Immunology, University of MinnesotaMinneapolisUnited States
- Masonic Cancer Center, University of MinnesotaMinneapolisUnited States
| | - Nicholas M Levinson
- Department of Pharmacology, University of MinnesotaMinneapolisUnited States
- Masonic Cancer Center, University of MinnesotaMinneapolisUnited States
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13
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Song L, Yang Y, Tian X. Current knowledge about immunotherapy resistance for melanoma and potential predictive and prognostic biomarkers. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024; 7:17. [PMID: 38835341 PMCID: PMC11149101 DOI: 10.20517/cdr.2023.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 06/06/2024]
Abstract
Melanoma still reaches thousands of new diagnoses per year, and its aggressiveness makes recovery challenging, especially for those with stage III/IV unresectable melanoma. Immunotherapy, emerging as a beacon of hope, stands at the forefront of treatments for advanced melanoma. This review delves into the various immunotherapeutic strategies, prominently featuring cytokine immunotherapy, adoptive cell therapy, immune checkpoint inhibitors, and vaccinations. Among these, immune checkpoint inhibitors, notably anti-programmed cell death-1 (PD-1) and anti-cytotoxic T lymphocyte antigen-4 (CTLA-4) antibodies, emerge as the leading strategy. However, a significant subset of melanoma patients remains unresponsive to these inhibitors, underscoring the need for potent biomarkers. Efficient biomarkers have the potential to revolutionize the therapeutic landscape by facilitating the design of personalized treatments for patients with melanoma. This comprehensive review highlights the latest advancements in melanoma immunotherapy and potential biomarkers at the epicenter of recent research endeavors.
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Affiliation(s)
- Lanni Song
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Bio-pharmaceutical Informatics, Wenzhou-Kean University, Wenzhou 325060, Zhejiang, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Wenzhou 325060, Zhejiang, China
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou 325060, Zhejiang, China
| | - Yixin Yang
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Bio-pharmaceutical Informatics, Wenzhou-Kean University, Wenzhou 325060, Zhejiang, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Wenzhou 325060, Zhejiang, China
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou 325060, Zhejiang, China
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, Union, NJ 07083, USA
| | - Xuechen Tian
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Bio-pharmaceutical Informatics, Wenzhou-Kean University, Wenzhou 325060, Zhejiang, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Wenzhou 325060, Zhejiang, China
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou 325060, Zhejiang, China
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14
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Yin H, Tang Q, Xia H, Bi F. Targeting RAF dimers in RAS mutant tumors: From biology to clinic. Acta Pharm Sin B 2024; 14:1895-1923. [PMID: 38799634 PMCID: PMC11120325 DOI: 10.1016/j.apsb.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/02/2024] [Accepted: 02/20/2024] [Indexed: 05/29/2024] Open
Abstract
RAS mutations occur in approximately 30% of tumors worldwide and have a poor prognosis due to limited therapies. Covalent targeting of KRAS G12C has achieved significant success in recent years, but there is still a lack of efficient therapeutic approaches for tumors with non-G12C KRAS mutations. A highly promising approach is to target the MAPK pathway downstream of RAS, with a particular focus on RAF kinases. First-generation RAF inhibitors have been authorized to treat BRAF mutant tumors for over a decade. However, their use in RAS-mutated tumors is not recommended due to the paradoxical ERK activation mainly caused by RAF dimerization. To address the issue of RAF dimerization, type II RAF inhibitors have emerged as leading candidates. Recent clinical studies have shown the initial effectiveness of these agents against RAS mutant tumors. Promisingly, type II RAF inhibitors in combination with MEK or ERK inhibitors have demonstrated impressive efficacy in RAS mutant tumors. This review aims to clarify the importance of RAF dimerization in cellular signaling and resistance to treatment in tumors with RAS mutations, as well as recent progress in therapeutic approaches to address the problem of RAF dimerization in RAS mutant tumors.
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Affiliation(s)
- Huanhuan Yin
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiulin Tang
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongwei Xia
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Feng Bi
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
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15
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Wang R, Yan Q, Liu X, Wu J. Unraveling lipid metabolism reprogramming for overcoming drug resistance in melanoma. Biochem Pharmacol 2024; 223:116122. [PMID: 38467377 DOI: 10.1016/j.bcp.2024.116122] [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: 01/17/2024] [Revised: 02/27/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024]
Abstract
Cutaneous melanoma is the deadliest form of skin cancer, and its incidence is continuing to increase worldwide in the last decades. Traditional therapies for melanoma can easily cause drug resistance, thus the treatment of melanoma remains a challenge. Various studies have focused on reversing the drug resistance. As tumors grow and progress, cancer cells face a constantly changing microenvironment made up of different nutrients, metabolites, and cell types. Multiple studies have shown that metabolic reprogramming of cancer is not static, but a highly dynamic process. There is a growing interest in exploring the relationship between melanoma andmetabolic reprogramming, one of which may belipid metabolism. This review frames the recent research progresses on lipid metabolism in melanoma.In addition, we emphasize the dynamic ability of metabolism during tumorigenesis as a target for improving response to different therapies and for overcoming drug resistance in melanoma.
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Affiliation(s)
- Ruilong Wang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qin Yan
- Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiao Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.
| | - Jinfeng Wu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.
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16
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Haugh A, Daud AI. Therapeutic Strategies in BRAF V600 Wild-Type Cutaneous Melanoma. Am J Clin Dermatol 2024; 25:407-419. [PMID: 38329690 DOI: 10.1007/s40257-023-00841-0] [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: 12/19/2023] [Indexed: 02/09/2024]
Abstract
There have been many recent advances in melanoma therapy. While 50% of melanomas have a BRAF mutation and are a target for BRAF inhibitors, the remaining 50% are BRAF wild-type. Immune checkpoint inhibitors targeting PD-1, cytotoxic T-lymphocyte-associated protein 4 (CTLA4) and lymphocyte activated gene-3 (Lag-3) are all approved for the treatment of patients with advanced BRAF wild-type melanoma; however, treatment of this patient population following initial immune checkpoint blockade is a current therapeutic challenge given the lack of other efficacious options. Here, we briefly review available US FDA-approved therapies for BRAF wild-type melanoma and focus on developing treatment avenues for this heterogeneous group of patients. We review the basics of genomic features of both BRAF mutant and BRAF wild-type melanoma as well as efforts underway to develop new targeted therapies involving the mitogen-activated protein kinase (MAPK) pathway for patients with BRAF wild-type tumors. We then focus on novel immunotherapies, including developing checkpoint inhibitors and agonists, cytokine therapies, oncolytic viruses and tumor-infiltrating lymphocytes, all of which represent potential therapeutic avenues for patients with BRAF wild-type melanoma who progress on currently approved immune checkpoint inhibitors.
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Affiliation(s)
- Alexandra Haugh
- Department of Medicine, University of California San Francisco, 550 16th Street, 6809, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adil I Daud
- Department of Medicine, University of California San Francisco, 550 16th Street, 6809, San Francisco, CA, 94158, USA.
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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17
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Clayton J, Romany A, Matenoglou E, Gavathiotis E, Poulikakos PI, Shen J. Mechanism of Dimer Selectivity and Binding Cooperativity of BRAF Inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571293. [PMID: 38168366 PMCID: PMC10760002 DOI: 10.1101/2023.12.12.571293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Aberrant signaling of BRAFV600E is a major cancer driver. Current FDA-approved RAF inhibitors selectively inhibit the monomeric BRAFV600E and suffer from tumor resistance. Recently, dimer-selective and equipotent RAF inhibitors have been developed; however, the mechanism of dimer selectivity is poorly understood. Here, we report extensive molecular dynamics (MD) simulations of the monomeric and dimeric BRAFV600E in the apo form or in complex with one or two dimer-selective (PHI1) or equipotent (LY3009120) inhibitor(s). The simulations uncovered the unprecedented details of the remarkable allostery in BRAFV600E dimerization and inhibitor binding. Specifically, dimerization retrains and shifts the αC helix inward and increases the flexibility of the DFG motif; dimer compatibility is due to the promotion of the αC-in conformation, which is stabilized by a hydrogen bond formation between the inhibitor and the αC Glu501. A more stable hydrogen bond further restrains and shifts the αC helix inward, which incurs a larger entropic penalty that disfavors monomer binding. This mechanism led us to propose an empirical way based on the co-crystal structure to assess the dimer selectivity of a BRAFV600E inhibitor. Simulations also revealed that the positive cooperativity of PHI1 is due to its ability to preorganize the αC and DFG conformation in the opposite protomer, priming it for binding the second inhibitor. The atomically detailed view of the interplay between BRAF dimerization and inhibitor allostery as well as cooperativity has implications for understanding kinase signaling and contributes to the design of protomer selective RAF inhibitors.
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Affiliation(s)
- Joseph Clayton
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, United States
| | - Aarion Romany
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States
| | - Evangelia Matenoglou
- Department of Biochemistry, Department of Medicine, Department of Oncology, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, New York, NY 10461, United States
| | - Evripidis Gavathiotis
- Department of Biochemistry, Department of Medicine, Department of Oncology, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, New York, NY 10461, United States
| | - Poulikos I Poulikakos
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, United States
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18
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Hanrahan AJ, Chen Z, Rosen N, Solit DB. BRAF - a tumour-agnostic drug target with lineage-specific dependencies. Nat Rev Clin Oncol 2024; 21:224-247. [PMID: 38278874 DOI: 10.1038/s41571-023-00852-0] [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: 12/12/2023] [Indexed: 01/28/2024]
Abstract
In June 2022, the FDA granted Accelerated Approval to the BRAF inhibitor dabrafenib in combination with the MEK inhibitor trametinib for the treatment of adult and paediatric patients (≥6 years of age) with unresectable or metastatic BRAFV600E-mutant solid tumours, except for BRAFV600E-mutant colorectal cancers. The histology-agnostic approval of dabrafenib plus trametinib marks the culmination of two decades of research into the landscape of BRAF mutations in human cancers, the biochemical mechanisms underlying BRAF-mediated tumorigenesis, and the clinical development of selective RAF and MEK inhibitors. Although the majority of patients with BRAFV600E-mutant tumours derive clinical benefit from BRAF inhibitor-based combinations, resistance to treatment develops in most. In this Review, we describe the biochemical basis for oncogenic BRAF-induced activation of MAPK signalling and pan-cancer and lineage-specific mechanisms of intrinsic, adaptive and acquired resistance to BRAF inhibitors. We also discuss novel RAF inhibitors and drug combinations designed to delay the emergence of treatment resistance and/or expand the population of patients with BRAF-mutant cancers who benefit from molecularly targeted therapies.
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Affiliation(s)
- Aphrothiti J Hanrahan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ziyu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics & Systems Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Neal Rosen
- Molecular Pharmacology Program, Sloan Kettering Institute for Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, Cornell University, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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19
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Riaud M, Maxwell J, Soria-Bretones I, Dankner M, Li M, Rose AAN. The role of CRAF in cancer progression: from molecular mechanisms to precision therapies. Nat Rev Cancer 2024; 24:105-122. [PMID: 38195917 DOI: 10.1038/s41568-023-00650-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
The RAF family of kinases includes key activators of the pro-tumourigenic mitogen-activated protein kinase pathway. Hyperactivation of RAF proteins, particularly BRAF and CRAF, drives tumour progression and drug resistance in many types of cancer. Although BRAF is the most studied RAF protein, partially owing to its high mutation incidence in melanoma, the role of CRAF in tumourigenesis and drug resistance is becoming increasingly clinically relevant. Here, we summarize the main known regulatory mechanisms and gene alterations that contribute to CRAF activity, highlighting the different oncogenic roles of CRAF, and categorize RAF1 (CRAF) mutations according to the effect on kinase activity. Additionally, we emphasize the effect that CRAF alterations may have on drug resistance and how precision therapies could effectively target CRAF-dependent tumours. Here, we discuss preclinical and clinical findings that may lead to improved treatments for all types of oncogenic RAF1 alterations in cancer.
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Affiliation(s)
- Melody Riaud
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jennifer Maxwell
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Isabel Soria-Bretones
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Matthew Dankner
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Meredith Li
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - April A N Rose
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada.
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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20
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Bao Y, Jia F, Li M, Xu R, Xie Y, Zhang F, Guo J. Characterizing the Molecular Mechanism of the Lethal C423D Mutation in FgMyoI: A Molecular Perspective. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1539-1549. [PMID: 38226494 DOI: 10.1021/acs.jafc.3c08648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The lethal mutation C423D in Fusarium graminearum myosin I (FgMyoI) occurs close to the binding pocket of the allosteric inhibitor phenamacril and causes severe inhibition on mycelial growth of F. graminearum strain PH-1. Here, based on extensive Gaussian accelerated molecular dynamics simulations and wet experiments, we elucidate the underlying molecular mechanism of the abnormal functioning of the FgMyoIC423D mutant at the atomistic level. Our results suggest that the damaging mutation C423D exhibits a synergistic allosteric inhibition mechanism similar to but more robust than that of phenamacril, including effects on the active site and actin binding. Unlike phenamacril-induced closure of Switch2, the mutation results in unfolding of the N-terminal relay helix with a partially opened Switch2 and blocks the structural rearrangement of the relay/SH1 helices, impairing the proper initiation of the recovery stroke. Due to the significant influence of C423D mutation on the function of FgMyoI, designing covalent inhibitors targeting this site holds tremendous potential.
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Affiliation(s)
- Yiqiong Bao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fangying Jia
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengrong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ran Xu
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Yanjie Xie
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingjing Guo
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
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Li X, Guan H, Ma C, Dai Y, Su J, Chen X, Yuan Q, Wang J. Combination of bulk RNA sequencing and scRNA sequencing uncover the molecular characteristics of MAPK signaling in kidney renal clear cell carcinoma. Aging (Albany NY) 2024; 16:1414-1439. [PMID: 38217548 PMCID: PMC10866414 DOI: 10.18632/aging.205436] [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: 07/11/2023] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
The MAPK signaling pathway significantly impacts cancer progression and resistance; however, its functions remain incompletely assessed across various cancers, particularly in kidney renal clear cell carcinoma (KIRC). Therefore, there is an urgent need for comprehensive pan-cancer investigations of MAPK signaling, particularly within the context of KIRC. In this research, we obtained TCGA pan-cancer multi-omics data and conducted a comprehensive analysis of the genomic and transcriptomic characteristics of the MAPK signaling pathway. For in-depth investigation in KIRC, status of MAPK pathway was quantitatively estimated by ssGSEA and Ward algorithm was utilized for cluster analysis. Molecular characteristics and clinical prognoses of KIRC patients with distinct MAPK activities were comprehensively explored using a series of bioinformatics algorithms. Subsequently, a combination of LASSO and COX regression analyses were utilized sequentially to construct a MAPK-related signature to help identify the risk level of each sample. Patients in the C1 subtype exhibited relatively higher levels of MAPK signaling activity, which were associated with abundant immune cell infiltration and favorable clinical outcomes. Single-cell RNA sequencing (scRNA-seq) analysis of KIRC samples identified seven distinct cell types, and endothelial cells in tumor tissues had obviously higher MAPK scores than normal tissues. The immunohistochemistry results indicated the reduced expression levels of PAPSS1, MAP3K11, and SPRED1 in KIRC samples. In conclusion, our study represents the first integration of bulk RNA sequencing and single-cell RNA sequencing to elucidate the molecular characteristics of MAPK signaling in KIRC, providing a solid foundation for precision oncology.
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Affiliation(s)
- Xiunan Li
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hewen Guan
- Department of Dermatology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Chuanyu Ma
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yunfei Dai
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Ji Su
- Department of Urology, Central Hospital of Benxi, Benxi, Liaoning, China
| | - Xu Chen
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jianbo Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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22
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Hajjo R, Sabbah DA, Bardaweel SK, Zhong HA. Targeting the EGFR/RAS/RAF signaling pathway in anticancer research: a recent update on inhibitor design and clinical trials (2020-2023). Expert Opin Ther Pat 2024; 34:51-69. [PMID: 38450537 DOI: 10.1080/13543776.2024.2327307] [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: 11/01/2023] [Accepted: 01/25/2024] [Indexed: 03/08/2024]
Abstract
INTRODUCTION Recent years have seen significant strides in drug developmenttargeting the EGFR/RAS/RAF signaling pathway which is critical forcell growth and proliferation. Protein-protein interaction networksamong EGFR, RAS, and RAF proteins offer insights for drug discovery. This review discusses the drug design and development efforts ofinhibitors targeting these proteins over the past 3 years, detailingtheir structures, selectivity, efficacy, and combination therapy.Strategies to combat drug resistance and minimize toxicities areexplored, along with future research directions. AREA COVERED This review encompasses clinical trials and patents on EGFR, KRAS,and BRAF inhibitors from 2020 to 2023, including advancements indesign and synthesis of proteolysis targeting chimeras (PROTACs) forprotein degradation. EXPERT OPINION To tackle drug resistance, designing allosteric fourth-generationEGFR inhibitors is vital. Covalent, allosteric, or combinationaltherapies, along with PROTAC degraders, are key methods to addressresistance and toxicity in KRAS and BRAF inhibitors.
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Affiliation(s)
- Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Board Member, National Center for Epidemics and Communicable Disease Control (JCDC), Amman, Jordan
| | - Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Sanaa K Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman, Jordan
| | - Haizhen A Zhong
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, Omaha, NE, USA
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23
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Wang P, Laster K, Jia X, Dong Z, Liu K. Targeting CRAF kinase in anti-cancer therapy: progress and opportunities. Mol Cancer 2023; 22:208. [PMID: 38111008 PMCID: PMC10726672 DOI: 10.1186/s12943-023-01903-x] [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: 08/31/2023] [Accepted: 11/16/2023] [Indexed: 12/20/2023] Open
Abstract
The RAS/mitogen-activated protein kinase (MAPK) signaling cascade is commonly dysregulated in human malignancies by processes driven by RAS or RAF oncogenes. Among the members of the RAF kinase family, CRAF plays an important role in the RAS-MAPK signaling pathway, as well as in the progression of cancer. Recent research has provided evidence implicating the role of CRAF in the physiological regulation and the resistance to BRAF inhibitors through MAPK-dependent and MAPK-independent mechanisms. Nevertheless, the effectiveness of solely targeting CRAF kinase activity remains controversial. Moreover, the kinase-independent function of CRAF may be essential for lung cancers with KRAS mutations. It is imperative to develop strategies to enhance efficacy and minimize toxicity in tumors driven by RAS or RAF oncogenes. The review investigates CRAF alterations observed in cancers and unravels the distinct roles of CRAF in cancers propelled by diverse oncogenes. This review also seeks to summarize CRAF-interacting proteins and delineate CRAF's regulation across various cancer hallmarks. Additionally, we discuss recent advances in pan-RAF inhibitors and their combination with other therapeutic approaches to improve treatment outcomes and minimize adverse effects in patients with RAF/RAS-mutant tumors. By providing a comprehensive understanding of the multifaceted role of CRAF in cancers and highlighting the latest developments in RAF inhibitor therapies, we endeavor to identify synergistic targets and elucidate resistance pathways, setting the stage for more robust and safer combination strategies for cancer treatment.
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Affiliation(s)
- Penglei Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
- Tianjian Laboratory for Advanced Biomedical Sciences, Zhengzhou, 450052, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Kyle Laster
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
- Tianjian Laboratory for Advanced Biomedical Sciences, Zhengzhou, 450052, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.
- Tianjian Laboratory for Advanced Biomedical Sciences, Zhengzhou, 450052, Henan, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China.
- Department of Pathophysiology, School of Basic Medical Sciences, China-US (Henan) Hormel Cancer Institute, AMS, College of Medicine, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.
- Tianjian Laboratory for Advanced Biomedical Sciences, Zhengzhou, 450052, Henan, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China.
- Department of Pathophysiology, School of Basic Medical Sciences, China-US (Henan) Hormel Cancer Institute, AMS, College of Medicine, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China.
- Basic Medicine Sciences Research Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, 450000, Henan, China.
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24
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Dalby KN. Raf protomers: Drug binding preferences in living cells. Cell Chem Biol 2023; 30:1329-1331. [PMID: 37977126 PMCID: PMC10954368 DOI: 10.1016/j.chembiol.2023.10.002] [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: 10/02/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
The precise and selective quantification of drug-target interactions within the context of RAS-RAF heterodimers in live cells offers a powerful tool for drug development and personalized medicine, particularly in cancer research, where the RAS-RAF pathway is pivotal.
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Affiliation(s)
- Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
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25
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Vasta JD, Michaud A, Zimprich CA, Beck MT, Swiatnicki MR, Zegzouti H, Thomas MR, Wilkinson J, Crapster JA, Robers MB. Protomer selectivity of type II RAF inhibitors within the RAS/RAF complex. Cell Chem Biol 2023; 30:1354-1365.e6. [PMID: 37643616 DOI: 10.1016/j.chembiol.2023.07.019] [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: 02/08/2023] [Revised: 05/12/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023]
Abstract
RAF dimer inhibitors offer therapeutic potential in RAF- and RAS-driven cancers. The utility of such drugs is predicated on their capacity to occupy both RAF protomers in the RAS-RAF signaling complex. Here we describe a method to conditionally quantify drug-target occupancy at selected RAF protomers within an active RAS-RAF complex in cells. RAF target engagement can be measured in the presence or absence of any mutant KRAS allele, enabling the high-affinity state of RAF dimer inhibitors to be quantified in the cellular milieu. The intracellular protomer selectivity of clinical-stage type II RAF inhibitors revealed that ARAF protomer engagement, but not engagement of BRAF or CRAF, is commensurate with inhibition of MAPK signaling in various mutant RAS cell lines. Our results support a fundamental role for ARAF in mutant RAS signaling and reveal poor ARAF protomer vulnerability for a cohort of RAF inhibitors undergoing clinical evaluation.
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26
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Ji H, Lu X, Zhao S, Wang Q, Liao B, Bauer LG, Huber KVM, Luo R, Tian R, Tan CSH. Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions. Cell Chem Biol 2023; 30:1478-1487.e7. [PMID: 37652024 PMCID: PMC10840709 DOI: 10.1016/j.chembiol.2023.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 05/18/2023] [Accepted: 08/09/2023] [Indexed: 09/02/2023]
Abstract
Target deconvolution is a crucial but costly and time-consuming task that hinders large-scale profiling for drug discovery. We present a matrix-augmented pooling strategy (MAPS) which mixes multiple drugs into samples with optimized permutation and delineates targets of each drug simultaneously with mathematical processing. We validated this strategy with thermal proteome profiling (TPP) testing of 15 drugs concurrently, increasing experimental throughput by 60x while maintaining high sensitivity and specificity. Benefiting from the lower cost and higher throughput of MAPS, we performed target deconvolution of the 15 drugs across 5 cell lines. Our profiling revealed that drug-target interactions can differ vastly in targets and binding affinity across cell lines. We further validated BRAF and CSNK2A2 as potential off-targets of bafetinib and abemaciclib, respectively. This work represents the largest thermal profiling of structurally diverse drugs across multiple cell lines to date.
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Affiliation(s)
- Hongchao Ji
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xue Lu
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR
| | - Shiji Zhao
- Department of Molecular Biology and Biochemistry, Department of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Qiqi Wang
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR
| | - Bin Liao
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR
| | - Ludwig G Bauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, OX3 7FZ Oxford, UK; Target Discovery Institute, Nuffield Department of Medicine, OX3 7FZ Oxford, UK
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, OX3 7FZ Oxford, UK; Target Discovery Institute, Nuffield Department of Medicine, OX3 7FZ Oxford, UK
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Department of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Ruijun Tian
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR
| | - Chris Soon Heng Tan
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR.
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27
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Rasmussen DM, Semonis MM, Greene JT, Muretta JM, Thompson AR, Ramos ST, Thomas DD, Pomerantz WC, Freedman TS, Levinson NM. Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.536450. [PMID: 37131649 PMCID: PMC10153139 DOI: 10.1101/2023.04.18.536450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The type II class of RAF inhibitors currently in clinical trials paradoxically activate BRAF at subsaturating concentrations. Activation is mediated by induction of BRAF dimers, but why activation rather than inhibition occurs remains unclear. Using biophysical methods tracking BRAF dimerization and conformation we built an allosteric model of inhibitor-induced dimerization that resolves the allosteric contributions of inhibitor binding to the two active sites of the dimer, revealing key differences between type I and type II RAF inhibitors. For type II inhibitors the allosteric coupling between inhibitor binding and BRAF dimerization is distributed asymmetrically across the two dimer binding sites, with binding to the first site dominating the allostery. This asymmetry results in efficient and selective induction of dimers with one inhibited and one catalytically active subunit. Our allosteric models quantitatively account for paradoxical activation data measured for 11 RAF inhibitors. Unlike type II inhibitors, type I inhibitors lack allosteric asymmetry and do not activate BRAF homodimers. Finally, NMR data reveal that BRAF homodimers are dynamically asymmetric with only one of the subunits locked in the active αC-in state. This provides a structural mechanism for how binding of only a single αC-in inhibitor molecule can induce potent BRAF dimerization and activation.
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Affiliation(s)
- Damien M. Rasmussen
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | - Manny M. Semonis
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
| | - Joseph T. Greene
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
| | - Joseph M. Muretta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | - Andrew R. Thompson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | | | - David D. Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455
| | | | - Tanya S. Freedman
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
- Center for Immunology, University of Minnesota, Minneapolis, MN, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455
| | - Nicholas M. Levinson
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455
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28
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Zhu EY, Schillo JL, Murray SD, Riordan JD, Dupuy AJ. Understanding cancer drug resistance with Sleeping Beauty functional genomic screens: Application to MAPK inhibition in cutaneous melanoma. iScience 2023; 26:107805. [PMID: 37860756 PMCID: PMC10582486 DOI: 10.1016/j.isci.2023.107805] [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: 02/27/2023] [Revised: 07/10/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023] Open
Abstract
Combined BRAF and MEK inhibition is an effective treatment for BRAF-mutant cutaneous melanoma. However, most patients progress on this treatment due to drug resistance. Here, we applied the Sleeping Beauty transposon system to understand how melanoma evades MAPK inhibition. We found that the specific drug resistance mechanisms differed across melanomas in our genetic screens of five cutaneous melanoma cell lines. While drivers that reactivated MAPK were highly conserved, many others were cell-line specific. One such driver, VAV1, activated a de-differentiated transcriptional program like that of hyperactive RAC1, RAC1P29S. To target this mechanism, we showed that an inhibitor of SRC, saracatinib, blunts the VAV1-induced transcriptional reprogramming. Overall, we highlighted the importance of accounting for melanoma heterogeneity in treating cutaneous melanoma with MAPK inhibitors. Moreover, we demonstrated the utility of the Sleeping Beauty transposon system in understanding cancer drug resistance.
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Affiliation(s)
- Eliot Y. Zhu
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jacob L. Schillo
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Sarina D. Murray
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jesse D. Riordan
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
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29
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Su D, Zhu S, Hou Z, Hao F, Xu K, Xu F, Zhu Y, Liu D, Xu J, Tao J. Toxoplasma gondii infection regulates apoptosis of host cells via miR-185/ARAF axis. Parasit Vectors 2023; 16:371. [PMID: 37858158 PMCID: PMC10585723 DOI: 10.1186/s13071-023-05991-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Toxoplasmosis is a zoonosis with a worldwide presence that is caused by the intracellular parasite Toxoplasma gondii. Active regulation of apoptosis is an important immune mechanism by which host cells resist the growth of T. gondii or avoid excessive pathological damage induced by this parasite. Previous studies found that upregulated expression of microRNA-185 (miR-185) during T. gondii infection has a potential role in regulating the expression of the ARAF gene, which is reported to be associated with cell proliferation and apoptosis. METHODS The expression levels of miR-185 and the ARAF gene were evaluated by qPCR and Western blot, respectively, in mice tissues, porcine kidney epithelial cells (PK-15) and porcine alveolar macrophages (3D4/21) following infection with the T. gondii ToxoDB#9 and RH strains. The dual luciferase reporter assay was then used to verify the relationship between miR-185 and ARAF targets in PK-15 cells. PK-15 and 3D4/21 cell lines with stable knockout of the ARAF gene were established by CRISPR, and then the apoptosis rates of the cells following T. gondii infection were detected using cell flow cytometry assays. Simultaneously, the activities of cleaved caspase-3, as a key apoptosis executive protein, were detected by Western blot to evaluate the apoptosis levels of cells. RESULTS Infection with both the T. gondii ToxoDB#9 and RH strains induced an increased expression of miR-185 and a decreased expression of ARAF in mice tissues, PK-15 and 3D4/21 cells. MiR-185 mimic transfections showed a significantly negative correlation in expression levels between miR-185 and the ARAF gene. The dual luciferase reporter assay confirmed that ARAF was a target of miR-185. Functional investigation revealed that T. gondii infection induced the apoptosis of PK-15 and 3D4/21 cells, which could be inhibited by ARAF knockout or overexpression of miR-185. The expression levels of cleaved caspase-3 protein were significantly lower in cells with ARAF knockout than in normal cells, which were consistent with the results of the cell flow cytometry assays. CONCLUSIONS Toxoplasma gondii infection could lead to the upregulation of miR-185 and the downregulation of ARAF, which was not related to the strain of T. gondii and the host cells. Toxoplasma gondii infection could regulate the apoptosis of host cells via the miR-185/ARAF axis, which represents an additional strategy used by T. gondii to counteract host-cell apoptosis in order to maintain survival and reproduce in the host cells.
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Affiliation(s)
- Dingzeyang Su
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009 Jiangsu People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009 People’s Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009 People’s Republic of China
| | - Shifan Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009 Jiangsu People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009 People’s Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009 People’s Republic of China
| | - Zhaofeng Hou
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009 Jiangsu People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009 People’s Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009 People’s Republic of China
| | - Fuxing Hao
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, 225300 People’s Republic of China
| | - Kangzhi Xu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009 Jiangsu People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009 People’s Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009 People’s Republic of China
| | - Fan Xu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009 Jiangsu People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009 People’s Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009 People’s Republic of China
| | - Yuyang Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009 Jiangsu People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009 People’s Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009 People’s Republic of China
| | - Dandan Liu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009 Jiangsu People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009 People’s Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009 People’s Republic of China
| | - Jinjun Xu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009 Jiangsu People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009 People’s Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009 People’s Republic of China
| | - Jianping Tao
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009 Jiangsu People’s Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009 People’s Republic of China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009 People’s Republic of China
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30
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Chehrazi-Raffle A, Tukachinsky H, Toye E, Sivakumar S, Schrock AB, Bergom HE, Ebrahimi H, Pal S, Dorff T, Agarwal N, Mahal BA, Oxnard GR, Hwang J, Antonarakis ES. Unique Spectrum of Activating BRAF Alterations in Prostate Cancer. Clin Cancer Res 2023; 29:3948-3957. [PMID: 37477913 PMCID: PMC10543965 DOI: 10.1158/1078-0432.ccr-23-1393] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/17/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
PURPOSE Alterations in BRAF have been reported in 3% to 5% of prostate cancer, although further characterization is lacking. Here, we describe the nature of BRAF alterations in prostate cancer using a large cohort from commercially available tissue and liquid biopsies subjected to comprehensive genomic profiling (CGP). EXPERIMENTAL DESIGN Tissue and liquid biopsies from patients with prostate cancer were profiled using FoundationOne CDx and FoundationOne Liquid CDx CGP assays, respectively. Tissue biopsies from non-prostate cancer types were used for comparison (n = 275,151). Genetic ancestry was predicted using a single-nucleotide polymorphism (SNP) based approach. RESULTS Among 15,864 tissue biopsies, BRAF-activating alterations were detected in 520 cases (3.3%). The majority (463 samples, 2.9%) harbored class II alterations, including BRAF rearrangements (243 samples, 1.5%), K601E (101 samples, 0.6%), and G469A (58 samples, 0.4%). BRAF-altered prostate cancers were enriched for CDK12 mutations (OR, 1.87; 9.2% vs. 5.2%; P = 0.018), but depleted in TMPRSS2 fusions (OR, 0.25; 11% vs. 32%; P < 0.0001), PTEN alterations (OR, 0.47; 17% vs. 31%; P < 0.0001), and APC alterations (OR, 0.48; 4.4% vs. 8.9%; P = 0.018) relative to BRAF wild-type (WT) disease. Compared with patients of European ancestry, BRAF alterations were more common in tumors from patients of African ancestry (5.1% vs. 2.9%, P < 0.0001) and Asian ancestry (6.0% vs. 2.9%, P < 0.001). CONCLUSIONS Activating BRAF alterations were detected in approximately 3% of prostate cancers, and most were class II mutations and rearrangements; BRAF V600 mutations were exceedingly rare. These findings suggest that BRAF activation in prostate cancer is unique from other cancers and supports further clinical investigation of therapeutics targeting the mitogen-activated protein kinase (MAPK) pathway.
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Affiliation(s)
| | | | - Eamon Toye
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | | | | | - Hannah E. Bergom
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Hedyeh Ebrahimi
- City of Hope Comprehensive Cancer Center, Duarte, California
| | - Sumanta Pal
- City of Hope Comprehensive Cancer Center, Duarte, California
| | - Tanya Dorff
- City of Hope Comprehensive Cancer Center, Duarte, California
| | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Brandon A. Mahal
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | | | - Justin Hwang
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
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Lauinger M, Christen D, Klar RFU, Roubaty C, Heilig CE, Stumpe M, Knox JJ, Radulovich N, Tamblyn L, Xie IY, Horak P, Forschner A, Bitzer M, Wittel UA, Boerries M, Ball CR, Heining C, Glimm H, Fröhlich M, Hübschmann D, Gallinger S, Fritsch R, Fröhling S, O'Kane GM, Dengjel J, Brummer T. BRAF Δβ3-αC in-frame deletion mutants differ in their dimerization propensity, HSP90 dependence, and druggability. SCIENCE ADVANCES 2023; 9:eade7486. [PMID: 37656784 DOI: 10.1126/sciadv.ade7486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
In-frame BRAF exon 12 deletions are increasingly identified in various tumor types. The resultant BRAFΔβ3-αC oncoproteins usually lack five amino acids in the β3-αC helix linker and sometimes contain de novo insertions. The dimerization status of BRAFΔβ3-αC oncoproteins, their precise pathomechanism, and their direct druggability by RAF inhibitors (RAFi) has been under debate. Here, we functionally characterize BRAFΔLNVTAP>F and two novel mutants, BRAFdelinsFS and BRAFΔLNVT>F, and compare them with other BRAFΔβ3-αC oncoproteins. We show that BRAFΔβ3-αC oncoproteins not only form stable homodimers and large multiprotein complexes but also require dimerization. Nevertheless, details matter as aromatic amino acids at the deletion junction of some BRAFΔβ3-αC oncoproteins, e.g., BRAFΔLNVTAP>F, increase their stability and dimerization propensity while conferring resistance to monomer-favoring RAFi such as dabrafenib or HSP 90/CDC37 inhibition. In contrast, dimer-favoring inhibitors such as naporafenib inhibit all BRAFΔβ3-αC mutants in cell lines and patient-derived organoids, suggesting that tumors driven by such oncoproteins are vulnerable to these compounds.
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Affiliation(s)
- Manuel Lauinger
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Daniel Christen
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rhena F U Klar
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carole Roubaty
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christoph E Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laura Tamblyn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Irene Y Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrea Forschner
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
| | - Michael Bitzer
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
- Center for Personalized Medicine Tübingen, Eberhard Karls University, Tübingen, Germany
- Department of Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Uwe A Wittel
- Department of General and Visceral Surgery, University of Freiburg Medical Center, Faculty of Medicine, 79106 Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Technische Universität Dresden, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Christoph Heining
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ralph Fritsch
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Department of Medical Oncology and Haematology, University Hospital of Zurich, Zurich, Switzerland
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Tilman Brummer
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany
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Song L, Wei X, Zhang X, Lu Y. Combining single-cell and transcriptomic analysis revealed the immunomodulatory effect of GOT2 on a glutamine-dependent manner in cutaneous melanoma. Front Pharmacol 2023; 14:1241454. [PMID: 37693904 PMCID: PMC10483140 DOI: 10.3389/fphar.2023.1241454] [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: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023] Open
Abstract
Background: Reprogramming in glutamine metabolism is a hallmark of cancers, while its role in cutaneous melanoma has not been studied at great length. Methods: Here, we constructed a glutamine metabolism-related prognostic signature in cutaneous melanoma with a variety of bioinformatics methods according to the glutamine metabolism regulatory molecules. Moreover, experimental verification was carried out for the key gene. Results: We have identified two subgroups of cutaneous melanoma patients, each with different prognoses, immune characteristics, and genetic mutations. GOT2 was the most concerned key gene among the model genes. We verified its role in promoting tumor cell proliferation by CCK-8 and clone formation assays. Conclusion: Our study cast new light on the prognosis of cutaneous melanoma, and the internal mechanism regulating glutamine metabolism of GOT2 may provide a new avenue for treating the cutaneous melanoma disease precisely.
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Affiliation(s)
- Lebin Song
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiyi Wei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xi Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Lu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Affiliation(s)
- Jaishri O Blakeley
- From the Johns Hopkins University School of Medicine, Baltimore (J.O.B.); and the University of California San Francisco, San Francisco (K.S.)
| | - Kevin Shannon
- From the Johns Hopkins University School of Medicine, Baltimore (J.O.B.); and the University of California San Francisco, San Francisco (K.S.)
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Fernandez MF, Choi J, Sosman J. New Approaches to Targeted Therapy in Melanoma. Cancers (Basel) 2023; 15:3224. [PMID: 37370834 PMCID: PMC10296143 DOI: 10.3390/cancers15123224] [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: 05/29/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
It was just slightly more than a decade ago when metastatic melanoma carried a dismal prognosis with few, if any, effective therapies. Since then, the evolution of cancer immunotherapy has led to new and effective treatment approaches for melanoma. However, despite these advances, a sizable portion of patients with advanced melanoma have de novo or acquired resistance to immune checkpoint inhibitors. At the same time, therapies (BRAF plus MEK inhibitors) targeting the BRAFV600 mutations found in 40-50% of cutaneous melanomas have also been critical for optimizing management and improving patient outcomes. Even though immunotherapy has been established as the initial therapy in most patients with cutaneous melanoma, subsequent effective therapy is limited to BRAFV600 melanoma. For all other melanoma patients, driver mutations have not been effectively targeted. Numerous efforts are underway to target melanomas with NRAS mutations, NF-1 LOF mutations, and other genetic alterations leading to activation of the MAP kinase pathway. In this era of personalized medicine, we will review the current genetic landscape, molecular classifications, emerging drug targets, and the potential for combination therapies for non-BRAFV600 melanoma.
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Affiliation(s)
| | | | - Jeffrey Sosman
- Robert H. Lurie Comprehensive Cancer Center, Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (M.F.F.); (J.C.)
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35
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Rohrer L, Spohr C, Beha C, Griffin R, Braun S, Halbach S, Brummer T. Analysis of RAS and drug induced homo- and heterodimerization of RAF and KSR1 proteins in living cells using split Nanoluc luciferase. Cell Commun Signal 2023; 21:136. [PMID: 37316874 DOI: 10.1186/s12964-023-01146-9] [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: 11/11/2022] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The dimerization of RAF kinases represents a key event in their activation cycle and in RAS/ERK pathway activation. Genetic, biochemical and structural approaches provided key insights into this process defining RAF signaling output and the clinical efficacy of RAF inhibitors (RAFi). However, methods reporting the dynamics of RAF dimerization in living cells and in real time are still in their infancy. Recently, split luciferase systems have been developed for the detection of protein-protein-interactions (PPIs), incl. proof-of-concept studies demonstrating the heterodimerization of the BRAF and RAF1 isoforms. Due to their small size, the Nanoluc luciferase moieties LgBiT and SmBiT, which reconstitute a light emitting holoenzyme upon fusion partner promoted interaction, appear as well-suited to study RAF dimerization. Here, we provide an extensive analysis of the suitability of the Nanoluc system to study the homo- and heterodimerization of BRAF, RAF1 and the related KSR1 pseudokinase. We show that KRASG12V promotes the homo- and heterodimerization of BRAF, while considerable KSR1 homo- and KSR1/BRAF heterodimerization already occurs in the absence of this active GTPase and requires a salt bridge between the CC-SAM domain of KSR1 and the BRAF-specific region. We demonstrate that loss-of-function mutations impairing key steps of the RAF activation cycle can be used as calibrators to gauge the dynamics of heterodimerization. This approach identified the RAS-binding domains and the C-terminal 14-3-3 binding motifs as particularly critical for the reconstitution of RAF mediated LgBiT/SmBiT reconstitution, while the dimer interface was less important for dimerization but essential for downstream signaling. We show for the first time that BRAFV600E, the most common BRAF oncoprotein whose dimerization status is controversially portrayed in the literature, forms homodimers in living cells more efficiently than its wildtype counterpart. Of note, Nanoluc activity reconstituted by BRAFV600E homodimers is highly sensitive to the paradox-breaking RAFi PLX8394, indicating a dynamic and specific PPI. We report the effects of eleven ERK pathway inhibitors on RAF dimerization, incl. third-generation compounds that are less-defined in terms of their dimer promoting abilities. We identify Naporafenib as a potent and long-lasting dimerizer and show that the split Nanoluc approach discriminates between type I, I1/2 and II RAFi. Video Abstract.
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Affiliation(s)
- Lino Rohrer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Carina Beha
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany.
- Center for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, 79104, Germany.
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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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Tkacik E, Li K, Gonzalez-Del Pino G, Ha BH, Vinals J, Park E, Beyett TS, Eck MJ. Structure and RAF family kinase isoform selectivity of type II RAF inhibitors tovorafenib and naporafenib. J Biol Chem 2023; 299:104634. [PMID: 36963492 PMCID: PMC10149214 DOI: 10.1016/j.jbc.2023.104634] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 03/26/2023] Open
Abstract
Upon activation by RAS, RAF family kinases initiate signaling through the MAP kinase cascade to control cell growth, proliferation, and differentiation. Among RAF isoforms (ARAF, BRAF, and CRAF), oncogenic mutations are by far most frequent in BRAF. The BRAFV600E mutation drives more than half of all malignant melanoma and is also found in many other cancers. Selective inhibitors of BRAFV600E (vemurafenib, dabrafenib, encorafenib) are used clinically for these indications, but they are not effective inhibitors in the context of oncogenic RAS, which drives dimerization and activation of RAF, nor for malignancies driven by aberrantly dimerized truncation/fusion variants of BRAF. By contrast, a number of "type II" RAF inhibitors have been developed as potent inhibitors of RAF dimers. Here, we compare potency of type II inhibitors tovorafenib (TAK-580) and naporafenib (LHX254) in biochemical assays against the three RAF isoforms and describe crystal structures of both compounds in complex with BRAF. We find that tovorafenib and naporafenib are most potent against CRAF but markedly less potent against ARAF. Crystal structures of both compounds with BRAFV600E or WT BRAF reveal the details of their molecular interactions, including the expected type II-binding mode, with full occupancy of both subunits of the BRAF dimer. Our findings have important clinical ramifications. Type II RAF inhibitors are generally regarded as pan-RAF inhibitors, but our studies of these two agents, together with recent work with type II inhibitors belvarafenib and naporafenib, indicate that relative sparing of ARAF may be a property of multiple drugs of this class.
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Affiliation(s)
- Emre Tkacik
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kunhua Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gonzalo Gonzalez-Del Pino
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Byung Hak Ha
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Javier Vinals
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Tyler S Beyett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
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Kim YY, Park H, Song T, Choi K, Dolton M, Mao J, Kim J, Ahn YG, Suh KH, Kim YH. Belvarafenib penetrates the BBB and shows potent antitumor activity in a murine melanoma brain metastasis model. Clin Exp Metastasis 2023; 40:137-148. [PMID: 36763292 DOI: 10.1007/s10585-023-10198-7] [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: 08/08/2022] [Accepted: 01/06/2023] [Indexed: 02/11/2023]
Abstract
Brain metastasis is a common complication in melanoma patients with BRAF and NRAS mutations and has a poor prognosis. Although BRAF inhibitors are clinically approved, their poor brain penetration limits their efficacy in brain metastasis. Thus, melanoma brain metastasis still requires better treatment. Belvarafenib, a pan-RAF inhibitor, has reported antitumor activity in melanoma with RAF and RAS mutations in animal models and patients. However, brain permeability and antitumor efficacy on brain metastasis have not been determined. This study confirmed the brain penetration of belvarafenib, the antitumor activity on BRAF and NRAS mutant melanoma, and the efficacy on melanoma within the brain. Belvarafenib strongly suppressed melanoma in BRAF V600E mutant A375SM tumor-bearing mice. It also significantly inhibited tumor growth in NRAS mutant SK-MEL-30 and K1735 tumor-bearing mice and synergized to enhance the antitumor activity combined with cobimetinib or atezolizumab. Belvarafenib was penetrated at considerable levels into the brains of mice and rats following oral administration. The exposure of belvarafenib in the brain was similar to or higher than that in plasma, and this high brain penetration differed significantly from that of other BRAF inhibitors with low brain penetration. Most importantly, belvarafenib strongly reduced tumor burden and markedly improved survival benefits in mice intracranially implanted with A375SM melanoma. These results demonstrated that belvarafenib, which has favorable BBB permeability, and potent antitumor activity on the tumors with BRAF/NRAS mutations, may be a promising therapeutic option for patients with BRAF/NRAS mutant melanoma brain metastasis.
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Affiliation(s)
- Yu-Yon Kim
- Hanmi Research Center, Hanmi Pharm. Co. Ltd, Gyeonggi-Do, Korea
| | - Hyunjin Park
- Hanmi Research Center, Hanmi Pharm. Co. Ltd, Gyeonggi-Do, Korea
| | - Taehun Song
- Hanmi Research Center, Hanmi Pharm. Co. Ltd, Gyeonggi-Do, Korea
| | - Kyungjin Choi
- Hanmi Research Center, Hanmi Pharm. Co. Ltd, Gyeonggi-Do, Korea
| | | | - Jialin Mao
- Genentech Inc, South San Francisco, CA, USA
| | - Jisook Kim
- Hanmi Research Center, Hanmi Pharm. Co. Ltd, Gyeonggi-Do, Korea
| | - Young Gil Ahn
- Hanmi Research Center, Hanmi Pharm. Co. Ltd, Gyeonggi-Do, Korea
| | - Kwee Hyun Suh
- Hanmi Research Center, Hanmi Pharm. Co. Ltd, Gyeonggi-Do, Korea
| | - Young Hoon Kim
- Hanmi Research Center, Hanmi Pharm. Co. Ltd, Gyeonggi-Do, Korea.
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Fröhlich F, Gerosa L, Muhlich J, Sorger PK. Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance. Mol Syst Biol 2023; 19:e10988. [PMID: 36700386 PMCID: PMC9912026 DOI: 10.15252/msb.202210988] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 11/29/2022] [Accepted: 12/15/2022] [Indexed: 01/27/2023] Open
Abstract
BRAF is prototypical of oncogenes that can be targeted therapeutically and the treatment of BRAFV600E melanomas with RAF and MEK inhibitors results in rapid tumor regression. However, drug-induced rewiring generates a drug adapted state thought to be involved in acquired resistance and disease recurrence. In this article, we study mechanisms of adaptive rewiring in BRAFV600E melanoma cells using an energy-based implementation of ordinary differential equation (ODE) modeling in combination with proteomic, transcriptomic and imaging data. We develop a method for causal tracing of ODE models and identify two parallel MAPK reaction channels that are differentially sensitive to RAF and MEK inhibitors due to differences in protein oligomerization and drug binding. We describe how these channels, and timescale separation between immediate-early signaling and transcriptional feedback, create a state in which the RAS-regulated MAPK channel can be activated by growth factors under conditions in which the BRAFV600E -driven channel is fully inhibited. Further development of the approaches in this article is expected to yield a unified model of adaptive drug resistance in melanoma.
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Affiliation(s)
- Fabian Fröhlich
- Laboratory of Systems Pharmacology, Department of Systems BiologyHarvard Medical SchoolBostonMAUSA
| | - Luca Gerosa
- Laboratory of Systems Pharmacology, Department of Systems BiologyHarvard Medical SchoolBostonMAUSA,Present address:
Genentech, Inc.South San FranciscoCAUSA
| | - Jeremy Muhlich
- Laboratory of Systems Pharmacology, Department of Systems BiologyHarvard Medical SchoolBostonMAUSA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems BiologyHarvard Medical SchoolBostonMAUSA
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Yang H, Zhou X, Fu D, Le C, Wang J, Zhou Q, Liu X, Yuan Y, Ding K, Xiao Q. Targeting RAS mutants in malignancies: successes, failures, and reasons for hope. Cancer Commun (Lond) 2023; 43:42-74. [PMID: 36316602 PMCID: PMC9859734 DOI: 10.1002/cac2.12377] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/15/2022] [Accepted: 10/13/2022] [Indexed: 01/22/2023] Open
Abstract
RAS genes are the most frequently mutated oncogenes and play critical roles in the development and progression of malignancies. The mutation, isoform (KRAS, HRAS, and NRAS), position, and type of substitution vary depending on the tissue types. Despite decades of developing RAS-targeted therapies, only small subsets of these inhibitors are clinically effective, such as the allele-specific inhibitors against KRASG12C . Targeting the remaining RAS mutants would require further experimental elucidation of RAS signal transduction, RAS-altered metabolism, and the associated immune microenvironment. This study reviews the mechanisms and efficacy of novel targeted therapies for different RAS mutants, including KRAS allele-specific inhibitors, combination therapies, immunotherapies, and metabolism-associated therapies.
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Affiliation(s)
- Hang Yang
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
| | - Xinyi Zhou
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
| | - Dongliang Fu
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
| | - Chenqin Le
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
| | - Jiafeng Wang
- Department of Pharmacology and Department of Gastroenterology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058P. R. China
| | - Quan Zhou
- Department of Cell BiologySchool of Basic Medical SciencesZhejiang UniversityHangzhouZhejiang310058P. R. China
| | - Xiangrui Liu
- Department of Pharmacology and Department of Gastroenterology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058P. R. China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058P. R. China
| | - Ying Yuan
- Department of Medical Oncologythe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310058P. R. China
| | - Kefeng Ding
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058P. R. China
| | - Qian Xiao
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
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Gelb BD, Yohe ME, Wolf C, Andelfinger G. New prospectives on treatment opportunities in RASopathies. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:541-560. [PMID: 36533679 PMCID: PMC10150944 DOI: 10.1002/ajmg.c.32024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]
Abstract
The RASopathies are a group of clinically defined developmental syndromes caused by germline variants of the RAS/mitogen-activated protein (MAPK) cascade. The prototypic RASopathy is Noonan syndrome, which has phenotypic overlap with related disorders such as cardiofaciocutaneous syndrome, Costello syndrome, Noonan syndrome with multiple lentigines, and others. In this state-of-the-art review, we summarize current knowledge on unmet therapeutic needs in these diseases and novel treatment approaches informed by insights from RAS/MAPK-associated cancer therapies, in particular through inhibition of MEK1/2 and mTOR in patients with severe disease manifestations. We explore the possibilities of integrating a larger arsenal of molecules currently under development into future care plans. Lastly, we describe both medical and ethical challenges and opportunities for future clinical trials in the field.
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Affiliation(s)
- Bruce D. Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marielle E. Yohe
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Cordula Wolf
- Department of Congenital Heart Defects and Pediatric Cardiology, German Heart Center Munich, School of Medicine & Health, Technical University of Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Gregor Andelfinger
- CHU Sainte Justine, Department of Pediatrics, Université de Montréal, Montréal, Quebec, Canada
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Liu G, Chen T, Zhang X, Ma X, Shi H. Small molecule inhibitors targeting the cancers. MedComm (Beijing) 2022; 3:e181. [PMID: 36254250 PMCID: PMC9560750 DOI: 10.1002/mco2.181] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Compared with traditional therapies, targeted therapy has merits in selectivity, efficacy, and tolerability. Small molecule inhibitors are one of the primary targeted therapies for cancer. Due to their advantages in a wide range of targets, convenient medication, and the ability to penetrate into the central nervous system, many efforts have been devoted to developing more small molecule inhibitors. To date, 88 small molecule inhibitors have been approved by the United States Food and Drug Administration to treat cancers. Despite remarkable progress, small molecule inhibitors in cancer treatment still face many obstacles, such as low response rate, short duration of response, toxicity, biomarkers, and resistance. To better promote the development of small molecule inhibitors targeting cancers, we comprehensively reviewed small molecule inhibitors involved in all the approved agents and pivotal drug candidates in clinical trials arranged by the signaling pathways and the classification of small molecule inhibitors. We discussed lessons learned from the development of these agents, the proper strategies to overcome resistance arising from different mechanisms, and combination therapies concerned with small molecule inhibitors. Through our review, we hoped to provide insights and perspectives for the research and development of small molecule inhibitors in cancer treatment.
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Affiliation(s)
- Gui‐Hong Liu
- Department of BiotherapyState Key Laboratory of BiotherapyCancer Center, West China HospitalSichuan UniversityChengduChina
| | - Tao Chen
- Department of CardiologyThe First Affiliated Hospital of China Medical UniversityShenyangLiaoningChina
| | - Xin Zhang
- Department of BiotherapyState Key Laboratory of BiotherapyCancer Center, West China HospitalSichuan UniversityChengduChina
| | - Xue‐Lei Ma
- Department of BiotherapyState Key Laboratory of BiotherapyCancer Center, West China HospitalSichuan UniversityChengduChina
| | - Hua‐Shan Shi
- Department of BiotherapyState Key Laboratory of BiotherapyCancer Center, West China HospitalSichuan UniversityChengduChina
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Caksa S, Baqai U, Aplin AE. The future of targeted kinase inhibitors in melanoma. Pharmacol Ther 2022; 239:108200. [PMID: 35513054 PMCID: PMC10187889 DOI: 10.1016/j.pharmthera.2022.108200] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022]
Abstract
Melanoma is a cancer of the pigment-producing cells of the body and its incidence is rising. Targeted inhibitors that act against kinases in the MAPK pathway are approved for BRAF-mutant metastatic cutaneous melanoma and increase patients' survival. Response to these therapies is limited by drug resistance and is less durable than with immune checkpoint inhibition. Conversely, rare melanoma subtypes have few therapeutic options for advanced disease and MAPK pathway targeting agents show minimal anti-tumor effects. Nevertheless, there is a future for targeted kinase inhibitors in melanoma: in new applications such as adjuvant or neoadjuvant therapy and in novel combinations with immunotherapies or other targeted therapies. Pre-clinical studies continue to identify tumor dependencies and their corresponding actionable drug targets, paving the way for rational targeted kinase inhibitor combinations as a personalized medicine approach for melanoma.
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Affiliation(s)
- Signe Caksa
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Usman Baqai
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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Poulikakos PI, Sullivan RJ, Yaeger R. Molecular Pathways and Mechanisms of BRAF in Cancer Therapy. Clin Cancer Res 2022; 28:4618-4628. [PMID: 35486097 PMCID: PMC9616966 DOI: 10.1158/1078-0432.ccr-21-2138] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/08/2022] [Accepted: 03/30/2022] [Indexed: 01/24/2023]
Abstract
With the identification of activating mutations in BRAF across a wide variety of malignancies, substantial effort was placed in designing safe and effective therapeutic strategies to target BRAF. These efforts have led to the development and regulatory approval of three BRAF inhibitors as well as five combinations of a BRAF inhibitor plus an additional agent(s) to manage cancer such as melanoma, non-small cell lung cancer, anaplastic thyroid cancer, and colorectal cancer. To date, each regimen is effective only in patients with tumors harboring BRAFV600 mutations and the duration of benefit is often short-lived. Further limitations preventing optimal management of BRAF-mutant malignancies are that treatments of non-V600 BRAF mutations have been less profound and combination therapy is likely necessary to overcome resistance mechanisms, but multi-drug regimens are often too toxic. With the emergence of a deeper understanding of how BRAF mutations signal through the RAS/MAPK pathway, newer RAF inhibitors are being developed that may be more effective and potentially safer and more rational combination therapies are being tested in the clinic. In this review, we identify the mechanics of RAF signaling through the RAS/MAPK pathway, present existing data on single-agent and combination RAF targeting efforts, describe emerging combinations, summarize the toxicity of the various agents in clinical testing, and speculate as to where the field may be headed.
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Affiliation(s)
- Poulikos I. Poulikakos
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ryan J. Sullivan
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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Schulz A, Raetz J, Karitzky PC, Dinter L, Tietze JK, Kolbe I, Käubler T, Renner B, Beissert S, Meier F, Westphal D. Head-to-Head Comparison of BRAF/MEK Inhibitor Combinations Proposes Superiority of Encorafenib Plus Trametinib in Melanoma. Cancers (Basel) 2022; 14:cancers14194930. [PMID: 36230853 PMCID: PMC9564158 DOI: 10.3390/cancers14194930] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary A decade ago, the diagnosis of metastatic melanoma was mostly a death sentence. This has changed since new therapies became widely available in the clinical setting. In addition to checkpoint inhibitors, targeted therapy with BRAF and MEK inhibitors is standard care for BRAF-mutated melanoma, which accounts for almost half of all melanoma cases. The second largest group of melanoma patients, whose tumors harbor a mutation in the NRAS gene, demonstrates only a limited response to targeted therapy with MEK inhibitors. The aim of this investigation was to directly compare all possible BRAF/MEK inhibitor combinations in addition to the currently applied regimens. The analyzed data suggested that the combination of the BRAF inhibitor encorafenib and the MEK inhibitor trametinib demonstrated the highest anti-tumor activity in both, BRAF- and NRAS-mutated melanoma. This combination is not presently used in patient treatment, and therefore, deserves an opportunity to become part of clinical trials. Abstract BRAFV600 mutations in melanoma are targeted with mutation-specific BRAF inhibitors in combination with MEK inhibitors, which have significantly increased overall survival, but eventually lead to resistance in most cases. Additionally, targeted therapy for patients with NRASmutant melanoma is difficult. Our own studies showed that BRAF inhibitors amplify the effects of MEK inhibitors in NRASmutant melanoma. This study aimed at identifying a BRAF and MEK inhibitor combination with superior anti-tumor activity to the three currently approved combinations. We, thus, assessed anti-proliferative and pro-apoptotic activities of all nine as well as resistance-delaying capabilities of the three approved inhibitor combinations in a head-to-head comparison in vitro. The unconventional combination encorafenib/trametinib displayed the highest activity to suppress proliferation and induce apoptosis, acting in an additive manner in BRAFmutant and in a synergistic manner in NRASmutant melanoma cells. Correlating with current clinical studies of approved inhibitor combinations, encorafenib/binimetinib prolonged the time to resistance most efficiently in BRAFmutant cells. Conversely, NRASmutant cells needed the longest time to establish resistance when treated with dabrafenib/trametinib. Together, our data indicate that the most effective combination might not be currently used in clinical settings and could lead to improved overall responses.
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Affiliation(s)
- Alexander Schulz
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, 01307 Dresden, Germany; Helmholtz-Zentrum Dresden–Rossendorf (HZDR), 01328 Dresden, Germany
| | - Jennifer Raetz
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Paula C. Karitzky
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Lisa Dinter
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, 01307 Dresden, Germany; Helmholtz-Zentrum Dresden–Rossendorf (HZDR), 01328 Dresden, Germany
| | - Julia K. Tietze
- Clinic and Polyclinic for Dermatology and Venereology, University Medical Center Rostock, 18055 Rostock, Germany
| | - Isabell Kolbe
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Theresa Käubler
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Bertold Renner
- Institute of Clinical Pharmacology, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
| | - Stefan Beissert
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, 01307 Dresden, Germany; Helmholtz-Zentrum Dresden–Rossendorf (HZDR), 01328 Dresden, Germany
| | - Friedegund Meier
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, 01307 Dresden, Germany; Helmholtz-Zentrum Dresden–Rossendorf (HZDR), 01328 Dresden, Germany
- Skin Cancer Center at the University Cancer Center (UCC) Dresden, University Hospital Carl Gustav Carus at TU Dresden, 01307 Dresden, Germany
| | - Dana Westphal
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, 01307 Dresden, Germany; Helmholtz-Zentrum Dresden–Rossendorf (HZDR), 01328 Dresden, Germany
- Correspondence: ; Tel.: +49-351-458-82274
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Liau NPD, Johnson MC, Izadi S, Gerosa L, Hammel M, Bruning JM, Wendorff TJ, Phung W, Hymowitz SG, Sudhamsu J. Structural basis for SHOC2 modulation of RAS signalling. Nature 2022; 609:400-407. [PMID: 35768504 PMCID: PMC9452301 DOI: 10.1038/s41586-022-04838-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 05/05/2022] [Indexed: 12/12/2022]
Abstract
The RAS-RAF pathway is one of the most commonly dysregulated in human cancers1-3. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation4 of the kinase RAF remains limited. Recent structures of inactive RAF monomer5 and active RAF dimer5-8 bound to 14-3-39,10 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF11 to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS11-13, but the structure of SHOC2 and the architecture of the presumptive SHOC2-PP1C-RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2-PP1C-MRAS complex to an overall resolution of 3 Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.
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Affiliation(s)
- Nicholas P D Liau
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Matthew C Johnson
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Saeed Izadi
- Pharmaceutical Development, Genentech, South San Francisco, CA, USA
| | - Luca Gerosa
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Michal Hammel
- Physical Bioscience Division, Lawrence Berkeley National Labs, Berkeley, CA, USA
| | - John M Bruning
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Timothy J Wendorff
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Wilson Phung
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Sarah G Hymowitz
- Department of Structural Biology, Genentech, South San Francisco, CA, USA.
- The Column Group, San Francisco, CA, USA.
| | - Jawahar Sudhamsu
- Department of Structural Biology, Genentech, South San Francisco, CA, USA.
- Department of Discovery Oncology, Genentech, South San Francisco, CA, USA.
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Sun N, Tian Y, Chen Y, Guo W, Li C. Metabolic rewiring directs melanoma immunology. Front Immunol 2022; 13:909580. [PMID: 36003368 PMCID: PMC9393691 DOI: 10.3389/fimmu.2022.909580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/13/2022] [Indexed: 11/22/2022] Open
Abstract
Melanoma results from the malignant transformation of melanocytes and accounts for the most lethal type of skin cancers. In the pathogenesis of melanoma, disordered metabolism is a hallmark characteristic with multiple metabolic paradigms involved in, e.g., glycolysis, lipid metabolism, amino acid metabolism, oxidative phosphorylation, and autophagy. Under the driving forces of oncogenic mutations, melanoma metabolism is rewired to provide not only building bricks for macromolecule synthesis and sufficient energy for rapid proliferation and metastasis but also various metabolic intermediates for signal pathway transduction. Of note, metabolic alterations in tumor orchestrate tumor immunology by affecting the functions of surrounding immune cells, thereby interfering with their antitumor capacity, in addition to the direct influence on tumor cell intrinsic biological activities. In this review, we first introduced the epidemiology, clinical characteristics, and treatment proceedings of melanoma. Then, the components of the tumor microenvironment, especially different populations of immune cells and their roles in antitumor immunity, were reviewed. Sequentially, how metabolic rewiring contributes to tumor cell malignant behaviors in melanoma pathogenesis was discussed. Following this, the proceedings of metabolism- and metabolic intermediate-regulated tumor immunology were comprehensively dissertated. Finally, we summarized currently available drugs that can be employed to target metabolism to intervene tumor immunology and modulate immunotherapy.
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Affiliation(s)
- Ningyue Sun
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- School of Basic Medical Sciences, Fourth Military Medical University, Xi’an, China
| | - Yangzi Tian
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yuhan Chen
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- School of Basic Medical Sciences, Fourth Military Medical University, Xi’an, China
| | - Weinan Guo
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- *Correspondence: Chunying Li, ; Weinan Guo,
| | - Chunying Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- *Correspondence: Chunying Li, ; Weinan Guo,
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Porcelli L, Di Fonte R, Pierri CL, Fucci L, Saponaro C, Armenio A, Serratì S, Strippoli S, Fasano R, Volpicella M, Daprile R, Tommasi S, Ressa CM, Guida M, Azzariti A. BRAF V600E;K601Q metastatic melanoma patient-derived organoids and docking analysis to predict the response to targeted therapy. Pharmacol Res 2022; 182:106323. [PMID: 35752358 DOI: 10.1016/j.phrs.2022.106323] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/31/2022] [Accepted: 06/19/2022] [Indexed: 10/17/2022]
Abstract
The V600E mutation in BRAF is associated with increased phosphorylation of Erk1/2 and high sensitivity to BRAFi/MEKi combination in metastatic melanoma. In very few patients, a tandem mutation in BRAF, V600 and K601, causes a different response to BRAFi/MEKi combination. BRAFV600E;K601Q patient-derived organoids (PDOs) were generated to investigate targeted therapy efficacy and docking analysis was used to assess BRAFV600E;K601Q interactions with Vemurafenib. PDOs were not sensitive to Vemurafenib and Cobimetinib given alone and sensitive to their combination, although not as responsive as BRAFV600E PDOs. The docking analysis justified such a result showing that the tandem mutation in BRAF reduced the affinity for Vemurafenib. Tumor analysis showed that BRAFV600E;K601Q displayed both increased phosphorylation of Erk1/2 at cytoplasmic level and activation of Notch resistance signaling. This prompted us to inhibit Notch signaling with Nirogacestat, achieving a greater antitumor response and providing PDOs-based evaluation of treatment efficacy in such rare metastatic melanoma.
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Affiliation(s)
- Letizia Porcelli
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Roberta Di Fonte
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Ciro L Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Livia Fucci
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Concetta Saponaro
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Andrea Armenio
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Simona Serratì
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Sabino Strippoli
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Rossella Fasano
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Rossana Daprile
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Stefania Tommasi
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Cosmo M Ressa
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Michele Guida
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Amalia Azzariti
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy.
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Hu D, Guo E, Yang B, Qin X, Fu Y, Fan J, Zhuang X, Yao Q, Lu F, Li W, Xiao R, Wu X, Yang X, Wang Z, Liu C, You L, Zang R, Zhou Q, Zhao W, Chen G, Sun C. Mutation profiles in circulating cell‐free
DNA
predict acquired resistance to Olaparib in high‐grade serous ovarian carcinoma. Cancer Sci 2022; 113:2849-2861. [PMID: 35661486 PMCID: PMC9357630 DOI: 10.1111/cas.15456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/23/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Dianxing Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Ensong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Bin Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xu Qin
- Department of Stomatology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Junpeng Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xucui Zhuang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Qianqian Yao
- Department of Medical Science Shanghai AccuraGen Biotechnology Co., Ltd Shanghai China
| | - Funian Lu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wenting Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xue Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xiaohang Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Zizhuo Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Chen Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Lixin You
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Rongyu Zang
- Department of Gynecologic Oncology, Zhongshan Hospital Fudan University Shanghai China
| | - Qi Zhou
- Department of Gynecology Oncology Chongqing University Cancer Hospital Chongqing China
| | - Weidong Zhao
- Department of Gynecologic Oncology Anhui Provincial Cancer Hospital Hefei China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
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50
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dos Santos IV, Borges RS, Silva GM, de Lima LR, Bastos RS, Ramos RS, Silva LB, da Silva CHTP, dos Santos CBR. Hierarchical Virtual Screening Based on Rocaglamide Derivatives to Discover New Potential Anti-Skin Cancer Agents. Front Mol Biosci 2022; 9:836572. [PMID: 35720115 PMCID: PMC9201829 DOI: 10.3389/fmolb.2022.836572] [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: 12/15/2021] [Accepted: 01/26/2022] [Indexed: 12/04/2022] Open
Abstract
Skin Cancer (SC) is among the most common type of cancers worldwide. The search for SC therapeutics using molecular modeling strategies as well as considering natural plant-derived products seems to be a promising strategy. The phytochemical Rocaglamide A (Roc-A) and its derivatives rise as an interesting set of reference compounds due to their in vitro cytotoxic activity with SC cell lines. In view of this, we performed a hierarchical virtual screening study considering Roc-A and its derivatives, with the aim to find new chemical entities with potential activity against SC. For this, we selected 15 molecules (Roc-A and 14 derivatives) and initially used them in docking studies to predict their interactions with Checkpoint kinase 1 (Chk1) as a target for SC. This allowed us to compile and use them as a training set to build robust pharmacophore models, validated by Pearson’s correlation (p) values and hierarchical cluster analysis (HCA), subsequentially submitted to prospective virtual screening using the Molport® database. Outputted compounds were then selected considering their similarities to Roc-A, followed by analyses of predicted toxicity and pharmacokinetic properties as well as of consensus molecular docking using three software. 10 promising compounds were selected and analyzed in terms of their properties and structural features and, also, considering their previous reports in literature. In this way, the 10 promising virtual hits found in this work may represent potential anti-SC agents and further investigations concerning their biological tests shall be conducted.
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Affiliation(s)
- Igor V.F. dos Santos
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil
| | - Rosivaldo S. Borges
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
| | - Guilherme M. Silva
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto - Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto - Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Lúcio R. de Lima
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
| | - Ruan S. Bastos
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
| | - Ryan S. Ramos
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil
| | - Luciane B. Silva
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
| | - Carlos H. T. P. da Silva
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto - Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto - Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Cleydson B. R. dos Santos
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
- *Correspondence: Cleydson B. R. dos Santos,
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