1
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Lee S, Kim HJ, Choi JH, Jang HJ, Cho HB, Kim HR, Park JI, Park KS, Park KH. Light emitting diode (LED) irradiation of liposomes enhances drug encapsulation and delivery for improved cancer eradication. J Control Release 2024; 368:756-767. [PMID: 38499090 DOI: 10.1016/j.jconrel.2024.03.027] [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: 12/19/2023] [Revised: 02/26/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Liposomes are widely used as drug delivery nanoplatforms because of their versatility and biocompatibility; however, their ability to load certain drugs may be suboptimal. In this study, we generated liposomes using a combination of DSPE and DSPE-PEG-2 k lipids and loaded them with doxorubicin (DOX) and paclitaxel (PTX), to investigate the effects of light emitting diode (LED) irradiation on liposome structure and drug loading efficiency. Scanning and transmission electron microscopy revealed that the surface of liposomes irradiated with blue or near-infrared LEDs (LsLipo) was rougher and more irregular than that of non-LED-irradiated liposomes (NsLipo). Nuclear magnetic resonance analysis showed that the hydrogen peak originating from the lipid head groups was lower in LsLipo than in NsLipo preparations, indicating that LED irradiation changed the chemical and physical properties of the liposome. Structural changes, such as reduced rigidity, induced by LED irradiation, increased the loading efficiency of DOX and PTX. In vitro and in vivo experiments showed that LsLipo were more effective at inhibiting the growth of cancer cells than NsLipo. Our findings suggest that LED irradiation enhances the drug delivery efficacy of liposomes and offer new possibilities for improving drug delivery systems.
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Affiliation(s)
- Sujeong Lee
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si 13488, Republic of Korea
| | - Hye Jin Kim
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si 13488, Republic of Korea
| | - Jin-Ho Choi
- Department of Biomedical Science, CHA University, Seongnam, Republic of Korea
| | - Hye Jung Jang
- Department of Biomedical Science, CHA University, Seongnam, Republic of Korea
| | - Hui Bang Cho
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si 13488, Republic of Korea
| | - Hye-Ryoung Kim
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si 13488, Republic of Korea
| | - Ji-In Park
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si 13488, Republic of Korea
| | - Kyung-Soon Park
- Department of Biomedical Science, CHA University, Seongnam, Republic of Korea.
| | - Keun-Hong Park
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si 13488, Republic of Korea.
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2
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Nair NU, Greninger P, Zhang X, Friedman AA, Amzallag A, Cortez E, Sahu AD, Lee JS, Dastur A, Egan RK, Murchie E, Ceribelli M, Crowther GS, Beck E, McClanaghan J, Klump-Thomas C, Boisvert JL, Damon LJ, Wilson KM, Ho J, Tam A, McKnight C, Michael S, Itkin Z, Garnett MJ, Engelman JA, Haber DA, Thomas CJ, Ruppin E, Benes CH. A landscape of response to drug combinations in non-small cell lung cancer. Nat Commun 2023; 14:3830. [PMID: 37380628 PMCID: PMC10307832 DOI: 10.1038/s41467-023-39528-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023] Open
Abstract
Combination of anti-cancer drugs is broadly seen as way to overcome the often-limited efficacy of single agents. The design and testing of combinations are however very challenging. Here we present a uniquely large dataset screening over 5000 targeted agent combinations across 81 non-small cell lung cancer cell lines. Our analysis reveals a profound heterogeneity of response across the tumor models. Notably, combinations very rarely result in a strong gain in efficacy over the range of response observable with single agents. Importantly, gain of activity over single agents is more often seen when co-targeting functionally proximal genes, offering a strategy for designing more efficient combinations. Because combinatorial effect is strongly context specific, tumor specificity should be achievable. The resource provided, together with an additional validation screen sheds light on major challenges and opportunities in building efficacious combinations against cancer and provides an opportunity for training computational models for synergy prediction.
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Affiliation(s)
- Nishanth Ulhas Nair
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xiaohu Zhang
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Adam A Friedman
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eliane Cortez
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Avinash Das Sahu
- University of New Mexico, Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Joo Sang Lee
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Anahita Dastur
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Regina K Egan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ellen Murchie
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Erin Beck
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | | | | | | | - Leah J Damon
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jeffrey Ho
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Angela Tam
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Sam Michael
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Zina Itkin
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Mathew J Garnett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | | | - Daniel A Haber
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, Rockville, MD, 20850, USA
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Cyril H Benes
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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3
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Tiedt R, King FJ, Stamm C, Niederst MJ, Delach S, Zumstein-Mecker S, Meltzer J, Mulford IJ, Labrot E, Engstler BS, Baltschukat S, Kerr G, Golji J, Wyss D, Schnell C, Ainscow E, Engelman JA, Sellers WR, Barretina J, Caponigro G, Porta DG. Integrated CRISPR screening and drug profiling identifies combination opportunities for EGFR, ALK, and BRAF/MEK inhibitors. Cell Rep 2023; 42:112297. [PMID: 36961816 DOI: 10.1016/j.celrep.2023.112297] [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: 05/06/2021] [Revised: 01/11/2022] [Accepted: 03/03/2023] [Indexed: 03/25/2023] Open
Abstract
Anti-tumor efficacy of targeted therapies is variable across patients and cancer types. Even in patients with initial deep response, tumors are typically not eradicated and eventually relapse. To address these challenges, we present a systematic screen for targets that limit the anti-tumor efficacy of EGFR and ALK inhibitors in non-small cell lung cancer and BRAF/MEK inhibitors in colorectal cancer. Our approach includes genome-wide CRISPR screens with or without drugs targeting the oncogenic driver ("anchor therapy"), and large-scale pairwise combination screens of anchor therapies with 351 other drugs. Interestingly, targeting of a small number of genes, including MCL1, BCL2L1, and YAP1, sensitizes multiple cell lines to the respective anchor therapy. Data from drug combination screens with EGF816 and ceritinib indicate that dasatinib and agents disrupting microtubules act synergistically across many cell lines. Finally, we show that a higher-order-combination screen with 26 selected drugs in two resistant EGFR-mutant lung cancer cell lines identified active triplet combinations.
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Affiliation(s)
- Ralph Tiedt
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Frederick J King
- Novartis Institutes for BioMedical Research, Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - Christelle Stamm
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Matthew J Niederst
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA.
| | - Scott Delach
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | | | - Jodi Meltzer
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Iain J Mulford
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | | | - Sabrina Baltschukat
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Grainne Kerr
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Javad Golji
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Daniel Wyss
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Christian Schnell
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Edward Ainscow
- Novartis Institutes for BioMedical Research, Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - Jeffrey A Engelman
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - William R Sellers
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Giordano Caponigro
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Diana Graus Porta
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
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4
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Ramzy GM, Norkin M, Koessler T, Voirol L, Tihy M, Hany D, McKee T, Ris F, Buchs N, Docquier M, Toso C, Rubbia-Brandt L, Bakalli G, Guerrier S, Huelsken J, Nowak-Sliwinska P. Platform combining statistical modeling and patient-derived organoids to facilitate personalized treatment of colorectal carcinoma. J Exp Clin Cancer Res 2023; 42:79. [PMID: 37013646 PMCID: PMC10069117 DOI: 10.1186/s13046-023-02650-z] [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: 01/17/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND We propose a new approach for designing personalized treatment for colorectal cancer (CRC) patients, by combining ex vivo organoid efficacy testing with mathematical modeling of the results. METHODS The validated phenotypic approach called Therapeutically Guided Multidrug Optimization (TGMO) was used to identify four low-dose synergistic optimized drug combinations (ODC) in 3D human CRC models of cells that are either sensitive or resistant to first-line CRC chemotherapy (FOLFOXIRI). Our findings were obtained using second order linear regression and adaptive lasso. RESULTS The activity of all ODCs was validated on patient-derived organoids (PDO) from cases with either primary or metastatic CRC. The CRC material was molecularly characterized using whole-exome sequencing and RNAseq. In PDO from patients with liver metastases (stage IV) identified as CMS4/CRIS-A, our ODCs consisting of regorafenib [1 mM], vemurafenib [11 mM], palbociclib [1 mM] and lapatinib [0.5 mM] inhibited cell viability up to 88%, which significantly outperforms FOLFOXIRI administered at clinical doses. Furthermore, we identified patient-specific TGMO-based ODCs that outperform the efficacy of the current chemotherapy standard of care, FOLFOXIRI. CONCLUSIONS Our approach allows the optimization of patient-tailored synergistic multi-drug combinations within a clinically relevant timeframe.
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Affiliation(s)
- George M Ramzy
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CMU, 1211, Geneva 4, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211, Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211, Geneva, Switzerland
| | - Maxim Norkin
- Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne-(EPFL-SV), 1015, Lausanne, Switzerland
| | - Thibaud Koessler
- Department of Oncology, Geneva University Hospitals, 1205, Geneva, Switzerland
| | - Lionel Voirol
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, 1205, Geneva, Switzerland
| | - Mathieu Tihy
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), 1205, Geneva, Switzerland
| | - Dina Hany
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CMU, 1211, Geneva 4, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211, Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211, Geneva, Switzerland
| | - Thomas McKee
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), 1205, Geneva, Switzerland
| | - Frédéric Ris
- Translational Department of Digestive and Transplant Surgery, Geneva University Hospitals and Faculty of Medicine, 1205, Geneva, Switzerland
| | - Nicolas Buchs
- Translational Department of Digestive and Transplant Surgery, Geneva University Hospitals and Faculty of Medicine, 1205, Geneva, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, 1211, Geneva, Switzerland
- Department of Genetics & Evolution, University of Geneva, 1211, Geneva, Switzerland
| | - Christian Toso
- Department of Visceral Surgery, Geneva University Hospital, 1211, Geneva, Switzerland
| | - Laura Rubbia-Brandt
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), 1205, Geneva, Switzerland
| | - Gaetan Bakalli
- EMLYON Business School, Artificial Intelligence in Management Institute, Ecully, France
| | - Stéphane Guerrier
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211, Geneva, Switzerland
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, 1205, Geneva, Switzerland
| | - Joerg Huelsken
- Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne-(EPFL-SV), 1015, Lausanne, Switzerland
| | - Patrycja Nowak-Sliwinska
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CMU, 1211, Geneva 4, Switzerland.
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211, Geneva, Switzerland.
- Translational Research Center in Oncohaematology, 1211, Geneva, Switzerland.
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5
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Zhu M, Tse MW, Weller J, Chen J, Blainey PC. The future of antibiotics begins with discovering new combinations. Ann N Y Acad Sci 2021; 1496:82-96. [PMID: 34212403 PMCID: PMC8290516 DOI: 10.1111/nyas.14649] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/20/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
Antibiotic resistance is a worldwide and growing clinical problem. With limited drug development in the antibacterial space, combination therapy has emerged as a promising strategy to combat multidrug-resistant bacteria. Antibacterial combinations can improve antibiotic efficacy and suppress antibacterial resistance through independent, synergistic, or even antagonistic activities. Combination therapies are famously used to treat viral and mycobacterial infections and cancer. However, antibacterial combinations are only now emerging as a common treatment strategy for other bacterial infections owing to challenges in their discovery, development, regulatory approval, and commercial/clinical deployment. Here, we focus on discovery-where the sheer scale of combinatorial chemical spaces represents a significant challenge-and discuss how combination therapy can impact the treatment of bacterial infections. Despite these challenges, recent advancements, including new in silico methods, theoretical frameworks, and microfluidic platforms, are poised to identify the new and efficacious antibacterial combinations needed to revitalize the antibacterial drug pipeline.
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Affiliation(s)
- Meilin Zhu
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
| | - Megan W. Tse
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
| | - Juliane Weller
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
| | - Julie Chen
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
- Microbiology Graduate ProgramMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Paul C. Blainey
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of TechnologyCambridgeMassachusetts
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6
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Rosati G, Aprile G, Basile D, Avallone A. Perspectives in the Treatment of RAS or BRAF Mutated Metastatic Colorectal Cancer Patients. Front Oncol 2021; 11:602596. [PMID: 33738249 PMCID: PMC7960908 DOI: 10.3389/fonc.2021.602596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/18/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Gerardo Rosati
- Medical Oncology Unit, "S. Carlo" Hospital, Potenza, Italy
| | - Giuseppe Aprile
- Medical Oncology Unit, "San Bortolo" Hospital, Vicenza, Italy
| | - Debora Basile
- Department of Medical Oncology (DAME), University of Udine, Udine, Italy
| | - Antonio Avallone
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
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7
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Zoetemelk M, Ramzy GM, Rausch M, Koessler T, van Beijnum JR, Weiss A, Mieville V, Piersma SR, de Haas RR, Delucinge-Vivier C, Andres A, Toso C, Henneman AA, Ragusa S, Petrova TV, Docquier M, McKee TA, Jimenez CR, Daali Y, Griffioen AW, Rubbia-Brandt L, Dietrich PY, Nowak-Sliwinska P. Optimized low-dose combinatorial drug treatment boosts selectivity and efficacy of colorectal carcinoma treatment. Mol Oncol 2020; 14:2894-2919. [PMID: 33021054 PMCID: PMC7607171 DOI: 10.1002/1878-0261.12797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/24/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022] Open
Abstract
The current standard of care for colorectal cancer (CRC) is a combination of chemotherapeutics, often supplemented with targeted biological drugs. An urgent need exists for improved drug efficacy and minimized side effects, especially at late‐stage disease. We employed the phenotypically driven therapeutically guided multidrug optimization (TGMO) technology to identify optimized drug combinations (ODCs) in CRC. We identified low‐dose synergistic and selective ODCs for a panel of six human CRC cell lines also active in heterotypic 3D co‐culture models. Transcriptome sequencing and phosphoproteome analyses showed that the mechanisms of action of these ODCs converged toward MAP kinase signaling and cell cycle inhibition. Two cell‐specific ODCs were translated to in vivo mouse models. The ODCs reduced tumor growth by ~80%, outperforming standard chemotherapy (FOLFOX). No toxicity was observed for the ODCs, while significant side effects were induced in the group treated with FOLFOX therapy. Identified ODCs demonstrated significantly enhanced bioavailability of the individual components. Finally, ODCs were also active in primary cells from CRC patient tumor tissues. Taken together, we show that the TGMO technology efficiently identifies selective and potent low‐dose drug combinations, optimized regardless of tumor mutation status, outperforming conventional chemotherapy.
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Affiliation(s)
- Marloes Zoetemelk
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.,Translational Research Center in Oncohaematology, Geneva, Switzerland
| | - George M Ramzy
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.,Translational Research Center in Oncohaematology, Geneva, Switzerland
| | - Magdalena Rausch
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.,Translational Research Center in Oncohaematology, Geneva, Switzerland
| | - Thibaud Koessler
- Department of Oncology, Geneva University Hospitals and Faculty of Medicine, Switzerland
| | - Judy R van Beijnum
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC-location VUmc, VU University Amsterdam, The Netherlands
| | - Andrea Weiss
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland
| | - Valentin Mieville
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland
| | - Sander R Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands.,OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | - Richard R de Haas
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands.,OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | | | - Axel Andres
- Translational Department of Digestive and Transplant Surgery, Geneva University Hospitals and Faculty of Medicine, Switzerland.,Hepato-Pancreato-Biliary Centre, Geneva University Hospitals and Faculty of Medicine, Switzerland
| | - Christian Toso
- Translational Department of Digestive and Transplant Surgery, Geneva University Hospitals and Faculty of Medicine, Switzerland.,Hepato-Pancreato-Biliary Centre, Geneva University Hospitals and Faculty of Medicine, Switzerland
| | - Alexander A Henneman
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands.,OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | - Simone Ragusa
- Department of Oncology, University of Lausanne, Switzerland.,Ludwig Institute for Cancer Research Lausanne, Switzerland
| | - Tatiana V Petrova
- Department of Oncology, University of Lausanne, Switzerland.,Ludwig Institute for Cancer Research Lausanne, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, Switzerland.,Department of Genetics & Evolution, University of Geneva, Switzerland
| | - Thomas A McKee
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), Switzerland
| | - Connie R Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands.,OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | - Youssef Daali
- Division of Clinical Pharmacology and Toxicology, Department of Anaesthesiology, Intensive Care and Emergency Medicine, Geneva University Hospitals, Pharmacology, Switzerland
| | - Arjan W Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC-location VUmc, VU University Amsterdam, The Netherlands
| | - Laura Rubbia-Brandt
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), Switzerland
| | - Pierre-Yves Dietrich
- Translational Research Center in Oncohaematology, Geneva, Switzerland.,Department of Oncology, Geneva University Hospitals and Faculty of Medicine, Switzerland
| | - Patrycja Nowak-Sliwinska
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.,Translational Research Center in Oncohaematology, Geneva, Switzerland
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8
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Folkesson E, Niederdorfer B, Nakstad VT, Thommesen L, Klinkenberg G, Lægreid A, Flobak Å. High-throughput screening reveals higher synergistic effect of MEK inhibitor combinations in colon cancer spheroids. Sci Rep 2020; 10:11574. [PMID: 32665693 PMCID: PMC7360566 DOI: 10.1038/s41598-020-68441-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/19/2020] [Indexed: 11/27/2022] Open
Abstract
Drug combinations have been proposed to combat drug resistance, but putative treatments are challenged by low bench-to-bed translational efficiency. To explore the effect of cell culture format and readout methods on identification of synergistic drug combinations in vitro, we studied response to 21 clinically relevant drug combinations in standard planar (2D) layouts and physiologically more relevant spheroid (3D) cultures of HCT-116, HT-29 and SW-620 cells. By assessing changes in viability, confluency and spheroid size, we were able to identify readout- and culture format-independent synergies, as well as synergies specific to either culture format or readout method. In particular, we found that spheroids, compared to 2D cultures, were generally both more sensitive and showed greater synergistic response to combinations involving a MEK inhibitor. These results further shed light on the importance of including more complex culture models in order to increase the efficiency of drug discovery pipelines.
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Affiliation(s)
- Evelina Folkesson
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Barbara Niederdorfer
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Vu To Nakstad
- Department of Biotechnology, SINTEF Materials and Chemistry, Trondheim, Norway
| | - Liv Thommesen
- Department of Biomedical Laboratory Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Geir Klinkenberg
- Department of Biotechnology, SINTEF Materials and Chemistry, Trondheim, Norway
| | - Astrid Lægreid
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Åsmund Flobak
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
- The Cancer Clinic, St Olav's University Hospital, Trondheim, Norway.
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9
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Georgiou A, Stewart A, Cunningham D, Banerji U, Whittaker SR. Inactivation of NF1 Promotes Resistance to EGFR Inhibition in KRAS/NRAS/BRAFV600 -Wild-Type Colorectal Cancer. Mol Cancer Res 2020; 18:835-846. [PMID: 32098826 PMCID: PMC7611272 DOI: 10.1158/1541-7786.mcr-19-1201] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/21/2020] [Accepted: 02/20/2020] [Indexed: 12/26/2022]
Abstract
Through the use of an unbiased, genome-scale CRISPR modifier screen, we identified NF1 suppression as a mechanism of resistance to EGFR inhibition in NRAS/KRAS/BRAFV600 -wild-type colorectal cancer cells. Reduced NF1 expression permitted sustained signaling through the MAPK pathway to promote cell proliferation in the presence of EGFR inhibition. Targeting of MEK in combination with EGFR inhibition leads to synergistic antiproliferative activity. Human KRAS/NRAS/BRAFV600 -wild-type colorectal cancer cell lines with NF1 mutations displayed reduced NF1 mRNA or protein expression and were resistant to EGFR blockade by gefitinib or cetuximab. Cooccurring loss-of-function mutations in PTEN were associated with resistance to dual EGFR/MEK inhibition but cotreatment with a PI3K inhibitor further suppressed proliferation. Loss of NF1 may be a useful biomarker to identify patients that are less likely to benefit from single-agent anti-EGFR therapy in colorectal cancer and may direct potential combination strategies. IMPLICATIONS: This study suggests that further clinical validation of NF1 status as predictor of response to anti-EGFR targeting antibodies in patients with colorectal cancer with KRAS/NRAS/BRAFV600 -wild-type tumors is warranted.
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Affiliation(s)
- Alexandros Georgiou
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Adam Stewart
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - David Cunningham
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Udai Banerji
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom.
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom.
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10
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Identification of low-dose multidrug combinations for sunitinib-naive and pre-treated renal cell carcinoma. Br J Cancer 2020; 123:556-567. [PMID: 32439932 PMCID: PMC7435198 DOI: 10.1038/s41416-020-0890-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 04/04/2020] [Accepted: 04/23/2020] [Indexed: 12/11/2022] Open
Abstract
Background Combinations of drugs can improve the efficacy of cancer treatment, enable the reduction of side effects and the occurrence of acquired drug resistance. Methods We approached this challenge mathematically by using the validated technology called the Therapeutically Guided Multidrug Optimization (TGMO) method. In a set of genetically distinct human renal cell carcinoma (RCC) cell lines, either treated chronically with sunitinib (−ST) or sunitinib-naive, we identified cell line-specific low-dose-optimised drug combinations (ODC). Results Six cell-type-specific low-dose drug combinations for three sunitinib-naive as well as three sunitinib pre-treated cells were established. These ODCs effectively inhibited the RCC cell metabolic activity while being ineffective in non-cancerous cells. Based on a single screening test and three searches, starting with ten drugs, we identified highly efficacious drug mixtures containing four drugs. All ODCs contained AZD4547 (FGFR signalling pathway inhibitor) and pictilisib (pan-phosphatidylinositol 3-kinase inhibitor), but varied in the third and fourth drug. ODC treatment significantly decreased cell metabolic activity (up to 70%) and induced apoptosis, independent of the pretreatment with sunitinib. The ODCs outperformed sunitinib, the standard care for RCC. Moreover, short-term starvation potentiated the ODC activity. The translation of the 2D-based results to 3D heterotypic co-culture models revealed significant inhibition of the spheroid growth (up to 95%). Conclusion We demonstrate a promising low-dose drug combination development to obtain drug combinations effective in naive as well as resistant tumours. Nevertheless, we emphasise the need for further mechanistic investigation and preclinical development.
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11
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Meyer CT, Wooten DJ, Lopez CF, Quaranta V. Charting the Fragmented Landscape of Drug Synergy. Trends Pharmacol Sci 2020; 41:266-280. [PMID: 32113653 PMCID: PMC7986484 DOI: 10.1016/j.tips.2020.01.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/16/2020] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
Even as the clinical impact of drug combinations continues to accelerate, no consensus on how to quantify drug synergy has emerged. Rather, surveying the landscape of drug synergy reveals the persistence of historical fissures regarding the appropriate domains of conflicting synergy models - fissures impacting all aspects of combination therapy discovery and deployment. Herein we chronicle the impact of these divisions on: (i) the design, interpretation, and reproducibility of high-throughput combination screens; (ii) the performance of algorithms to predict synergistic mixtures; and (iii) the search for higher-order synergistic interactions. Further progress in each of these subfields hinges on reaching a consensus regarding the long-standing rifts in the field.
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Affiliation(s)
- Christian T Meyer
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA
| | - David J Wooten
- Department of Physics, Pennsylvania State University, University Park, PA, USA
| | - Carlos F Lopez
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Vito Quaranta
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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12
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Rusiecki R, Witkowski J, Jaszczewska-Adamczak J. MDM2-p53 Interaction Inhibitors: The Current State-of-Art and Updated Patent Review (2010-Present). Recent Pat Anticancer Drug Discov 2020; 14:324-369. [DOI: 10.2174/1574892814666191022163540] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/10/2023]
Abstract
Background:
Mouse Double Minute 2 protein (MDM2) is a cellular regulator of p53 tumor
suppressor (p53). Inhibition of the interaction between MDM2 and p53 proteins is a promising anticancer
therapy.
Objective:
This updated patent review is an attempt to compile the research and achievements of the
various researchers working on small molecule MDM2 inhibitors from 2010 to date. We provide an
outlook into the future for therapy based on MDM2 inhibition by presenting an overview of the most
relevant patents which have recently appeared in the literature.
Methods:
Literature and recent patents focusing on the anticancer potential of MDM2-p53 interaction
inhibitors and its applications have been analyzed. We put the main emphasis on the most perspective
compounds which are or were examined in clinical trials.
Results:
Literature data indicated that MDM2 inhibitors are therapeutically effective in specific types
of cancer or non-cancer diseases. A great number of patents and research work around new MDM2-
p53 interaction inhibitors, possible combinations, new indications, clinical regimens in previous years
prove that this targeted therapy is in the scope of interest for many business and academic research
groups.
Conclusion:
Novel MDM2 inhibitors thanks to higher potency and better ADME properties have
shown effectiveness in preclinical and clinical development however the final improvement of therapeutic
potential for MDM2 inhibitors might depend on the useful combination therapy and exploring
new cancer and non-cancer indications.
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Affiliation(s)
- Rafał Rusiecki
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
| | - Jakub Witkowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
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13
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Yang W, Li Y, Ai Y, Obianom ON, Guo D, Yang H, Sakamuru S, Xia M, Shu Y, Xue F. Pyrazole-4-Carboxamide (YW2065): A Therapeutic Candidate for Colorectal Cancer via Dual Activities of Wnt/β-Catenin Signaling Inhibition and AMP-Activated Protein Kinase (AMPK) Activation. J Med Chem 2019; 62:11151-11164. [PMID: 31769984 DOI: 10.1021/acs.jmedchem.9b01252] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Dysregulation of the Wnt/β-catenin signaling pathway has been widely recognized as a pathogenic mechanism for colorectal cancer (CRC). Although numerous Wnt inhibitors have been developed, they commonly suffer from toxicity and unintended effects. Moreover, concerns have been raised in targeting this pathway because of its critical roles in maintaining stem cells and regenerating tissues and organs. On the basis of the anthelmintic drug pyrvinium and previous lead FX1128, we have developed a compound YW2065 (1c) which demonstrated excellent anti-CRC effects in vitro and in vivo. YW2065 achieves its inhibitory activity for Wnt signaling by stabilizing Axin-1, a scaffolding protein that regulates proteasome degradation of β-catenin. Simultaneously, YW2065 also led to the activation of the tumor suppressor AMPK, providing an additional anticancer mechanism. In addition, YW2065 showed favorable pharmacokinetic properties without obvious toxicity. The anti-CRC effect of YW2065 was highlighted by its promising efficacy in a mice xenograft model.
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Affiliation(s)
- Wei Yang
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Yingjun Li
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Yong Ai
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Obinna N Obianom
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Dong Guo
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Hong Yang
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Srilatha Sakamuru
- National Center for Advancing Translational Sciences , National Institutes of Health , 9800 Medical Center Drive , Bethesda , Maryland 20892 , United States
| | - Menghang Xia
- National Center for Advancing Translational Sciences , National Institutes of Health , 9800 Medical Center Drive , Bethesda , Maryland 20892 , United States
| | - Yan Shu
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States.,School and Hospital of Stomatology , Guangzhou Medical University , Guangzhou 510140 , China
| | - Fengtian Xue
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
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14
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Ianevski A, Giri AK, Gautam P, Kononov A, Potdar S, Saarela J, Wennerberg K, Aittokallio T. Prediction of drug combination effects with a minimal set of experiments. NAT MACH INTELL 2019; 1:568-577. [PMID: 32368721 DOI: 10.1038/s42256-019-0122-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
High-throughput drug combination screening provides a systematic strategy to discover unexpected combinatorial synergies in pre-clinical cell models. However, phenotypic combinatorial screening with multi-dose matrix assays is experimentally expensive, especially when the aim is to identify selective combination synergies across a large panel of cell lines or patient samples. Here we implemented DECREASE, an efficient machine learning model that requires only a limited set of pairwise dose-response measurements for accurate prediction of drug combination synergy and antagonism. Using a compendium of 23,595 drug combination matrices tested in various cancer cell lines, and malaria and Ebola infection models, we demonstrate how cost-effective experimental designs with DECREASE capture almost the same degree of information for synergy and antagonism detection as the fully-measured dose-response matrices. Measuring only the diagonal of the matrix provides an accurate and practical option for combinatorial screening. The open-source web-implementation enables applications of DECREASE to both pre-clinical and translational studies.
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Affiliation(s)
- Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland.,Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto University, FI-02150 Espoo, Finland
| | - Anil K Giri
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland
| | - Prson Gautam
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland
| | - Alexander Kononov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland.,Biotech Research & Innovation Centre (BRIC) and the Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland.,Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto University, FI-02150 Espoo, Finland.,Department of Mathematics and Statistics, University of Turku, Quantum, FI-20014 Turku, Finland
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15
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Weiss A, Le Roux-Bourdieu M, Zoetemelk M, Ramzy GM, Rausch M, Harry D, Miljkovic-Licina M, Falamaki K, Wehrle-Haller B, Meraldi P, Nowak-Sliwinska P. Identification of a Synergistic Multi-Drug Combination Active in Cancer Cells via the Prevention of Spindle Pole Clustering. Cancers (Basel) 2019; 11:E1612. [PMID: 31652588 PMCID: PMC6826636 DOI: 10.3390/cancers11101612] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
A major limitation of clinically used cancer drugs is the lack of specificity resulting in toxicity. To address this, we performed a phenotypically-driven screen to identify optimal multidrug combinations acting with high efficacy and selectivity in clear cell renal cell carcinoma (ccRCC). The search was performed using the Therapeutically Guided Multidrug Optimization (TGMO) method in ccRCC cells (786-O) and nonmalignant renal cells and identified a synergistic low-dose four-drug combination (C2) with high efficacy and negligible toxicity. We discovered that C2 inhibits multipolar spindle pole clustering, a survival mechanism employed by cancer cells with spindle abnormalities. This phenotype was also observed in 786-O cells resistant to sunitinib, the first line ccRCC treatment, as well as in melanoma cells with distinct percentages of supernumerary centrosomes. We conclude that C2-treatment shows a high efficacy in cells prone to form multipolar spindles. Our data suggest a highly effective and selective C2 treatment strategy for malignant and drug-resistant cancers.
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Affiliation(s)
- Andrea Weiss
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Morgan Le Roux-Bourdieu
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Marloes Zoetemelk
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - George M Ramzy
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Magdalena Rausch
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Daniela Harry
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Marijana Miljkovic-Licina
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Department of Pathology and Immunology, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Katayoun Falamaki
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Bernard Wehrle-Haller
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Patrick Meraldi
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Patrycja Nowak-Sliwinska
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
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16
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Abstract
RAS genes are the most commonly mutated oncogenes in cancer, but effective therapeutic strategies to target RAS-mutant cancers have proved elusive. A key aspect of this challenge is the fact that direct inhibition of RAS proteins has proved difficult, leading researchers to test numerous alternative strategies aimed at exploiting RAS-related vulnerabilities or targeting RAS effectors. In the past few years, we have witnessed renewed efforts to target RAS directly, with several promising strategies being tested in clinical trials at different stages of completion. Important advances have also been made in approaches designed to indirectly target RAS by improving inhibition of RAS effectors, exploiting synthetic lethal interactions or metabolic dependencies, using therapeutic combination strategies or harnessing the immune system. In this Review, we describe historical and ongoing efforts to target RAS-mutant cancers and outline the current therapeutic landscape in the collective quest to overcome the effects of this crucial oncogene.
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17
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Tendler A, Zimmer A, Mayo A, Alon U. Noise-precision tradeoff in predicting combinations of mutations and drugs. PLoS Comput Biol 2019; 15:e1006956. [PMID: 31116755 PMCID: PMC6548401 DOI: 10.1371/journal.pcbi.1006956] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 06/04/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023] Open
Abstract
Many biological problems involve the response to multiple perturbations. Examples include response to combinations of many drugs, and the effects of combinations of many mutations. Such problems have an exponentially large space of combinations, which makes it infeasible to cover the entire space experimentally. To overcome this problem, several formulae that predict the effect of drug combinations or fitness landscape values have been proposed. These formulae use the effects of single perturbations and pairs of perturbations to predict triplets and higher order combinations. Interestingly, different formulae perform best on different datasets. Here we use Pareto optimality theory to quantitatively explain why no formula is optimal for all datasets, due to an inherent bias-variance (noise-precision) tradeoff. We calculate the Pareto front of log-linear formulae and find that the optimal formula depends on properties of the dataset: the typical interaction strength and the experimental noise. This study provides an approach to choose a suitable prediction formula for a given dataset, in order to best overcome the combinatorial explosion problem. Sometimes a combination of drugs works much better than each drug alone. Finding such drug cocktails is a pressing challenge in order to combat drug resistance and to improve drug effects. However, it is impossible to test all combinations of multiple drug experimentally. Therefore, researchers are looking for computational rather than experimental approaches to overcome this problem. One approach is to measure the effect of few drugs and plug it into a formula that predicts the effect of many drugs together. Existing prediction formulae typically perform best on the dataset that they were developed on, but less well on other datasets. Here we explain this observation and give a guide for the choice of an optimal prediction formula for a given dataset. The optimal formula depends on two main properties of the dataset: 1) The interaction strength between the drugs and 2) The experimental noise in the data. This study may help researchers discover effective combinations of multiple drugs and multiple perturbations in general.
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Affiliation(s)
- Avichai Tendler
- Dept. Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Zimmer
- Dept. Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avi Mayo
- Dept. Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Alon
- Dept. Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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18
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Chantzi E, Jarvius M, Niklasson M, Segerman A, Gustafsson MG. COMBImage: a modular parallel processing framework for pairwise drug combination analysis that quantifies temporal changes in label-free video microscopy movies. BMC Bioinformatics 2018; 19:453. [PMID: 30477419 PMCID: PMC6257977 DOI: 10.1186/s12859-018-2458-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 10/03/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Large-scale pairwise drug combination analysis has lately gained momentum in drug discovery and development projects, mainly due to the employment of advanced experimental-computational pipelines. This is fortunate as drug combinations are often required for successful treatment of complex diseases. Furthermore, most new drugs cannot totally replace the current standard-of-care medication, but rather have to enter clinical use as add-on treatment. However, there is a clear deficiency of computational tools for label-free and temporal image-based drug combination analysis that go beyond the conventional but relatively uninformative end point measurements. RESULTS COMBImage is a fast, modular and instrument independent computational framework for in vitro pairwise drug combination analysis that quantifies temporal changes in label-free video microscopy movies. Jointly with automated analyses of temporal changes in cell morphology and confluence, it performs and displays conventional cell viability and synergy end point analyses. The image processing algorithms are parallelized using Google's MapReduce programming model and optimized with respect to method-specific tuning parameters. COMBImage is shown to process time-lapse microscopy movies from 384-well plates within minutes on a single quad core personal computer. This framework was employed in the context of an ongoing drug discovery and development project focused on glioblastoma multiforme; the most deadly form of brain cancer. Interesting add-on effects of two investigational cytotoxic compounds when combined with vorinostat were revealed on recently established clonal cultures of glioma-initiating cells from patient tumor samples. Therapeutic synergies, when normal astrocytes were used as a toxicity cell model, reinforced the pharmacological interest regarding their potential clinical use. CONCLUSIONS COMBImage enables, for the first time, fast and optimized pairwise drug combination analyses of temporal changes in label-free video microscopy movies. Providing this jointly with conventional cell viability based end point analyses, it could help accelerating and guiding any drug discovery and development project, without use of cell labeling and the need to employ a particular live cell imaging instrument.
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Affiliation(s)
- Efthymia Chantzi
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala, Sweden
| | - Malin Jarvius
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala, Sweden
- SciLifeLab Drug Discovery and Development, In Vitro Systems Pharmacology Facility, Uppsala University, Uppsala, Sweden
| | - Mia Niklasson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Segerman
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mats G. Gustafsson
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala, Sweden
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19
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Kim S, Tiedt R, Loo A, Horn T, Delach S, Kovats S, Haas K, Engstler BS, Cao A, Pinzon-Ortiz M, Mulford I, Acker MG, Chopra R, Brain C, di Tomaso E, Sellers WR, Caponigro G. The potent and selective cyclin-dependent kinases 4 and 6 inhibitor ribociclib (LEE011) is a versatile combination partner in preclinical cancer models. Oncotarget 2018; 9:35226-35240. [PMID: 30443290 PMCID: PMC6219668 DOI: 10.18632/oncotarget.26215] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/15/2018] [Indexed: 01/18/2023] Open
Abstract
Inhibition of cyclin-dependent kinases 4 and 6 (CDK4/6) is associated with robust antitumor activity. Ribociclib (LEE011) is an orally bioavailable CDK4/6 inhibitor that is approved for the treatment of hormone receptor-positive, human epidermal growth factor receptor 2-negative advanced breast cancer, in combination with an aromatase inhibitor, and is currently being evaluated in several additional trials. Here, we report the preclinical profile of ribociclib. When tested across a large panel of kinase active site binding assays, ribociclib and palbociclib were highly selective for CDK4, while abemaciclib showed affinity to several other kinases. Both ribociclib and abemaciclib showed slightly higher potency in CDK4-dependent cells than in CDK6-dependent cells, while palbociclib did not show such a difference. Profiling CDK4/6 inhibitors in large-scale cancer cell line screens in vitro confirmed that RB1 loss of function is a negative predictor of sensitivity. We also found that routinely used cellular viability assays measuring adenosine triphosphate levels as a proxy for cell numbers underestimated the effects of CDK4/6 inhibition, which contrasts with assays that assess cell number more directly. Robust antitumor efficacy and combination benefit was detected when ribociclib was added to encorafenib, nazartinib, or endocrine therapies in patient-derived xenografts.
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Affiliation(s)
- Sunkyu Kim
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Ralph Tiedt
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland, USA
| | - Alice Loo
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Thomas Horn
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Scott Delach
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Steven Kovats
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Kristy Haas
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | | | - Alexander Cao
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Maria Pinzon-Ortiz
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Iain Mulford
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Michael G Acker
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Rajiv Chopra
- Novartis Institutes for BioMedical Research, Chemical Biology & Therapeutics, Cambridge, MA, USA
| | - Christopher Brain
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Cambridge, MA, USA
| | - Emmanuelle di Tomaso
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - William R Sellers
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Giordano Caponigro
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
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20
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Weinstein ZB, Kuru N, Kiriakov S, Palmer AC, Khalil AS, Clemons PA, Zaman MH, Roth FP, Cokol M. Modeling the impact of drug interactions on therapeutic selectivity. Nat Commun 2018; 9:3452. [PMID: 30150706 PMCID: PMC6110842 DOI: 10.1038/s41467-018-05954-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 07/27/2018] [Indexed: 01/12/2023] Open
Abstract
Combination therapies that produce synergistic growth inhibition are widely sought after for the pharmacotherapy of many pathological conditions. Therapeutic selectivity, however, depends on the difference between potency on disease-causing cells and potency on non-target cell types that cause toxic side effects. Here, we examine a model system of antimicrobial compound combinations applied to two highly diverged yeast species. We find that even though the drug interactions correlate between the two species, cell-type-specific differences in drug interactions are common and can dramatically alter the selectivity of compounds when applied in combination vs. single-drug activity-enhancing, diminishing, or inverting therapeutic windows. This study identifies drug combinations with enhanced cell-type-selectivity with a range of interaction types, which we experimentally validate using multiplexed drug-interaction assays for heterogeneous cell cultures. This analysis presents a model framework for evaluating drug combinations with increased efficacy and selectivity against pathogens or tumors.
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Affiliation(s)
- Zohar B Weinstein
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02115, USA
| | - Nurdan Kuru
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Szilvia Kiriakov
- Program in Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA, 02215, USA
- Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Adam C Palmer
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Paul A Clemons
- Chemical Biology & Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Muhammad H Zaman
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Boston University, Boston, MA, 02215, USA
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, M5S 3E1, Canada
- Canadian Institute for Advanced Research, Toronto, ON, M5S 3E1, Canada
| | - Murat Cokol
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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21
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Cokol-Cakmak M, Bakan F, Cetiner S, Cokol M. Diagonal Method to Measure Synergy Among Any Number of Drugs. J Vis Exp 2018. [PMID: 29985330 PMCID: PMC6101960 DOI: 10.3791/57713] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A synergistic drug combination has a higher efficacy compared to the effects of individual drugs. Checkerboard assays, where drugs are combined in many doses, allow sensitive measurement of drug interactions. However, these assays are costly and do not scale well for measuring interaction among many drugs. Several recent studies have reported drug interaction measurements using a diagonal sampling of the traditional checkerboard assay. This alternative methodology greatly decreases the cost of drug interaction experiments and allows interaction measurement for combinations with many drugs. Here, we describe a protocol to measure the three pairwise interactions and one three-way interaction among three antibiotics in duplicate, in five days, using only three 96-well microplates and standard laboratory equipment. We present representative results showing that the three-antibiotic combination of Levofloxacin + Nalidixic Acid + Penicillin G is synergistic. Our protocol scales up to measure interactions among many drugs and in other biological contexts, allowing for efficient screens for multi-drug synergies against pathogens and tumors.
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Affiliation(s)
| | - Feray Bakan
- Nanotechnology Research and Application Center, Sabanci University
| | - Selim Cetiner
- Faculty of Engineering and Natural Sciences, Sabanci University
| | - Murat Cokol
- Faculty of Engineering and Natural Sciences, Sabanci University; Nanotechnology Research and Application Center, Sabanci University; Laboratory of Systems Pharmacology, Harvard Medical School;
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22
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Ravikumar B, Aittokallio T. Improving the efficacy-safety balance of polypharmacology in multi-target drug discovery. Expert Opin Drug Discov 2017; 13:179-192. [DOI: 10.1080/17460441.2018.1413089] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Balaguru Ravikumar
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
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23
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Zimmer A, Tendler A, Katzir I, Mayo A, Alon U. Prediction of drug cocktail effects when the number of measurements is limited. PLoS Biol 2017; 15:e2002518. [PMID: 29073201 PMCID: PMC5675459 DOI: 10.1371/journal.pbio.2002518] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 11/07/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022] Open
Abstract
Cocktails of drugs can be more effective than single drugs, because they can potentially work at lower doses and avoid resistance. However, it is impossible to test all drug cocktails drawn from a large set of drugs because of the huge number of combinations. To overcome this combinatorial explosion problem, one can sample a relatively small number of combinations and use a model to predict the rest. Recently, Zimmer and Katzir et al. presented a model that accurately predicted the effects of cocktails at all doses based on measuring pairs of drugs. This model requires measuring each pair at several different doses and uses interpolation to reduce experimental noise. However, often, it is not possible to measure each pair at multiple doses (for example, in scarce patient-derived tumor material or in large screens). Here, we ask whether measurements at only a single dose can also predict high-order drug cocktails. To address this, we present a fully factorial experimental dataset on all drug cocktails built of 6 chemotherapy drugs on 2 cancer cell lines. We develop a formula that uses only pair measurements at a single dose to predict much of the variation up to 6-drug cocktails in the present data, outperforming commonly used Bliss independence and regression approaches. This model, called the pairs model, is an extension of the Bliss independence model to pairs: For M drugs, it equals the product of all pair effects to the power 1/(M−1). The pairs model also shows good agreement with previously published data on antibiotic triplets and quadruplets. The present model can only predict combinations at the same doses in which the pairs were measured and is not able to predict effects at other doses. This study indicates that pair-based approaches might be able to usefully predict and prioritize high-order combinations, even in large screens or when material for testing is limited. Drug cocktails are a promising strategy for diseases such as cancer and infections, because cocktails can be more effective than individual drugs and can overcome problems of drug resistance. However, finding the best cocktail comprising a given set of drugs is challenging because the number of experiments needed is huge and grows exponentially with the number of drugs. This problem is exacerbated when the experiments are expensive and the material for testing is rare. Here, we present a way to address this challenge using a mathematical formula, called the pairs model, that requires relatively few experimental tests in order to estimate the effects of cocktails and to predict which cocktail is most effective. The formula does well on experimental data generated in this study using combinations of between 3 and 6 anticancer drugs, as well as on existing data that use combinations of antibiotics.
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Affiliation(s)
- Anat Zimmer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avichai Tendler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Itay Katzir
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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25
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Weinberg F, Reischmann N, Fauth L, Taromi S, Mastroianni J, Köhler M, Halbach S, Becker AC, Deng N, Schmitz T, Uhl FM, Herbener N, Riedel B, Beier F, Swarbrick A, Lassmann S, Dengjel J, Zeiser R, Brummer T. The Atypical Kinase RIOK1 Promotes Tumor Growth and Invasive Behavior. EBioMedicine 2017; 20:79-97. [PMID: 28499923 PMCID: PMC5478185 DOI: 10.1016/j.ebiom.2017.04.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 12/27/2022] Open
Abstract
Despite being overexpressed in different tumor entities, RIO kinases are hardly characterized in mammalian cells. We investigated the role of these atypical kinases in different cancer cells. Using isogenic colon-, breast- and lung cancer cell lines, we demonstrate that knockdown of RIOK1, but not of RIOK2 or RIOK3, strongly impairs proliferation and invasiveness in conventional and 3D culture systems. Interestingly, these effects were mainly observed in RAS mutant cancer cells. In contrast, growth of RAS wildtype Caco-2 and Bcr-Abl-driven K562 cells is not affected by RIOK1 knockdown, suggesting a specific requirement for RIOK1 in the context of oncogenic RAS signaling. Furthermore, we show that RIOK1 activates NF-κB signaling and promotes cell cycle progression. Using proteomics, we identified the pro-invasive proteins Metadherin and Stathmin1 to be regulated by RIOK1. Additionally, we demonstrate that RIOK1 promotes lung colonization in vivo and that RIOK1 is overexpressed in different subtypes of human lung- and breast cancer. Altogether, our data suggest RIOK1 as a potential therapeutic target, especially in RAS-driven cancers.
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Affiliation(s)
- Florian Weinberg
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany
| | - Nadine Reischmann
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Lisa Fauth
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Sanaz Taromi
- Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Justin Mastroianni
- Faculty of Biology, ALU, Freiburg, Germany; Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Martin Köhler
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Andrea C Becker
- Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany; Department of Dermatology, University Medical Center - ALU, Freiburg, Germany
| | - Niantao Deng
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Tatjana Schmitz
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany
| | - Franziska Maria Uhl
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Nicola Herbener
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Bianca Riedel
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Fabian Beier
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Alexander Swarbrick
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Silke Lassmann
- BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany; German Cancer Consortium (DKTK, Freiburg) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörn Dengjel
- BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany; Department of Dermatology, University Medical Center - ALU, Freiburg, Germany; Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Robert Zeiser
- BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; German Cancer Consortium (DKTK, Freiburg) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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26
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Resistance mechanisms to TP53-MDM2 inhibition identified by in vivo piggyBac transposon mutagenesis screen in an Arf -/- mouse model. Proc Natl Acad Sci U S A 2017; 114:3151-3156. [PMID: 28265066 DOI: 10.1073/pnas.1620262114] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Inhibitors of double minute 2 protein (MDM2)-tumor protein 53 (TP53) interaction are predicted to be effective in tumors in which the TP53 gene is wild type, by preventing TP53 protein degradation. One such setting is represented by the frequent CDKN2A deletion in human cancer that, through inactivation of p14ARF, activates MDM2 protein, which in turn degrades TP53 tumor suppressor. Here we used piggyBac (PB) transposon insertional mutagenesis to anticipate resistance mechanisms occurring during treatment with the MDM2-TP53 inhibitor HDM201. Constitutive PB mutagenesis in Arf-/- mice provided a collection of spontaneous tumors with characterized insertional genetic landscapes. Tumors were allografted in large cohorts of mice to assess the pharmacologic effects of HDM201. Sixteen out of 21 allograft models were sensitive to HDM201 but ultimately relapsed under treatment. A comparison of tumors with acquired resistance to HDM201 and untreated tumors identified 87 genes that were differentially and significantly targeted by the PB transposon. Resistant tumors displayed a complex clonality pattern suggesting the emergence of several resistant subclones. Among the most frequent alterations conferring resistance, we observed somatic and insertional loss-of-function mutations in transformation-related protein 53 (Trp53) in 54% of tumors and transposon-mediated gain-of-function alterations in B-cell lymphoma-extra large (Bcl-xL), Mdm4, and two TP53 family members, resulting in expression of the TP53 dominant negative truncations ΔNTrp63 and ΔNTrp73. Enhanced BCL-xL and MDM4 protein expression was confirmed in resistant tumors, as well as in HDM201-resistant patient-derived tumor xenografts. Interestingly, concomitant inhibition of MDM2 and BCL-xL demonstrated significant synergy in p53 wild-type cell lines in vitro. Collectively, our findings identify several potential mechanisms by which TP53 wild-type tumors may escape MDM2-targeted therapy.
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