1
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Dong Z, Zhang H, Chen Y, Payne PRO, Li F. Interpreting the Mechanism of Synergism for Drug Combinations Using Attention-Based Hierarchical Graph Pooling. Cancers (Basel) 2023; 15:4210. [PMID: 37686486 PMCID: PMC10486573 DOI: 10.3390/cancers15174210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Synergistic drug combinations provide huge potentials to enhance therapeutic efficacy and to reduce adverse reactions. However, effective and synergistic drug combination prediction remains an open question because of the unknown causal disease signaling pathways. Though various deep learning (AI) models have been proposed to quantitatively predict the synergism of drug combinations, the major limitation of existing deep learning methods is that they are inherently not interpretable, which makes the conclusions of AI models untransparent to human experts, henceforth limiting the robustness of the model conclusion and the implementation ability of these models in real-world human-AI healthcare. In this paper, we develop an interpretable graph neural network (GNN) that reveals the underlying essential therapeutic targets and the mechanism of the synergy (MoS) by mining the sub-molecular network of great importance. The key point of the interpretable GNN prediction model is a novel graph pooling layer, a self-attention-based node and edge pool (henceforth SANEpool), that can compute the attention score (importance) of genes and connections based on the genomic features and topology. As such, the proposed GNN model provides a systematic way to predict and interpret the drug combination synergism based on the detected crucial sub-molecular network. Experiments on various well-adopted drug-synergy-prediction datasets demonstrate that (1) the SANEpool model has superior predictive ability to generate accurate synergy score prediction, and (2) the sub-molecular networks detected by the SANEpool are self-explainable and salient for identifying synergistic drug combinations.
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Affiliation(s)
- Zehao Dong
- Department of Computer Science & Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; (Z.D.); (Y.C.)
| | - Heming Zhang
- Institute for Informatics, Data Science, and Biostatistics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; (H.Z.); (P.R.O.P.)
| | - Yixin Chen
- Department of Computer Science & Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; (Z.D.); (Y.C.)
| | - Philip R. O. Payne
- Institute for Informatics, Data Science, and Biostatistics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; (H.Z.); (P.R.O.P.)
| | - Fuhai Li
- Institute for Informatics, Data Science, and Biostatistics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; (H.Z.); (P.R.O.P.)
- Department of Pediatrics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
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2
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Grissenberger S, Sturtzel C, Wenninger-Weinzierl A, Radic-Sarikas B, Scheuringer E, Bierbaumer L, Etienne V, Némati F, Pascoal S, Tötzl M, Tomazou EM, Metzelder M, Putz EM, Decaudin D, Delattre O, Surdez D, Kovar H, Halbritter F, Distel M. High-content drug screening in zebrafish xenografts reveals high efficacy of dual MCL-1/BCL-X L inhibition against Ewing sarcoma. Cancer Lett 2023; 554:216028. [PMID: 36462556 DOI: 10.1016/j.canlet.2022.216028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Ewing sarcoma is a pediatric bone and soft tissue cancer with an urgent need for new therapies to improve disease outcome. To identify effective drugs, phenotypic drug screening has proven to be a powerful method, but achievable throughput in mouse xenografts, the preclinical Ewing sarcoma standard model, is limited. Here, we explored the use of xenografts in zebrafish for high-throughput drug screening to discover new combination therapies for Ewing sarcoma. We subjected xenografts in zebrafish larvae to high-content imaging and subsequent automated tumor size analysis to screen single agents and compound combinations. We identified three drug combinations effective against Ewing sarcoma cells: Irinotecan combined with either an MCL-1 or an BCL-XL inhibitor and in particular dual inhibition of the anti-apoptotic proteins MCL-1 and BCL-XL, which efficiently eradicated tumor cells in zebrafish xenografts. We confirmed enhanced efficacy of dual MCL-1/BCL-XL inhibition compared to single agents in a mouse PDX model. In conclusion, high-content screening of small compounds on Ewing sarcoma zebrafish xenografts identified dual MCL-1/BCL-XL targeting as a specific vulnerability and promising therapeutic strategy for Ewing sarcoma, which warrants further investigation towards clinical application.
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Affiliation(s)
| | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Andrea Wenninger-Weinzierl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Branka Radic-Sarikas
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Department of Pediatric Surgery, Medical University of Vienna, Vienna, Austria
| | - Eva Scheuringer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Lisa Bierbaumer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Vesnie Etienne
- Laboratory of Preclinical Investigation, Department of Translational Research, Institut Curie, PSL University, Paris, France
| | - Fariba Némati
- Laboratory of Preclinical Investigation, Department of Translational Research, Institut Curie, PSL University, Paris, France
| | - Susana Pascoal
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Marcus Tötzl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eleni M Tomazou
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Martin Metzelder
- Department of Pediatric Surgery, Medical University of Vienna, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Department of Translational Research, Institut Curie, PSL University, Paris, France; Department of Medical Oncology, Institut Curie Research Centre, Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Heinrich Kovar
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Dept. Pediatrics, Medical University Vienna, Vienna, Austria
| | | | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria.
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3
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Management of Unresectable Localized Pelvic Bone Sarcomas: Current Practice and Future Perspectives. Cancers (Basel) 2022; 14:cancers14102546. [PMID: 35626150 PMCID: PMC9139258 DOI: 10.3390/cancers14102546] [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: 04/04/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Some locally advanced pelvic bone tumors are deemed unresectable and, as such, not suitable for curative surgery. In this setting, treatment options are generally limited and not unanimous, with decisions being made on an individual basis after multidisciplinary discussion. Ultimately, and notwithstanding the bright prospects raised by novel therapeutic approaches, treatment should be patient-tailored, weighing a panoply of patient- and tumor-related factors. Abstract Bone sarcomas (BS) are rare mesenchymal tumors usually located in the extremities and pelvis. While surgical resection is the cornerstone of curative treatment, some locally advanced tumors are deemed unresectable and hence not suitable for curative intent. This is often true for pelvic sarcoma due to anatomic complexity and proximity to vital structures, making treatment options for these tumors generally limited and not unanimous, with decisions being made on an individual basis after multidisciplinary discussion. Several studies have been published in recent years focusing on innovative treatment options for patients with locally advanced sarcoma not amenable to local surgery. The present article reviews the evidence regarding the treatment of patients with locally advanced and unresectable pelvic BS, with the goal of providing an overview of treatment options for the main BS histologic subtypes involving this anatomic area and exploring future therapeutic perspectives. The management of unresectable localized pelvic BS represents a major challenge and is hampered by the lack of comprehensive and standardized guidelines. As such, the optimal treatment needs to be individually tailored, weighing a panoply of patient- and tumor-related factors. Despite the bright prospects raised by novel therapeutic approaches, the role of each treatment option in the therapeutic armamentarium of these patients requires solid clinical evidence before becoming fully established.
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4
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Fayzullina D, Tsibulnikov S, Stempen M, Schroeder BA, Kumar N, Kharwar RK, Acharya A, Timashev P, Ulasov I. Novel Targeted Therapeutic Strategies for Ewing Sarcoma. Cancers (Basel) 2022; 14:cancers14081988. [PMID: 35454895 PMCID: PMC9032664 DOI: 10.3390/cancers14081988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Ewing sarcoma is an uncommon cancer that arises in mesenchymal tissues and represents the second most widespread malignant bone neoplasm after osteosarcoma in children. Therapy has increased the 5-year survival rate in the last 40 years, although the recurrence rate has remained high. There is an immediate and unmet need for the development of novel Ewing sarcoma therapies. We offer new prospective targets for the therapy of Ewing sarcoma. The EWSR1/FLI1 fusion protein, which is identified in 85–90% of Ewing sarcoma tumors, and its direct targets are given special focus in this study. Experimantal therapy that targets multiple signaling pathways activated during ES progression, alone or in combination with existing regimens, may become the new standard of care for Ewing sarcoma patients, improving patient survival. Abstract Ewing sarcoma (ES) is an uncommon cancer that arises in mesenchymal tissues and represents the second most widespread malignant bone neoplasm after osteosarcoma in children. Amplifications in genomic, proteomic, and metabolism are characteristics of sarcoma, and targeting altered cancer cell molecular processes has been proposed as the latest promising strategy to fight cancer. Recent technological advancements have elucidated some of the underlying oncogenic characteristics of Ewing sarcoma. Offering new insights into the physiological basis for this phenomenon, our current review examines the dynamics of ES signaling as it related to both ES and the microenvironment by integrating genomic and proteomic analyses. An extensive survey of the literature was performed to compile the findings. We have also highlighted recent and ongoing studies integrating metabolomics and genomics aimed at better understanding the complex interactions as to how ES adapts to changing biochemical changes within the tumor microenvironment.
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Affiliation(s)
- Daria Fayzullina
- Group of Experimental Biotherapy and Diagnostic, Department of Advanced Materials, Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia; (D.F.); (S.T.); (M.S.); (P.T.)
| | - Sergey Tsibulnikov
- Group of Experimental Biotherapy and Diagnostic, Department of Advanced Materials, Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia; (D.F.); (S.T.); (M.S.); (P.T.)
| | - Mikhail Stempen
- Group of Experimental Biotherapy and Diagnostic, Department of Advanced Materials, Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia; (D.F.); (S.T.); (M.S.); (P.T.)
| | - Brett A. Schroeder
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA;
| | - Naveen Kumar
- Tumor Immunology Lab, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (N.K.); (A.A.)
| | - Rajesh Kumar Kharwar
- Endocrine Research Lab, Department of Zoology, Kutir Post Graduate College, Chakkey, Jaunpur 222146, India;
| | - Arbind Acharya
- Tumor Immunology Lab, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (N.K.); (A.A.)
| | - Peter Timashev
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia; (D.F.); (S.T.); (M.S.); (P.T.)
- Department of Advanced Materials, Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Ilya Ulasov
- Group of Experimental Biotherapy and Diagnostic, Department of Advanced Materials, Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia; (D.F.); (S.T.); (M.S.); (P.T.)
- Correspondence:
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5
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Tzanakakis GN, Giatagana EM, Berdiaki A, Spyridaki I, Hida K, Neagu M, Tsatsakis AM, Nikitovic D. The Role of IGF/IGF-IR-Signaling and Extracellular Matrix Effectors in Bone Sarcoma Pathogenesis. Cancers (Basel) 2021; 13:cancers13102478. [PMID: 34069554 PMCID: PMC8160938 DOI: 10.3390/cancers13102478] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/27/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Bone sarcomas are mesenchymal origin tumors. Bone sarcoma patients show a variable response or do not respond to chemotherapy. Notably, improving efficient chemotherapy approaches, dealing with chemoresistance, and preventing metastasis pose unmet challenges in sarcoma therapy. Insulin-like growth factors 1 and 2 (IGF-1 and -2) and their respective receptors are a multifactorial system that significantly contributes to bone sarcoma pathogenesis. Most clinical trials aiming at the IGF pathway have had limited success. Developing combinatorial strategies to enhance antitumor responses and better classify the patients that could best benefit from IGF-axis targeting therapies is in order. A plausible approach for developing a combinatorial strategy is to focus on the tumor microenvironment (TME) and processes executed therein. Herewith, we will discuss how the interplay between IGF-signaling and the TME constituents affects bone sarcomas’ basal functions and their response to therapy. Potential direct and adjunct therapeutical implications of the extracellular matrix (ECM) effectors will also be summarized. Abstract Bone sarcomas, mesenchymal origin tumors, represent a substantial group of varying neoplasms of a distinct entity. Bone sarcoma patients show a limited response or do not respond to chemotherapy. Notably, developing efficient chemotherapy approaches, dealing with chemoresistance, and preventing metastasis pose unmet challenges in sarcoma therapy. Insulin-like growth factors 1 and 2 (IGF-1 and -2) and their respective receptors are a multifactorial system that significantly contributes to bone sarcoma pathogenesis. Whereas failures have been registered in creating novel targeted therapeutics aiming at the IGF pathway, new agent development should continue, evaluating combinatorial strategies for enhancing antitumor responses and better classifying the patients that could best benefit from these therapies. A plausible approach for developing a combinatorial strategy is to focus on the tumor microenvironment (TME) and processes executed therein. Herewith, we will discuss how the interplay between IGF-signaling and the TME constituents affects sarcomas’ basal functions and their response to therapy. This review highlights key studies focusing on IGF signaling in bone sarcomas, specifically studies underscoring novel properties that make this system an attractive therapeutic target and identifies new relationships that may be exploited. Potential direct and adjunct therapeutical implications of the extracellular matrix (ECM) effectors will also be summarized.
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Affiliation(s)
- George N. Tzanakakis
- Laboratory of Histology-Embryology, School of Medicine, University of Crete, 71003 Heraklion, Greece; (G.N.T.); (E.-M.G.); (A.B.); (I.S.)
- Laboratory of Anatomy, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Eirini-Maria Giatagana
- Laboratory of Histology-Embryology, School of Medicine, University of Crete, 71003 Heraklion, Greece; (G.N.T.); (E.-M.G.); (A.B.); (I.S.)
| | - Aikaterini Berdiaki
- Laboratory of Histology-Embryology, School of Medicine, University of Crete, 71003 Heraklion, Greece; (G.N.T.); (E.-M.G.); (A.B.); (I.S.)
| | - Ioanna Spyridaki
- Laboratory of Histology-Embryology, School of Medicine, University of Crete, 71003 Heraklion, Greece; (G.N.T.); (E.-M.G.); (A.B.); (I.S.)
| | - Kyoko Hida
- Department of Vascular Biology and Molecular Pathology, Hokkaido University Graduate School of Dental Medicine, Sapporo 060-8586, Japan;
| | - Monica Neagu
- Department of Immunology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania;
| | - Aristidis M. Tsatsakis
- Laboratory of Toxicology, School of Medicine, University of Crete, 71003 Heraklion, Greece;
| | - Dragana Nikitovic
- Laboratory of Histology-Embryology, School of Medicine, University of Crete, 71003 Heraklion, Greece; (G.N.T.); (E.-M.G.); (A.B.); (I.S.)
- Correspondence:
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6
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Jin W. The Role of Tyrosine Kinases as a Critical Prognostic Parameter and Its Targeted Therapies in Ewing Sarcoma. Front Cell Dev Biol 2020; 8:613. [PMID: 32754598 PMCID: PMC7381324 DOI: 10.3389/fcell.2020.00613] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Ewing sarcoma (ES) is a rare, highly aggressive, bone, or soft tissue-associated tumor. Although this sarcoma often responds well to initial chemotherapy, 40% of the patients develop a lethal recurrence of the disease, with death recorded in 75-80% of patients with metastatic ES within 5 years, despite receiving high-dose chemotherapy. ES is genetically well-characterized, as indicated by the EWS-FLI1 fusion protein encoded as a result of chromosomal translocation in 80-90% of patients with ES, as well as in ES-related cancer cell lines. Recently, tyrosine kinases have been identified in the pathogenesis of ES. These tyrosine kinases, acting as oncoproteins, are associated with the clinical pathogenesis, metastasis, acquisition of self-renewal traits, and chemoresistance of ES, through the activation of various intracellular signaling pathways. This review describes the recent progress related to cellular and molecular functional roles of tyrosine kinases in the progression of ES.
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Affiliation(s)
- Wook Jin
- Laboratory of Molecular Disease and Cell Regulation, Department of Biochemistry, School of Medicine, Gachon University, Incheon, South Korea
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7
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Precision medicine in Ewing sarcoma: a translational point of view. Clin Transl Oncol 2020; 22:1440-1454. [PMID: 32026343 DOI: 10.1007/s12094-020-02298-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/09/2020] [Indexed: 12/19/2022]
Abstract
Ewing sarcoma is a rare tumor that arises in bones of children and teenagers but, in 15% of the patients it is presented as a primary soft tissue tumor. Balanced reciprocal chimeric translocation t(11;22)(q24;q12), which encodes an oncogenic protein fusion (EWSR1/FLI1), is the most generalized and characteristic molecular event. Using conventional treatments, (chemotherapy, surgery and radiotherapy) long-term overall survival rate is 30% for patients with disseminated disease and 65-75% for patients with localized tumors. Urgent new effective drug development is a challenge. This review summarizes the preclinical and clinical investigational knowledge about prognostic and targetable biomarkers in Ewing sarcoma, finally suggesting a workflow for precision medicine committees.
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8
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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: 68] [Impact Index Per Article: 13.6] [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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9
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Estupiñan O, Santos L, Rodriguez A, Fernandez‐Nevado L, Costales P, Perez‐Escuredo J, Hermosilla MA, Oro P, Rey V, Tornin J, Allonca E, Fernandez‐Garcia MT, Alvarez‐Fernandez C, Braña A, Astudillo A, Menendez ST, Moris F, Rodriguez R. The multikinase inhibitor EC‐70124 synergistically increased the antitumor activity of doxorubicin in sarcomas. Int J Cancer 2019; 145:254-266. [DOI: 10.1002/ijc.32081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/22/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Oscar Estupiñan
- Hospital Universitario Central de Asturias ‐ Instituto de Investigación Sanitaria del Principado de Asturias Oviedo Spain
- Instituto Universitario de Oncología del Principado de Asturias Oviedo Spain
- CIBER en oncología (CIBERONC) Madrid Spain
| | - Laura Santos
- Hospital Universitario Central de Asturias ‐ Instituto de Investigación Sanitaria del Principado de Asturias Oviedo Spain
| | - Aida Rodriguez
- Hospital Universitario Central de Asturias ‐ Instituto de Investigación Sanitaria del Principado de Asturias Oviedo Spain
| | - Lucia Fernandez‐Nevado
- Hospital Universitario Central de Asturias ‐ Instituto de Investigación Sanitaria del Principado de Asturias Oviedo Spain
| | | | | | | | | | - Veronica Rey
- Hospital Universitario Central de Asturias ‐ Instituto de Investigación Sanitaria del Principado de Asturias Oviedo Spain
- Instituto Universitario de Oncología del Principado de Asturias Oviedo Spain
| | - Juan Tornin
- Hospital Universitario Central de Asturias ‐ Instituto de Investigación Sanitaria del Principado de Asturias Oviedo Spain
- Instituto Universitario de Oncología del Principado de Asturias Oviedo Spain
| | - Eva Allonca
- Hospital Universitario Central de Asturias ‐ Instituto de Investigación Sanitaria del Principado de Asturias Oviedo Spain
| | | | | | - Alejandro Braña
- Servicio de Traumatología of the Hospital Universitario Central de Asturias Oviedo Spain
| | - Aurora Astudillo
- Servicio de Anatomía Patológica of the Hospital Universitario Central de Asturias Oviedo Spain
| | - Sofia T Menendez
- Hospital Universitario Central de Asturias ‐ Instituto de Investigación Sanitaria del Principado de Asturias Oviedo Spain
- Instituto Universitario de Oncología del Principado de Asturias Oviedo Spain
- CIBER en oncología (CIBERONC) Madrid Spain
| | | | - Rene Rodriguez
- Hospital Universitario Central de Asturias ‐ Instituto de Investigación Sanitaria del Principado de Asturias Oviedo Spain
- Instituto Universitario de Oncología del Principado de Asturias Oviedo Spain
- CIBER en oncología (CIBERONC) Madrid Spain
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10
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Pemovska T, Bigenzahn JW, Superti-Furga G. Recent advances in combinatorial drug screening and synergy scoring. Curr Opin Pharmacol 2018; 42:102-110. [PMID: 30193150 PMCID: PMC6219891 DOI: 10.1016/j.coph.2018.07.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022]
Abstract
Treatment of complex diseases such as cancer, cardiovascular disease, diabetes or neurological disorders frequently warrants the utilization of drug combinations for therapeutic intervention. In fact, the most successful example is the current standard of care for HIV patients. However, identification of successful drug cocktails is not a simple task and is hampered by lack of standardization in terminology, experimental protocols and models as well as data analysis. Here we discuss the most recent developments in combinatorial drug screening by covering technological advancements in screening strategies, cellular model systems as well as novel drug classes. We believe the research progress being made provides promising basis to build on and identify, develop and optimize efficacious clinically relevant combinatorial drug treatments.
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Affiliation(s)
- Tea Pemovska
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17A, 1090 Vienna, Austria.
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Kondo T. Current Status of Proteomics in Ewing's Sarcoma. Proteomics Clin Appl 2018; 13:e1700130. [PMID: 29992772 DOI: 10.1002/prca.201700130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 06/13/2018] [Indexed: 02/01/2023]
Abstract
Ewing's sarcoma is an extremely rare mesenchymal malignancy of the bone, which predominantly occurs in children and young adolescents. Ewing's sarcoma is characterized by chromosomal translocations resulting in the formation of chimeric fusions between the EWS gene and transcription factors of the ETS family, such as EWS-FLI-1. The clinical outcome of Ewing's sarcoma remains poor, and novel therapeutic approaches are required. Proteomic analyses have been applied to identify the functions of the fusion gene product, and a novel mechanism of EWS-FLI-1 turnover has been proposed. Furthermore, proteomics has revealed the regulation of IL-6 secretion by EWS-FLI-1, which may promote malignant behavior in tumor cells. In addition, proteomic approaches have been used to assess the effects of unique genes and drugs on Ewing's sarcoma and to determine specific biomarker candidates for the prediction of drug resistance and recurrence. By identifying the proteins relevant to the molecular backgrounds of clinical characters of Ewing's sarcoma, we can understand the biology of Ewing's sarcoma and develop clinical applications. Fundamental research systems such as tumor cell and tissue biobanks and databases are required to make effective use of the limited clinical materials and promote research into Ewing's sarcoma.
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Affiliation(s)
- Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, 104-0045 Tokyo, Japan
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Fuxreiter M. Fuzziness in Protein Interactions-A Historical Perspective. J Mol Biol 2018; 430:2278-2287. [PMID: 29477337 DOI: 10.1016/j.jmb.2018.02.015] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/09/2018] [Accepted: 02/16/2018] [Indexed: 12/22/2022]
Abstract
The proposal that coupled folding to binding is not an obligatory mechanism for intrinsically disordered (ID) proteins was put forward 10 years ago. The notion of fuzziness implies that conformational heterogeneity can be maintained upon interactions of ID proteins, which has a functional impact either on regulated assembly or activity of the corresponding complexes. Here I review how the concept has evolved in the past decade, via increasing experimental data providing insights into the mechanisms, pathways and regulatory modes. The effects of structural diversity and transient contacts on protein assemblies have been collected and systematically analyzed (Fuzzy Complexes Database, http://protdyn-database.org). Fuzziness has also been exploited as a framework to decipher molecular organization of higher-order protein structures. Quantification of conformational heterogeneity opens exciting future perspectives for drug discovery from small molecule-ID protein interactions to supramolecular assemblies.
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Affiliation(s)
- Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary.
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Goss KL, Koppenhafer SL, Harmoney KM, Terry WW, Gordon DJ. Inhibition of CHK1 sensitizes Ewing sarcoma cells to the ribonucleotide reductase inhibitor gemcitabine. Oncotarget 2017; 8:87016-87032. [PMID: 29152060 PMCID: PMC5675612 DOI: 10.18632/oncotarget.18776] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/22/2017] [Indexed: 12/22/2022] Open
Abstract
Ewing sarcoma is a bone and soft tissue sarcoma that occurs in children and young adults. The EWS-FLI1 gene fusion is the driver mutation in most Ewing sarcoma tumors and functions, in part, as an aberrant transcription factor. We recently identified that Ewing sarcoma cells are sensitive to inhibition of ribonucleotide reductase (RNR), which catalyzes the formation of deoxyribonucleotides from ribonucleotides. In this report, we show that Ewing sarcoma cells are sensitive to treatment with clofarabine, which is a nucleoside analogue and allosteric inhibitor of RNR. However, clofarabine is a reversible inhibitor of RNR and we found that the effect of clofarabine is limited when using a short (6-hour) drug treatment. Gemcitabine, on the other hand, is an irreversible inhibitor of the RRM1 subunit of RNR and this drug induces apoptosis in Ewing sarcoma cells when used in both 6-hour and longer drug treatments. Treatment of Ewing sarcoma cells with gemcitabine also results in activation of checkpoint kinase 1 (CHK1), which is a critical mediator of cell survival in the setting of impaired DNA replication. Notably, inhibition of CHK1 function in Ewing sarcoma cells using a small-molecule CHK1 inhibitor, or siRNA knockdown, in combination with gemcitabine results in increased toxicity both in vitro and in vivo in a mouse xenograft experiment. Overall, our results provide insight into Ewing sarcoma biology and identify a candidate therapeutic target, and drug combination, in Ewing sarcoma.
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Affiliation(s)
- Kelli L Goss
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Stacia L Koppenhafer
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Kathryn M Harmoney
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, Iowa 52242, USA
| | - William W Terry
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, Iowa 52242, USA
| | - David J Gordon
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Iowa, Iowa City, Iowa 52242, USA
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