Integrating Phenotypic Search and Phosphoproteomic Profiling of Active Kinases for Optimization of Drug Mixtures for RCC Treatment.

Combined application of multiple therapeutic agents presents the possibility of enhanced efficacy and reduced development of resistance. Definition of the most appropriate combination for any given disease phenotype is challenged by the vast number of theoretically possible combinations of drugs and doses, making extensive empirical testing a virtually impossible task. We have used the streamlined-feedback system control (s-FSC) technique, a phenotypic approach, which converges to optimized drug combinations (ODC) within a few experimental steps. Phosphoproteomics analysis coupled to kinase activity analysis using the novel INKA (integrative inferred kinase activity) pipeline was performed to evaluate ODC mechanisms in a panel of renal cell carcinoma (RCC) cell lines. We identified different ODC with up to 95% effectivity for each RCC cell line, with low doses (ED5-25) of individual drugs. Global phosphoproteomics analysis demonstrated inhibition of relevant kinases, and targeting remaining active kinases with additional compounds improved efficacy. In addition, we identified a common RCC ODC, based on kinase activity data, to be effective in all RCC cell lines under study. Combining s-FSC with a phosphoproteomic profiling approach provides valuable insight in targetable kinase activity and allows for the identification of superior drug combinations for the treatment of RCC.

Cancers. 2020 Sep 21*** epublish ***

Judy R van Beijnum, Andrea Weiss, Robert H Berndsen, Tse J Wong, Louise C Reckman, Sander R Piersma, Marloes Zoetemelk, Richard de Haas, Olivier Dormond, Axel Bex, Alexander A Henneman, Connie R Jimenez, Arjan W Griffioen, Patrycja Nowak-Sliwinska

Angiogenesis Laboratory, Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1081HV, 1182 DB Amsterdam, The Netherlands., Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland., Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, De Boelelaan 1117, 1081HV, 1182 DB Amsterdam, The Netherlands., Department of Visceral surgery, Lausanne University Hospital and University of Lausanne, 1015 Lausanne, Switzerland., Royal Free London NHS Foundation Trust, Renal Cancer Centre, University College London, Division of Surgical and Interventional Science, London NW3 2QG, UK.

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