Multiobjective optimization identifies cancer-selective combination therapies

PLoS Comput Biol. 2020 Dec 28;16(12):e1008538. doi: 10.1371/journal.pcbi.1008538. eCollection 2020 Dec.

Abstract

Combinatorial therapies are required to treat patients with advanced cancers that have become resistant to monotherapies through rewiring of redundant pathways. Due to a massive number of potential drug combinations, there is a need for systematic approaches to identify safe and effective combinations for each patient, using cost-effective methods. Here, we developed an exact multiobjective optimization method for identifying pairwise or higher-order combinations that show maximal cancer-selectivity. The prioritization of patient-specific combinations is based on Pareto-optimization in the search space spanned by the therapeutic and nonselective effects of combinations. We demonstrate the performance of the method in the context of BRAF-V600E melanoma treatment, where the optimal solutions predicted a number of co-inhibition partners for vemurafenib, a selective BRAF-V600E inhibitor, approved for advanced melanoma. We experimentally validated many of the predictions in BRAF-V600E melanoma cell line, and the results suggest that one can improve selective inhibition of BRAF-V600E melanoma cells by combinatorial targeting of MAPK/ERK and other compensatory pathways using pairwise and third-order drug combinations. Our mechanism-agnostic optimization method is widely applicable to various cancer types, and it takes as input only measurements of a subset of pairwise drug combinations, without requiring target information or genomic profiles. Such data-driven approaches may become useful for functional precision oncology applications that go beyond the cancer genetic dependency paradigm to optimize cancer-selective combinatorial treatments.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents / therapeutic use
  • Combined Modality Therapy
  • Humans
  • Melanoma / drug therapy*
  • Precision Medicine
  • Protein Kinase Inhibitors / therapeutic use
  • Proto-Oncogene Proteins B-raf / metabolism
  • Skin Neoplasms / drug therapy*

Substances

  • Antineoplastic Agents
  • Protein Kinase Inhibitors
  • Proto-Oncogene Proteins B-raf

Grants and funding

This work was supported by the Academy of Finland [grants 292611, 310507, 313267, 326238 to TA; grant 313270 to VM], the Cancer Society of Finland [TA] and the Sigrid Jusélius Foundation [TA]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.