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An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer

Nature Medicine volume 23, pages 929–937 (2017)Cite this article

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Abstract

The principles that govern the evolution of tumors exposed to targeted therapy are poorly understood. Here we modeled the selection and propagation of an amplification in the BRAF oncogene (BRAFamp) in patient-derived tumor xenografts (PDXs) that were treated with a direct inhibitor of the kinase ERK, either alone or in combination with other ERK signaling inhibitors. Single-cell sequencing and multiplex fluorescence in situ hybridization analyses mapped the emergence of extra-chromosomal amplification in parallel evolutionary trajectories that arose in the same tumor shortly after treatment. The evolutionary selection of BRAFamp was determined by the fitness threshold, the barrier that subclonal populations need to overcome to regain fitness in the presence of therapy. This differed for inhibitors of ERK signaling, suggesting that sequential monotherapy is ineffective and selects for a progressively higher BRAF copy number. Concurrent targeting of the RAF, MEK and ERK kinases, however, imposed a sufficiently high fitness threshold to prevent the propagation of subclones with high-level BRAFamp. When administered on an intermittent schedule, this treatment inhibited tumor growth in 11/11 PDXs of lung cancer or melanoma without apparent toxicity in mice. Thus, gene amplification can be acquired and expanded through parallel evolution, enabling tumors to adapt while maintaining their intratumoral heterogeneity. Treatments that impose the highest fitness threshold will likely prevent the evolution of resistance-causing alterations and, thus, merit testing in patients.

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Figure 1: ERK-inhibitor-resistant populations with extrachromosomal BRAF amplification.
Figure 2: BRAFamp emerges in parallel evolutionary tracts.
Figure 3: BRAFamp is sufficient to confer a selective advantage in the presence of ERKi treatment.
Figure 4: Fitness threshold model.
Figure 5: Identification of a treatment to suppress the evolution of BRAF-amplified clones.
Figure 6: An intermittent combination treatment inhibits tumor growth in BRAFV600E PDX models for lung cancer and melanoma.

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Acknowledgements

The authors thank D. Solit, N. Bouvier and the Center for Molecular Oncology at MSKCC for assistance with next-generation sequencing, Z. Yao (MSKCC) for providing the A375 doxycycline-inducible BRAFV600E cells, as well as C. Sawyers, C. Rudin, J. Poirier and M. Mroczkowski for reviewing the manuscript. This work was supported by the US National Institutes of Health (NIH) (grant K08 CA191082-01A1; P.L.), the Uniting Against Lung Cancer Foundation (P.L.), the Damon Runyon Clinical Investigator Award (P.L.), the Josie Robertson Investigator Program at MSKCC (P.L.), the Druckenmiller Center for Lung Cancer Center at MSKCC (P.L.) and a Medical Scientist Training Program grant from the National Institute of General Medical Sciences of the NIH under award number T32GM007739 to the Weill Cornell–Rockefeller–Sloan Kettering Tri-institutional MD–PhD Program (Y.X.). E.d.S. and S.W.L. are supported in part by the MSKCC Pilot Center for Precision Disease Modeling program (U54 OD020355). T.B. is supported by the William C. and Joyce C. O'Neil Charitable Trust, Memorial Sloan Kettering Single-Cell Sequencing Initiative. J.N. is supported by the Knut and Alice Wallenberg Foundation. The authors also acknowledge the MSKCC Support Grant–Core Grant program (P30 CA008748).

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Author notes

  1. Luciano Martelotto

    Present address: School of Clinical Sciences, Monash University, Clayton, Victoria, Australia

  2. Yaohua Xue and Luciano Martelotto: These authors contributed equally to this work.

Authors and Affiliations

  1. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA

    Yaohua Xue, Alberto Vides, Martha Solomon, Trang Thi Mai, Neelam Chaudhary & Piro Lito

  2. Weill Cornell–Rockefeller–Sloan Kettering Tri-institutional MD–PhD Program, New York, New York, USA

    Yaohua Xue

  3. Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Luciano Martelotto, Michael F Berger & Jorge S Reis-Filho

  4. Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Timour Baslan & Scott W Lowe

  5. Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Greg J Riely, Bob T Li & Piro Lito

  6. NantOmics, Rockville, Maryland, USA

    Kerry Scott, Fabiola Cechhi, Sarit Schwartz & Todd Hembrough

  7. Sahlgrenska Translational Melanoma Group, Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden

    Ulrika Stierner & Jonas Nilsson

  8. Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Kalyani Chadalavada & Gouri Nanjangud

  9. Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Elisa de Stanchina

  10. Weill Cornell Medical College, Cornell University, New York, New York, USA

    Michael F Berger & Piro Lito

  11. Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Neal Rosen

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Contributions

Y.X., L.M., A.V., M.S., T.T.M. and N.C. performed experiments; L.M., T.B. and J.S.R.-F. performed, analyzed and helped interpret the single-cell sequencing experiments; M.F.B. analyzed the bulk-sequencing data; G.J.R. and B.T.L. provided the patient samples; J.N. and U.S. provided the PDX models; E.d.S. performed the animal experiments; K.S., F.C., T.H. and S.S. performed the mass spectrometry experiments; K.C. performed the FISH experiments, and G.N. analyzed the results. N.R. and S.W.L. provided key scientific insights and reagents; P.L. conceived and supervised the study, designed and performed experiments, and interpreted data; Y.X. and P.L. were the principal writers of the manuscript; and all of the authors reviewed the manuscript and contributed in writing.

Corresponding author

Correspondence to Piro Lito.

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Competing interests

P.L. is listed as an inventor on a patent application filed by MSKCC that incorporates discoveries described in the manuscript. N.R. is on the scientific advisory board, and has received grant support from, Chugai Pharmaceutical and is on the SAB of Astra-Zeneca, Beigene and Kura. S.S., T.H., K.S. and F.C. are employees of NantOmics.

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Supplementary Tables 1 and 2 and Supplementary Figures 1–7 (PDF 11679 kb)

Supplementary Dataset (XLSX 2434 kb)

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Xue, Y., Martelotto, L., Baslan, T. et al. An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer. Nat Med 23, 929–937 (2017). https://doi.org/10.1038/nm.4369

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