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Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C

Oncogene volume 37, pages 2444–2455 (2018)Cite this article

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Abstract

Activating mutations in RAS genes are associated with approximately 20% of all human cancers. New targeted therapies show preclinical promise in inhibiting the KRAS G12C variant. However, concerns exist regarding the effectiveness of such therapies in vivo given the possibilities of existing intratumor heterogeneity or de novo mutation leading to treatment resistance. We performed deep sequencing of 27 KRAS G12-positive lung tumors to determine the prevalence of other oncogenic mutations within KRAS or within commonly mutated downstream genes that could confer resistance at the time of treatment. We also passaged patient-derived xenografts to assess the potential for novel KRAS mutation to arise during subsequent tumor evolution. Furthermore, we estimate the de novo mutation rate in KRAS position 12 and in genes downstream of KRAS. Finally, we present an approach for estimation of the selection intensity for these point mutations that explains their high prevalence in tumors. We find no evidence of heterogeneity that may compromise KRAS G12C targeted therapy within sequenced lung tumors or passaged xenografts. We find that mutations that confer resistance are even less likely to occur downstream of KRAS than to occur within KRAS. Our approach predicts that BRAF V600E would provide the highest fitness advantage for de novo-resistant subclones. Overall, our findings suggest that resistance to targeted therapy of KRAS G12C-positive tumors is unlikely to be present at the time of treatment and, among the de novo mutations likely to confer resistance, mutations in BRAF, a gene with targeted inhibitors presently available, result in subclones with the highest fitness advantage.

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This work was partially funded by Gilead Sciences, Inc.

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Authors and Affiliations

  1. Department of Biostatistics, Yale University, New Haven, CT, USA

    Vincent L. Cannataro, Stephen G. Gaffney, Carly Stender, Zi-Ming Zhao & Jeffrey P. Townsend

  2. Departments of Medicine, Cell Biology, and Pharmacology, New York University School of Medicine, New York, NY, USA

    Mark Philips

  3. Gilead Sciences, Foster City, CA, USA

    Andrew E. Greenstein

  4. Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA

    Jeffrey P. Townsend

  5. Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA

    Jeffrey P. Townsend

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  1. Vincent L. Cannataro
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Correspondence to Jeffrey P. Townsend.

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Cannataro, V.L., Gaffney, S.G., Stender, C. et al. Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C. Oncogene 37, 2444–2455 (2018). https://doi.org/10.1038/s41388-017-0105-z

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