Leveraging transcriptional dynamics to improve BRAF inhibitor responses in melanoma

Inna Smalley, Eunjung Kim, Jiannong Li, Paige Spence, Clayton J. Wyatt, Zeynep Eroglu, Vernon K. Sondak, Jane L. Messina, Nalan Akgul Babacan, Silvya Stuchi Maria-Engler, Lesley De Armas, Sion L. Williams, Robert A. Gatenby, Y. Ann Chen, Alexander R.A. Anderson, Keiran S.M. Smalley

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Background: Melanoma is a heterogeneous tumour, but the impact of this heterogeneity upon therapeutic response is not well understood. Methods: Single cell mRNA analysis was used to define the transcriptional heterogeneity of melanoma and its dynamic response to BRAF inhibitor therapy and treatment holidays. Discrete transcriptional states were defined in cell lines and melanoma patient specimens that predicted initial sensitivity to BRAF inhibition and the potential for effective re-challenge following resistance. A mathematical model was developed to maintain competition between the drug-sensitive and resistant states, which was validated in vivo. Findings: Our analyses showed melanoma cell lines and patient specimens to be composed of >3 transcriptionally distinct states. The cell state composition was dynamically regulated in response to BRAF inhibitor therapy and drug holidays. Transcriptional state composition predicted for therapy response. The differences in fitness between the different transcriptional states were leveraged to develop a mathematical model that optimized therapy schedules to retain the drug sensitive population. In vivo validation demonstrated that the personalized adaptive dosing schedules outperformed continuous or fixed intermittent BRAF inhibitor schedules. Interpretation: Our study provides the first evidence that transcriptional heterogeneity at the single cell level predicts for initial BRAF inhibitor sensitivity. We further demonstrate that manipulating transcriptional heterogeneity through personalized adaptive therapy schedules can delay the time to resistance. Funding: This work was funded by the National Institutes of Health. The funder played no role in assembly of the manuscript.

Original languageEnglish (US)
Pages (from-to)178-190
Number of pages13
JournalEBioMedicine
Volume48
DOIs
StatePublished - Oct 2019

Keywords

  • Heterogeneity
  • MITF
  • Mathematical modelling
  • Melanoma
  • Resistance

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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  • Cite this

    Smalley, I., Kim, E., Li, J., Spence, P., Wyatt, C. J., Eroglu, Z., Sondak, V. K., Messina, J. L., Babacan, N. A., Maria-Engler, S. S., De Armas, L., Williams, S. L., Gatenby, R. A., Chen, Y. A., Anderson, A. R. A., & Smalley, K. S. M. (2019). Leveraging transcriptional dynamics to improve BRAF inhibitor responses in melanoma. EBioMedicine, 48, 178-190. https://doi.org/10.1016/j.ebiom.2019.09.023