Non-genomic and Immune Evolution of Melanoma Acquiring MAPKi Resistance

Willy Hugo, Hubing Shi, Lu Sun, Marco Piva, Chunying Song, Xiangju Kong, Gatien Moriceau, Aayoung Hong, Kimberly B. Dahlman, Douglas B. Johnson, Jeffrey A. Sosman, Antoni Ribas, Roger S. Lo*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

299 Scopus citations

Abstract

Summary Clinically acquired resistance to MAPK inhibitor (MAPKi) therapies for melanoma cannot be fully explained by genomic mechanisms and may be accompanied by co-evolution of intra-tumoral immunity. We sought to discover non-genomic mechanisms of acquired resistance and dynamic immune compositions by a comparative, transcriptomic-methylomic analysis of patient-matched melanoma tumors biopsied before therapy and during disease progression. Transcriptomic alterations across resistant tumors were highly recurrent, in contrast to mutations, and were frequently correlated with differential methylation of tumor cell-intrinsic CpG sites. We identified in the tumor cell compartment supra-physiologic c-MET up-expression, infra-physiologic LEF1 down-expression and YAP1 signature enrichment as drivers of acquired resistance. Importantly, high intra-tumoral cytolytic T cell inflammation prior to MAPKi therapy preceded CD8 T cell deficiency/exhaustion and loss of antigen presentation in half of disease-progressive melanomas, suggesting cross-resistance to salvage anti-PD-1/PD-L1 immunotherapy. Thus, melanoma acquires MAPKi resistance with highly dynamic and recurrent non-genomic alterations and co-evolving intra-tumoral immunity.

Original languageEnglish (US)
Pages (from-to)1271-1285
Number of pages15
JournalCell
Volume162
Issue number6
DOIs
StatePublished - Sep 10 2015

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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