Editors' ChoiceCancer

Omic profiling of melanoma evolution

Sci. Signal.  06 Oct 2015:
Vol. 8, Issue 397, pp. ec285
DOI: 10.1126/scisignal.aad5259

Melanomas acquire resistance to MAPKi, which are various drugs that inhibit individual enzymes in the mitogen-activated protein kinase (MAPK) pathway. To understand the development of drug resistance, Hugo et al. performed whole-exome sequencing (WES), transcriptomic analysis, and analysis of the methylation status of DNA (methylomic analyses) on biopsies from patients with melanomas prior to drug therapy, after single-drug therapy with a MAPKi targeting the MAPK kinase BRAF, double-drug therapy with a MAPKi targeting BRAF and a MAPKi targeting the MAPK kinase MEK, and as the disease progressed. WES analysis revealed that the two most frequently occurring genetic mutations to MAPKi-resistant melanomas were amplifications of BRAF encoding the BRAFV600E/K mutant and RAS. However, not all of the drug-resistant melanomas exhibited these genetic changes. Transcriptomic profiling of the biopsies showed enrichment of 855 genes with significantly altered expression prior to therapy, after therapy, and after the recurrence of disease. Unexpectedly, many of the genes with altered expression were classified as related to the immune system or immune response; in particular the drug-resistant melanomas exhibited altered expression of genes associated with inflammation, monocyte function, and T cell function. The transcriptomic data indicated that the MAPKi-resistant melanomas may have fewer CD8+ T cells, which could be an indication that the melanomas were evading the immune system after drug treatment. Epigenetic chromatin modifications may underlie some of the differences in gene expression, because there was a positive correlation between differential genomic CpG methylation and mRNA abundance for a subset of the genes with altered expression. In particular, decreased CpG methylation was associated with increased abundance of the transcript for the hepatocyte growth factor receptor c-MET, whereas increased CpG methylation was associated with decreased abundance of the transcript for the transcription factor and β-catenin–binding partner LEF1. To verify the involvement of increased c-MET signaling and decreased LEF1-dependent transcription on MAPKi resistance, the authors examined how altering these two processes in MAPKi-resistant subclones of M229 and SKMEL28 melanoma cell lines, which have the BRAFV600E mutation, affected the response to MAPKi. Increased c-MET abundance in these MAPKi-resistant cell lines correlated with increased phosphorylation of the kinase AKT, which is part of a MAPK-independent survival pathway. Analysis of growth in a clonogenic assay indicated that knocking down c-MET reduced the growth of a subpopulation of the MAPKi-resistant cell lines, and application of the c-MET ligand enhanced the clonogenic survival of the MAPKi-resistant cells in the presence of the MAPKi, but did not enhance survival of the parental cell lines. Compared with the parental cell lines, a panel of MAPKi-resistant cells had decreased abundance of both LEF1 mRNA and LEF1 protein. In addition, expression of LEF1-related pathway genes was decreased, suggesting reduced signaling through the Wnt–β-catenin pathway. Consistent with reduced β-catenin signaling leading MAPKi resistance, exposure of MAPKi-resistant cell lines to an inhibitor of the kinase glycogen synthase kinase β (GSK-3β)—the kinase responsible for destabilizing cytosolic β-catenin—to increase the transcriptional-regulating activity of β-catenin resensitized the cells to MAPKi, and overexpression of LEF1 in the presence of GSK-3β inhibition further sensitized the cells to MAPKi.

Although the transcriptional regulator YAP1 was not identified as affected at the genetic, epigenetic, or transcriptional level in the melanoma patient samples, the gene signature of this transcriptional regulator was enriched in the MAPKi-resistant tumors and cell lines, suggesting a posttranscriptional change in YAP1 activity contributed to resistance. Indeed, the abundance of YAP1 and phosphorylated YAP1 was increased in MAPKi-resistant cell lines. YAP1 knockdown resensitized the MAPKi-resistant cell lines to MAPKi. Additionally, individually YAP1 knockdown and GSK-3β inhibition increased the abundance of a marker of apoptosis, and combined reduction in YAP1 and enhanced β-catenin signaling produced an even stronger increase in this apoptotic marker. This study provides insight into the diverse mechanisms by which melanoma becomes resistant to MAPKi and implies that changes not only in the melanoma cells but also in the immune system may contribute to the progression of this disease.

W. Hugo, H. Shi, L. Sun, M. Piva, C. Song, X. Kong, G. Moriceau, A. Hong, K. B. Dahlman, D. B, Johnson, J. A. Sosman, A. Ribas, R. S. Lo, Non-genomic and immune evolution of melanoma acquiring MAPKi resistance. Cell 162, 1271–1285 (2015). [PubMed]