Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma

Abstract

Systematic analyses of cancer genomes promise to unveil patterns of genetic alterations linked to the genesis and spread of human cancers. High-density single-nucleotide polymorphism (SNP) arrays enable detailed and genome-wide identification of both loss-of-heterozygosity events and copy-number alterations in cancer. Here, by integrating SNP array-based genetic maps with gene expression signatures derived from NCI60 cell lines, we identified the melanocyte master regulator MITF (microphthalmia-associated transcription factor) as the target of a novel melanoma amplification. We found that MITF amplification was more prevalent in metastatic disease and correlated with decreased overall patient survival. BRAF mutation and p16 inactivation accompanied MITF amplification in melanoma cell lines. Ectopic MITF expression in conjunction with the BRAF(V600E) mutant transformed primary human melanocytes, and thus MITF can function as a melanoma oncogene. Reduction of MITF activity sensitizes melanoma cells to chemotherapeutic agents. Targeting MITF in combination with BRAF or cyclin-dependent kinase inhibitors may offer a rational therapeutic avenue into melanoma, a highly chemotherapy-resistant neoplasm. Together, these data suggest that MITF represents a distinct class of 'lineage survival' or 'lineage addiction' oncogenes required for both tissue-specific cancer development and tumour progression.

Palmitoylation-dependent activation of MC1R prevents melanomagenesis

“…The clonogenic survival and soft agar assays for hTERT/p53DD/CDK4(R24C)/BRAF V600E melanocytes were performed as described previously 26 . Briefly, for the melanocyte growth promoting withdrawal experiments, hTERT/p53DD/CDK4(R24C)/BRAF V600E melanocytes were treated with 20 J/m 2 UVB in the presence of 1 μM α-MSH before plating into 6-well plate at 1,000 cells per well, and then subject to clonogenic survival assays 15 days after UVR.…”

“…In vivo tumorigenesis assay of hTERT/p53DD/CDK4(R24C)/BRAF V600E melanocytes was performed as described previously 26 . Briefly, 3×10 6 melanocytes were mixed with matrigel (1:1) and injected subcutaneously into the flanks of male nude mice.…”

“…4f). Using engineered human immortal melanocytes (hTERT/p53DD/CDK4(R24C) melanocytes) 25,26 in colony formation and soft agar growth assays we found that BRAF V600E -mediated cellular transformation was suppressed by WT MC1R, but not the C315S mutant, while the R151C and R160W variants exhibited an intermediate phenotype (Fig. 3a, Extended Data Fig.…”

“…Soft agar and colony formation assays using the human hTERT/p53DD/CDK4(R24C) melanocytes 25,26 revealed that ZDHHC13 depletion increased transformation by BRAF V600E in the presence of WT MC1R, whereas enhanced transformation by the R151C mutant was suppressed by ZDHHC13 overexpression (Fig. 3b, Extended Data Fig.…”

Molecular heterogeneity of TFE3 activation in renal cell carcinomas

“…Gain of function of these genes has been associated with different tumour entities such as malignant melanomas, clear cell sarcoma and renal cell carcinomas. 8,9 In addition to renal cell carcinomas, translocations of TFE3 have also been identified in alveolar soft part sarcoma and a subset of perivascular epithelioid cell neoplasms (PEComas). 10,11 The biological behaviour of Xp11 translocation renal cell carcinomas has recently been documented in children and young adults, poor clinical outcome and early metastasis have been reported.…”