Putative genomic characteristics of BRAF V600K versus V600E cutaneous melanoma

Abstract

Approximately 50% of all cutaneous melanomas harbor activating BRAF V600 mutations; among, these 10-30% carry the V600K mutation. Clinically, patients with V600K tumors experience distant metastases sooner and have an increased risk of relapse and shorter survival than patients with V600E tumors. Despite the clinical and other histopathological differences between these BRAF tumor subtypes, little is known about them at the genomic level. Herein, we systematically compared BRAF V600E and V600K skin cutaneous melanoma (SKCM) samples from the Cancer Genome Atlas (TCGA) for differential protein, gene, and microRNA expression genome-wide using the Mann-Whitney U-test. Our analyses showed that elements of energy-metabolism and protein-translation pathways were upregulated and that proapoptotic pathways were downregulated in V600K tumors compared with V600E tumors. We found that c-Kit protein and KIT gene expressions were significantly higher in V600K tumors than in V600E tumors, concurrent with significant downregulation of several KIT-targeting microRNAs (mir) including mir-222 in V600K tumors, suggesting KIT and mir-222 might be key genomic contributors toward the clinical differences observed. The relationship that we uncovered among KIT/c-Kit expression, mir-222 expression, and growth and prosurvival signals in V600 tumors is intriguing. We believe that the observed clinical aggressiveness of V600K tumors compared to V600E tumors may be attributable to the increased energy metabolism, protein translation and prosurvival signals compared with V600E tumors. If confirmed using larger numbers of V600K tumors, our results may prove useful for designing clinical management and targeted chemotherapeutical interventions for BRAF V600K-positive melanomas. Finally, the small sample size in V600K tumors is a major limitation of our study.

Figure 1

Fitted survival probabilities as function of days after diagnosis based on Cox regression model for two SKCM subtypes: BRAF V600K and V600E. Circles indicate censored patients. The plots are based on 13 subjects with V600K tumors and 106 with V600E tumors. The apparent difference between survival curves was not statistically significant (p=0.39).

Figure 2

Boxplots of expression levels of selected differentially expressed proteins between V600K and V600E tumors. The protein expression data were taken from TCGA RPPA analysis without further standardization and transformation.

Figure 3

Boxplots of expression levels of mTOR_pS2448-R-C protein between V600K and V600E tumors. The protein expression data were taken from TCGA RPPA analysis without further standardization and transformation.

Figure 4

Boxplots of mir-222 expression levels across two SKCM BRAF tumor subtypes defined by TCGA melanoma working group. The numbers of microRNA-seq samples for V600K and V600E subtypes were 17 and 121, respectively.

Figure 5

Boxplots of c-Kit protein (top) and KIT gene (bottom) expression across the two SKCM mutation subtypes (BRAF V600E and V600K) defined by TCGA melanoma working group. The numbers samples for V600K and V600E, respectively, were 13 and 91 for RPPA; and 17 and 124 for RNA-seq. Both RNA-seq and RPPA (protein expression) data were normalized by TCGA; we subsequently applied a log₂-transformation to the RNA-seq data before analysis.

Figure 6

Scatter plots of KIT and mir-222 expression in all SKCM tumors (top) and BRAF V600K only SKCM tumors (bottom). The red lines are the least-squares fits. In this Figure, we first identified matching RNA-seq and miRNA-seq samples and extracted KIT expression and mir-222 expression respectively.