In-depth genomic data analyses revealed complex transcriptional and epigenetic dysregulations of BRAF(V600E) in melanoma

BACKGROUND: The recurrent BRAF driver mutation V600E (BRAF(V600E)) is currently one of the most clinically relevant mutations in melanoma. However, the genome-wide transcriptional and epigenetic dysregulations induced by BRAF(V600E) are still unclear. The investigation of this driver mutation’s functional consequences is critical to the understanding of tumorigenesis and the development of therapeutic strategies. METHODS AND RESULTS: We performed an integrative analysis of transcriptomic and epigenomic changes disturbed by BRAF(V600E) by comparing the gene expression and methylation profiles of 34 primary cutaneous melanoma tumors harboring BRAF(V600E) with those of 27 BRAF(WT) samples available from The Cancer Genome Atlas (TCGA). A total of 711 significantly differentially expressed genes were identified as putative BRAF(V600E) target genes. Functional enrichment analyses revealed the transcription factor MITF (p < 3.6 × 10(−16)) and growth factor TGFB1 (p < 3.1 × 10(−9)) were the most significantly enriched up-regulators, with MITF being significantly up-regulated, whereas TGFB1 was significantly down-regulated in BRAF(V600E), suggesting that they may mediate tumorigenesis driven by BRAF(V600E). Further investigation using the MITF ChIP-Seq data confirmed that BRAF(V600E) led to an overall increased level of gene expression for the MITF targets. Furthermore, DNA methylation analysis revealed a global DNA methylation loss in BRAF(V600E) relative to BRAF(WT). This might be due to BRAF dysregulation of DNMT3A, which was identified as a potential target with significant down-regulation in BRAF(V600E). Finally, we demonstrated that BRAF(V600E) targets may play essential functional roles in cell growth and proliferation, measured by their effects on melanoma tumor growth using a short hairpin RNA silencing experimental dataset. CONCLUSIONS: Our integrative analysis identified a set of BRAF(V600E) target genes. Further analyses suggested a complex mechanism driven by mutation BRAF(V600E) on melanoma tumorigenesis that disturbs specific cancer-related genes, pathways, and methylation modifications. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12943-015-0328-y) contains supplementary material, which is available to authorized users.