In-depth genomic data analyses revealed complex transcriptional and epigenetic dysregulations of BRAFV600E in melanoma

Abstract

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.