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

Guo X, Xu Y, Zhao Z - Mol. Cancer (2015)

Bottom Line: 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.Further analyses suggested a complex mechanism driven by mutation BRAF (V600E) on melanoma tumorigenesis that disturbs specific cancer-related genes, pathways, and methylation modifications.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA. xingyi.guo@vanderbilt.edu.

ABSTRACT

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.

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Boxplot of gene expression fold changes (absolute value) on A375 melanoma cells before and after the treatment of vemurafenib, for Snowball identifiedBRAFV600Etargets from both TCGA primary and metastatic tumour samples, MITF targets from literature and control genes. P value for each comparison was derived from Wilcoxon test.
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Fig5: Boxplot of gene expression fold changes (absolute value) on A375 melanoma cells before and after the treatment of vemurafenib, for Snowball identifiedBRAFV600Etargets from both TCGA primary and metastatic tumour samples, MITF targets from literature and control genes. P value for each comparison was derived from Wilcoxon test.

Mentions: To further evaluate the identified BRAFV600E regulated genes, we analyzed a publicly available gene expression dataset of A375 melanoma cells that harbor the BRAFV600E mutation. This dataset contains the gene expression profiles before and after treatment with BRAF inhibitor vemurafenib (RAFi) [42]. Interestingly, we found that BRAFV600E regulated genes identified by Snowball from both the TCGA primary and metastasis tumor samples as well as the MTIF ChIP-Seq targets [41] showed a significant response when compared to randomly selected control genes (Figure 5). This suggested that BRAFV600E regulated genes identified by Snowball are highly reliable and BRAFV600E may regulate MITF targets likely mediated via MITF.Figure 5


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

Guo X, Xu Y, Zhao Z - Mol. Cancer (2015)

Boxplot of gene expression fold changes (absolute value) on A375 melanoma cells before and after the treatment of vemurafenib, for Snowball identifiedBRAFV600Etargets from both TCGA primary and metastatic tumour samples, MITF targets from literature and control genes. P value for each comparison was derived from Wilcoxon test.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4373107&req=5

Fig5: Boxplot of gene expression fold changes (absolute value) on A375 melanoma cells before and after the treatment of vemurafenib, for Snowball identifiedBRAFV600Etargets from both TCGA primary and metastatic tumour samples, MITF targets from literature and control genes. P value for each comparison was derived from Wilcoxon test.
Mentions: To further evaluate the identified BRAFV600E regulated genes, we analyzed a publicly available gene expression dataset of A375 melanoma cells that harbor the BRAFV600E mutation. This dataset contains the gene expression profiles before and after treatment with BRAF inhibitor vemurafenib (RAFi) [42]. Interestingly, we found that BRAFV600E regulated genes identified by Snowball from both the TCGA primary and metastasis tumor samples as well as the MTIF ChIP-Seq targets [41] showed a significant response when compared to randomly selected control genes (Figure 5). This suggested that BRAFV600E regulated genes identified by Snowball are highly reliable and BRAFV600E may regulate MITF targets likely mediated via MITF.Figure 5

Bottom Line: 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.Further analyses suggested a complex mechanism driven by mutation BRAF (V600E) on melanoma tumorigenesis that disturbs specific cancer-related genes, pathways, and methylation modifications.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA. xingyi.guo@vanderbilt.edu.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus