Limits...
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.

Show MeSH

Related in: MedlinePlus

MITFand its target genes dysregulated byBRAFV600Edriver mutation in primary tumor samples. A) and B) Boxplots show the relative gene expression level (median value) in tumor samples and fold changes (absolute value) between BRAFV600E and BRAFWT samples for:1) non-MITF target genes, 2) MITF ChIP-Seq binding targets), 3) MITF induced genes, and 4) MITF ChIP-Seq binding and induced targets.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: MITFand its target genes dysregulated byBRAFV600Edriver mutation in primary tumor samples. A) and B) Boxplots show the relative gene expression level (median value) in tumor samples and fold changes (absolute value) between BRAFV600E and BRAFWT samples for:1) non-MITF target genes, 2) MITF ChIP-Seq binding targets), 3) MITF induced genes, and 4) MITF ChIP-Seq binding and induced targets.

Mentions: To further evaluate whether BRAFV600E target genes are mostly mediated by MITF, we collected 5,579 MITF target genes that were reported in a ChIP-Seq experiment and 732 MITF-induced targets inferred from a small interfering RNA (siRNA)-mediated MITF knockdown (siMITF) experiment in a melanoma cell line [41]. We found that genes targeted by MITF ChIP-Seq binding and siMITF-induced genes were more highly expressed overall than randomly selected background genes, regardless of BRAFV600E mutation status (Figure 4A, Wilcoxon test, p < 5.0 × 10−30 for all comparisons). Furthermore, a random subset of non-target genes with the same range of expression levels was selected as a background to compare to MITF ChIP-Seq binding and siMITF induced target genes, and the result showed that both MITF ChIP-Seq binding and siMITF induced targets showed a significantly higher expression change in BRAFV600E versus BRAFWT than the randomly selected background genes (Figure 4B; Wilcoxon test, p < 3.0 × 10−11 for all comparisons). These results support the conclusion that BRAFV600E leads to an increased in the level of the MITF gene, which likely subsequently results in the overall activation of many MITF target genes.Figure 4


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

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

MITFand its target genes dysregulated byBRAFV600Edriver mutation in primary tumor samples. A) and B) Boxplots show the relative gene expression level (median value) in tumor samples and fold changes (absolute value) between BRAFV600E and BRAFWT samples for:1) non-MITF target genes, 2) MITF ChIP-Seq binding targets), 3) MITF induced genes, and 4) MITF ChIP-Seq binding and induced targets.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: MITFand its target genes dysregulated byBRAFV600Edriver mutation in primary tumor samples. A) and B) Boxplots show the relative gene expression level (median value) in tumor samples and fold changes (absolute value) between BRAFV600E and BRAFWT samples for:1) non-MITF target genes, 2) MITF ChIP-Seq binding targets), 3) MITF induced genes, and 4) MITF ChIP-Seq binding and induced targets.
Mentions: To further evaluate whether BRAFV600E target genes are mostly mediated by MITF, we collected 5,579 MITF target genes that were reported in a ChIP-Seq experiment and 732 MITF-induced targets inferred from a small interfering RNA (siRNA)-mediated MITF knockdown (siMITF) experiment in a melanoma cell line [41]. We found that genes targeted by MITF ChIP-Seq binding and siMITF-induced genes were more highly expressed overall than randomly selected background genes, regardless of BRAFV600E mutation status (Figure 4A, Wilcoxon test, p < 5.0 × 10−30 for all comparisons). Furthermore, a random subset of non-target genes with the same range of expression levels was selected as a background to compare to MITF ChIP-Seq binding and siMITF induced target genes, and the result showed that both MITF ChIP-Seq binding and siMITF induced targets showed a significantly higher expression change in BRAFV600E versus BRAFWT than the randomly selected background genes (Figure 4B; Wilcoxon test, p < 3.0 × 10−11 for all comparisons). These results support the conclusion that BRAFV600E leads to an increased in the level of the MITF gene, which likely subsequently results in the overall activation of many MITF target genes.Figure 4

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