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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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Functional analysis ofBRAFV600Etarget genes identified in primary tumor samples. A) Heat-map showing the differential signals for BRAFV600E target genes identified by Snowball approach. B) Enriched functional categories of the BRAFV600E target genes. * refers to genes in CGC catalogue.
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Fig2: Functional analysis ofBRAFV600Etarget genes identified in primary tumor samples. A) Heat-map showing the differential signals for BRAFV600E target genes identified by Snowball approach. B) Enriched functional categories of the BRAFV600E target genes. * refers to genes in CGC catalogue.

Mentions: To identify the genes and related pathways perturbed by BRAFV600E, we developed a novel statistical approach, named Snowball, to identify differentially expressed genes based on their aggregated association between co-expression patterns and BRAFV600E mutation status. We identified the regulatory network modules that were significantly associated with BRAFV600E with a permutation p < 0.05, followed by a Weighted Gene Co-expression Network analysis (see Materials and methods, Figure 1A) [21]. As a result, a total of 711 putative target genes were identified including 330 down-regulated and 381 up-regulated genes (Additional file 1). Figure 2A shows a heat-map of expression patterns in the BRAFV600E and BRAFWT samples for those significantly associated genes identified by Snowball.Figure 1


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

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

Functional analysis ofBRAFV600Etarget genes identified in primary tumor samples. A) Heat-map showing the differential signals for BRAFV600E target genes identified by Snowball approach. B) Enriched functional categories of the BRAFV600E target genes. * refers to genes in CGC catalogue.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Functional analysis ofBRAFV600Etarget genes identified in primary tumor samples. A) Heat-map showing the differential signals for BRAFV600E target genes identified by Snowball approach. B) Enriched functional categories of the BRAFV600E target genes. * refers to genes in CGC catalogue.
Mentions: To identify the genes and related pathways perturbed by BRAFV600E, we developed a novel statistical approach, named Snowball, to identify differentially expressed genes based on their aggregated association between co-expression patterns and BRAFV600E mutation status. We identified the regulatory network modules that were significantly associated with BRAFV600E with a permutation p < 0.05, followed by a Weighted Gene Co-expression Network analysis (see Materials and methods, Figure 1A) [21]. As a result, a total of 711 putative target genes were identified including 330 down-regulated and 381 up-regulated genes (Additional file 1). Figure 2A shows a heat-map of expression patterns in the BRAFV600E and BRAFWT samples for those significantly associated genes identified by Snowball.Figure 1

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