Abstract
BackgroundPrimary cutaneous malignant melanoma is a cancer of the pigment cells of the skin, some of which are accompanied by BRAF mutation. Melanoma incidence and mortality rates have been rising around the world. As the current knowledge about pathogenesis, clinical and genetic features of cutaneous melanoma is not very clear, we aim to use bioinformatics to identify the potential key genes involved in the expression and mutation status of BRAF.MethodsFirstly, we used UCSC public hub datasets of melanoma (Lin et al., Cancer Res 68(3):664, 2008) to perform weighted genes co-expression network analysis (WGCNA) and differentially expressed genes analysis (DEGs), respectively. Secondly, overlapping genes between significant gene modules and DEGs were screened and validated at transcriptional levels and overall survival in TCGA and GTEx datasets. Lastly, the functional enrichment analysis was accomplished to find biological functions on the web-server database.ResultsWe performed weighted correlation network and differential expression analyses, using gene expression data in melanoma samples. We identified 20 genes whose expression was correlated with the mutation status of BRAF. For further validation, three of these genes (CYR61, DUSP1, and RNASE4) were found to have similar expression patterns in skin tumors from TCGA compared with normal skin samples from GTEx. We also found that weak expression of these three genes was associated with worse overall survival in the TCGA data. These three genes were involved in the nucleic acid metabolic process.ConclusionIn this study, CYR61, DUSP1, and RNASE4 were identified as potential genes of interest for future molecular studies in melanoma, which would improve our understanding of its causes and underlying molecular events. These candidate genes may provide a promising avenue of future research for therapeutic targets in melanoma.
Highlights
Primary cutaneous malignant melanoma is a cancer of the pigment cells of the skin, some of which are accompanied by B-Raf proto-oncogene (BRAF) mutation
Skin cutaneous melanoma (SKCM) is a malignant cancer that originates from melanocytes and exists in different forms
It was clear that the MEbrown (1021 genes) was most positive associated with the expression of BRAF (Fig. 4a)
Summary
Primary cutaneous malignant melanoma is a cancer of the pigment cells of the skin, some of which are accompanied by BRAF mutation. As the current knowledge about pathogenesis, clinical and genetic features of cutaneous melanoma is not very clear, we aim to use bioinformatics to identify the potential key genes involved in the expression and mutation status of BRAF. Skin cutaneous melanoma (SKCM) is a malignant cancer that originates from melanocytes and exists in different forms. Melanoma is the most dangerous type of skin cancer. The primary cause of melanoma is ultraviolet light (UV) exposure in those with low levels of skin pigment [1, 2]. About 25 % of melanoma derives from moles Those with many moles, a history of affected family members, and who have poor immune function were at greater risk [2]. Diagnosis can be finished by biopsy of any concerning skin lesion [2]
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