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Published on: March 30, 2019
Bioinformatics analysis to identify the critical genes, microRNAs and long noncoding RNAs in melanoma
Qian Zhang1, Yang Wang, Jiulong Liang
1Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, Shenyang, Liaoning, China.
Abstract:
Melanoma, which is usually induced by ultraviolet light exposure and the following DNA damage, is the most dangerous skin cancer. The purpose of the present study was to screen key molecules involved in melanoma.Microarray data of E-MTAB-1862 were downloaded from the ArrayExpress database, which included 21 primary melanoma samples and 11 benign nevus samples. In addition, the RNASeq version 2 and microRNA (miRNA) sequencing data of cutaneous melanoma were downloaded from The Cancer Genome Atlas database. After identifying the differentially expressed genes (DEGs) using Limma package, enrichment analysis and protein-protein interaction (PPI) network analysis were performed separately for them using DAVID software and Cytoscape software. In addition, survival analysis and regulatory network analysis were further performed by log-rank test and Cytoscape software, respectively. Moreover, real-time reverse transcription polymerase chain reaction (RT-PCR) was performed to further verify the expression patterns of several selected DEGs.A total of 382 DEGs were identified in primary melanoma samples, including 206 upregulated genes and 176 downregulated genes. Functional enrichment analysis showed that COL17A1 was enriched in epidermis development. In the PPI network, CXCL8 (degree = 29) and STAT1 (degree = 28) had higher degrees and could interact with each other. Survival analysis showed that 21 DEGs, 55 long noncoding RNAs (lncRNAs) and 32 miRNAs were found to be associated with prognosis. Furthermore, several regulatory relationships were found in the lncRNA-gene regulatory network (such as RP11-361L15.4 targeting COL17A1) and the miRNA-gene regulatory network (such as hsa-miR-375 targeting CCL27 and hsa-miR-375 targeting insulin-like growth factor 1 receptor [IGF1R]). Real-time RT-PCR results showed that the overall direction of differential expression was consistent except COL17A1.CXCL8 interacted with STAT1, CCL27, and IGF1R targeted by hsa-miR-375, and COL17A1 targeted by RP11-361L15.4 might function in the development and progression of melanoma, which should be verified by more detailed experiments.
Insights
This study identifies key molecules like CXCL8 and STAT1 involved in melanoma development. It highlights potential regulatory networks, including microRNA targeting of CCL27 and IGF1R, crucial for understanding skin cancer progression.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Melanoma, a dangerous skin cancer, is often caused by ultraviolet light exposure and subsequent DNA damage.
- Identifying key molecular players is crucial for understanding melanoma pathogenesis and developing targeted therapies.
Purpose of the Study:
- To screen and identify key molecules and regulatory networks involved in melanoma development and progression.
- To analyze differentially expressed genes (DEGs), long noncoding RNAs (lncRNAs), and microRNAs (miRNAs) in melanoma samples.
Main Methods:
- Downloaded and analyzed microarray, RNA-Seq, and miRNA sequencing data from public databases (ArrayExpress, The Cancer Genome Atlas).
- Utilized Limma for DEG identification, DAVID and Cytoscape for enrichment and protein-protein interaction (PPI) network analysis.
- Performed survival analysis, regulatory network analysis, and real-time reverse transcription polymerase chain reaction (RT-PCR) for validation.
Main Results:
- Identified 382 DEGs (206 upregulated, 176 downregulated) in primary melanoma samples.
- CXCL8 and STAT1 emerged as key interacting molecules in the PPI network.
- Discovered prognostic associations for 21 DEGs, 55 lncRNAs, and 32 miRNAs, along with regulatory networks involving lncRNAs and miRNAs (e.g., hsa-miR-375 targeting CCL27 and IGF1R).
Conclusions:
- CXCL8-STAT1 interaction and hsa-miR-375-mediated targeting of CCL27 and IGF1R are potentially significant in melanoma.
- The lncRNA RP11-361L15.4 targeting COL17A1 may also play a role in melanoma development.
- Further experimental validation is warranted to confirm the functional roles of these identified molecules and networks in melanoma.
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