Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies.
Metastatic melanoma causes a high rate of mortality. We conducted an integrated analysis to identify critical regulators associated with the prognosis, pathogenesis, and targeted therapies of metastatic-melanoma. A microarray dataset, GSE15605, including 12 metastatic-melanoma and sixteen normal ski...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0312754 |
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| author | Zeinab Chaharlashkar Yousof Saeedi Honar Meghdad Abdollahpour-Alitappeh Sepideh Parvizpour Abolfazl Barzegar Effat Alizadeh |
| author_facet | Zeinab Chaharlashkar Yousof Saeedi Honar Meghdad Abdollahpour-Alitappeh Sepideh Parvizpour Abolfazl Barzegar Effat Alizadeh |
| author_sort | Zeinab Chaharlashkar |
| collection | DOAJ |
| description | Metastatic melanoma causes a high rate of mortality. We conducted an integrated analysis to identify critical regulators associated with the prognosis, pathogenesis, and targeted therapies of metastatic-melanoma. A microarray dataset, GSE15605, including 12 metastatic-melanoma and sixteen normal skin (NS) samples, were obtained from the GEO database. After exploration of DEGs of NS and metastatic-melanoma, identification of relevant transcription factors (TFs) and kinases, the Gene Ontology (GO), and pathways analyses of DEGs were performed. Protein-protein interaction (PPI) networks were evaluated by the STRING and Cytoscape. Subsequently, the hub genes were selected using GEPIA. Survival analysis was performed using the TCGA. To identify microRNA and lncRNA DEGs of the melanoma-associated genes miRwalk and FANTOM6 were employed. In metastatic-melanoma samples 285 and 1173 genes were up and down-regulated, respectively. The upregulated genes were mostly involved in granulocyte chemotaxis, positive regulation of calcium ion transmembrane transport, and melanin biosynthetic process. Five hub genes including CXCL11, ICAM1, LEF1, MITF, and STAT1 were identified, SUZ12, SOX2, TCF3, NANOG, and SMAD4 were determined as the most significant TFs in metastatic-melanoma. Furthermore, CDK2, GSK3B, CSNK2A1, and CDK1 target the highest amounts of genes associated with disease. The DGIdb analysis results show the match drugs for five hub genes. MiRNAs analysis revealed hsa-miR-181c-5p, hsa-miR-30b-3p, hsa-miR-3680-3P, hsa-miR-4659a-3p, hsa-miR-4687-3P, and hsa-miR-6808-3P could regulate the hub genes, whereas RP11-553K8.5 and SRP14-AS1 were identified as the top significant lncRNA. The items recognized in the current study can be used as potential biomarkers for diagnostic, predictive, and might helpful to develop targeted combined therapies. |
| format | Article |
| id | doaj-art-28f7f476e1d74a73b4dacd5e69aaed25 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-28f7f476e1d74a73b4dacd5e69aaed252025-02-05T05:31:22ZengPublic Library of Science (PLoS)PLoS ONE1932-62032025-01-01201e031275410.1371/journal.pone.0312754Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies.Zeinab ChaharlashkarYousof Saeedi HonarMeghdad Abdollahpour-AlitappehSepideh ParvizpourAbolfazl BarzegarEffat AlizadehMetastatic melanoma causes a high rate of mortality. We conducted an integrated analysis to identify critical regulators associated with the prognosis, pathogenesis, and targeted therapies of metastatic-melanoma. A microarray dataset, GSE15605, including 12 metastatic-melanoma and sixteen normal skin (NS) samples, were obtained from the GEO database. After exploration of DEGs of NS and metastatic-melanoma, identification of relevant transcription factors (TFs) and kinases, the Gene Ontology (GO), and pathways analyses of DEGs were performed. Protein-protein interaction (PPI) networks were evaluated by the STRING and Cytoscape. Subsequently, the hub genes were selected using GEPIA. Survival analysis was performed using the TCGA. To identify microRNA and lncRNA DEGs of the melanoma-associated genes miRwalk and FANTOM6 were employed. In metastatic-melanoma samples 285 and 1173 genes were up and down-regulated, respectively. The upregulated genes were mostly involved in granulocyte chemotaxis, positive regulation of calcium ion transmembrane transport, and melanin biosynthetic process. Five hub genes including CXCL11, ICAM1, LEF1, MITF, and STAT1 were identified, SUZ12, SOX2, TCF3, NANOG, and SMAD4 were determined as the most significant TFs in metastatic-melanoma. Furthermore, CDK2, GSK3B, CSNK2A1, and CDK1 target the highest amounts of genes associated with disease. The DGIdb analysis results show the match drugs for five hub genes. MiRNAs analysis revealed hsa-miR-181c-5p, hsa-miR-30b-3p, hsa-miR-3680-3P, hsa-miR-4659a-3p, hsa-miR-4687-3P, and hsa-miR-6808-3P could regulate the hub genes, whereas RP11-553K8.5 and SRP14-AS1 were identified as the top significant lncRNA. The items recognized in the current study can be used as potential biomarkers for diagnostic, predictive, and might helpful to develop targeted combined therapies.https://doi.org/10.1371/journal.pone.0312754 |
| spellingShingle | Zeinab Chaharlashkar Yousof Saeedi Honar Meghdad Abdollahpour-Alitappeh Sepideh Parvizpour Abolfazl Barzegar Effat Alizadeh Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies. PLoS ONE |
| title | Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies. |
| title_full | Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies. |
| title_fullStr | Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies. |
| title_full_unstemmed | Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies. |
| title_short | Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies. |
| title_sort | metastatic melanoma an integrated analysis to identify critical regulators associated with prognosis pathogenesis and targeted therapies |
| url | https://doi.org/10.1371/journal.pone.0312754 |
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