Re-Exploring Biomarkers and Therapeutic Targets in Primary Melanoma Patients: Insights from Network-Based Analysis of Microarray Data
ABSTRACT: Objective: To identify novel biomarkers and therapeutic targets for primary melanoma using network-based microarray data analysis. Methods: Eligible microarray datasets from the Gene Expression Omnibus (GEO) database were used to identify differentially expressed genes (DEGs). The protein...
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| Format: | Article |
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KeAi Communications Co. Ltd.
2020-12-01
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| Series: | Chinese Journal of Plastic and Reconstructive Surgery |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S209669112100042X |
| _version_ | 1811198687197528064 |
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| author | Kangjie SHEN Chuanyuan WEI Yi XIE Lu WANG Shuyu WANG Ming REN Xinyi DENG Daohe WANG Zixu GAO Zihao FENG Jianying GU |
| author_facet | Kangjie SHEN Chuanyuan WEI Yi XIE Lu WANG Shuyu WANG Ming REN Xinyi DENG Daohe WANG Zixu GAO Zihao FENG Jianying GU |
| author_sort | Kangjie SHEN |
| collection | DOAJ |
| description | ABSTRACT: Objective: To identify novel biomarkers and therapeutic targets for primary melanoma using network-based microarray data analysis. Methods: Eligible microarray datasets from the Gene Expression Omnibus (GEO) database were used to identify differentially expressed genes (DEGs). The protein-protein interaction (PPI) network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to identify hub genes and pathways that might affect the survival of melanoma patients. Immunohistochemistry results obtained from the Human Protein Atlas (HPA) database confirmed the protein expression levels of hub genes. The Cancer Genome Atlas (TCGA) database was used to further verify the gene expression levels and conduct survival analysis. Results: Three microarray datasets (GSE3189, GSE15605, and GSE46517) containing 122 melanoma and 30 normal skin tissue samples were included. A total of 262 common differentially expressed genes (cDEGs) were identified based on three statistical approaches (Fisher's method, the random effects model (REM), and vote counting) with strict criteria. Of these, two upregulated genes, centromere protein F (CENPF) and pituitary tumor-transforming gene 1 (PTTG1), were selected as hub genes. HPA and TCGA database analyses confirmed that CENPF and PTTG1 were overexpressed in melanoma. Survival analysis showed that high expression levels of CENPF were significantly correlated with decreased overall survival (OS) (P=0.028). Conclusion: The expression level of CENPF was significantly upregulated in melanoma and correlated with decreased OS. Thus, CENPF may represent a novel biomarker and therapeutic target for melanoma patients. |
| first_indexed | 2024-04-12T01:35:31Z |
| format | Article |
| id | doaj.art-af0cff4fda9b4f3987fc25f213ba67c1 |
| institution | Directory Open Access Journal |
| issn | 2096-6911 |
| language | English |
| last_indexed | 2024-04-12T01:35:31Z |
| publishDate | 2020-12-01 |
| publisher | KeAi Communications Co. Ltd. |
| record_format | Article |
| series | Chinese Journal of Plastic and Reconstructive Surgery |
| spelling | doaj.art-af0cff4fda9b4f3987fc25f213ba67c12022-12-22T03:53:20ZengKeAi Communications Co. Ltd.Chinese Journal of Plastic and Reconstructive Surgery2096-69112020-12-0124228240Re-Exploring Biomarkers and Therapeutic Targets in Primary Melanoma Patients: Insights from Network-Based Analysis of Microarray DataKangjie SHEN0Chuanyuan WEI1Yi XIE2Lu WANG3Shuyu WANG4Ming REN5Xinyi DENG6Daohe WANG7Zixu GAO8Zihao FENG9Jianying GU10Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China; The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaDepartment of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China; The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaDepartment of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, ChinaDepartment of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Department of Plastic Surgery, Xiamen Branch of Affiliated Zhongshan Hospital of Fudan University, Xiamen, Fujian 361015, China; Corresponding authors: Jianying Gu, MD, PhD & Zihao Feng, MD, Address: Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Xuhui District, Shanghai 200032, China, Tel./Fax: 021-64437963Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Department of Plastic Surgery, Xiamen Branch of Affiliated Zhongshan Hospital of Fudan University, Xiamen, Fujian 361015, China; Corresponding authors: Jianying Gu, MD, PhD & Zihao Feng, MD, Address: Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Xuhui District, Shanghai 200032, China, Tel./Fax: 021-64437963ABSTRACT: Objective: To identify novel biomarkers and therapeutic targets for primary melanoma using network-based microarray data analysis. Methods: Eligible microarray datasets from the Gene Expression Omnibus (GEO) database were used to identify differentially expressed genes (DEGs). The protein-protein interaction (PPI) network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to identify hub genes and pathways that might affect the survival of melanoma patients. Immunohistochemistry results obtained from the Human Protein Atlas (HPA) database confirmed the protein expression levels of hub genes. The Cancer Genome Atlas (TCGA) database was used to further verify the gene expression levels and conduct survival analysis. Results: Three microarray datasets (GSE3189, GSE15605, and GSE46517) containing 122 melanoma and 30 normal skin tissue samples were included. A total of 262 common differentially expressed genes (cDEGs) were identified based on three statistical approaches (Fisher's method, the random effects model (REM), and vote counting) with strict criteria. Of these, two upregulated genes, centromere protein F (CENPF) and pituitary tumor-transforming gene 1 (PTTG1), were selected as hub genes. HPA and TCGA database analyses confirmed that CENPF and PTTG1 were overexpressed in melanoma. Survival analysis showed that high expression levels of CENPF were significantly correlated with decreased overall survival (OS) (P=0.028). Conclusion: The expression level of CENPF was significantly upregulated in melanoma and correlated with decreased OS. Thus, CENPF may represent a novel biomarker and therapeutic target for melanoma patients.http://www.sciencedirect.com/science/article/pii/S209669112100042XMelanomaNetwork-based analysisMicroarrayCentromere protein FBiomarkers |
| spellingShingle | Kangjie SHEN Chuanyuan WEI Yi XIE Lu WANG Shuyu WANG Ming REN Xinyi DENG Daohe WANG Zixu GAO Zihao FENG Jianying GU Re-Exploring Biomarkers and Therapeutic Targets in Primary Melanoma Patients: Insights from Network-Based Analysis of Microarray Data Chinese Journal of Plastic and Reconstructive Surgery Melanoma Network-based analysis Microarray Centromere protein F Biomarkers |
| title | Re-Exploring Biomarkers and Therapeutic Targets in Primary Melanoma Patients: Insights from Network-Based Analysis of Microarray Data |
| title_full | Re-Exploring Biomarkers and Therapeutic Targets in Primary Melanoma Patients: Insights from Network-Based Analysis of Microarray Data |
| title_fullStr | Re-Exploring Biomarkers and Therapeutic Targets in Primary Melanoma Patients: Insights from Network-Based Analysis of Microarray Data |
| title_full_unstemmed | Re-Exploring Biomarkers and Therapeutic Targets in Primary Melanoma Patients: Insights from Network-Based Analysis of Microarray Data |
| title_short | Re-Exploring Biomarkers and Therapeutic Targets in Primary Melanoma Patients: Insights from Network-Based Analysis of Microarray Data |
| title_sort | re exploring biomarkers and therapeutic targets in primary melanoma patients insights from network based analysis of microarray data |
| topic | Melanoma Network-based analysis Microarray Centromere protein F Biomarkers |
| url | http://www.sciencedirect.com/science/article/pii/S209669112100042X |
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