Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma
Background Lung squamous cell carcinoma (LUSC) is a major subtype of lung cancer with limited therapeutic options and poor clinical prognosis. Methods Three datasets (GSE19188, GSE33532 and GSE33479) were obtained from the gene expression omnibus (GEO) database. Differentially expressed genes (DEGs)...
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PeerJ Inc.
2020-05-01
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| author | Xiaohan Ma Huijun Ren Ruoyu Peng Yi Li Liang Ming |
| author_facet | Xiaohan Ma Huijun Ren Ruoyu Peng Yi Li Liang Ming |
| author_sort | Xiaohan Ma |
| collection | DOAJ |
| description | Background Lung squamous cell carcinoma (LUSC) is a major subtype of lung cancer with limited therapeutic options and poor clinical prognosis. Methods Three datasets (GSE19188, GSE33532 and GSE33479) were obtained from the gene expression omnibus (GEO) database. Differentially expressed genes (DEGs) between LUSC and normal tissues were identified by GEO2R, and functional analysis was employed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Protein–protein interaction (PPI) and hub genes were identified via the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. Hub genes were further validated in The Cancer Genome Atlas (TCGA) database. Subsequently, survival analysis was performed using the Kapla–Meier curve and Cox progression analysis. Based on univariate and multivariate Cox progression analysis, a gene signature was established to predict overall survival. Receiver operating characteristic curve was used to evaluate the prognostic value of the model. Results A total of 116 up-regulated genes and 84 down-regulated genes were identified. These DEGs were mainly enriched in the two pathways: cell cycle and p53 signaling way. According to the degree of protein nodes in the PPI network, 10 hub genes were identified. The mRNA expression levels of the 10 hub genes in LUSC were also significantly up-regulated in the TCGA database. Furthermore, a novel seven-gene signature (FLRT3, PPP2R2C, MMP3, MMP12, CAPN8, FILIP1 and SPP1) from the DEGs was constructed and acted as a significant and independent prognostic signature for LUSC. Conclusions The 10 hub genes might be tightly correlated with LUSC progression. The seven-gene signature might be an independent biomarker with a significant predictive value in LUSC overall survival. |
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| last_indexed | 2024-03-09T06:39:53Z |
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| spelling | doaj.art-1c6449a1c62844d3974a5c2ad9286fa62023-12-03T10:51:44ZengPeerJ Inc.PeerJ2167-83592020-05-018e908610.7717/peerj.9086Identification of key genes associated with progression and prognosis for lung squamous cell carcinomaXiaohan Ma0Huijun Ren1Ruoyu Peng2Yi Li3Liang Ming4Department of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, ChinaDepartment of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, ChinaDepartment of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, ChinaDepartment of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, ChinaDepartment of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, ChinaBackground Lung squamous cell carcinoma (LUSC) is a major subtype of lung cancer with limited therapeutic options and poor clinical prognosis. Methods Three datasets (GSE19188, GSE33532 and GSE33479) were obtained from the gene expression omnibus (GEO) database. Differentially expressed genes (DEGs) between LUSC and normal tissues were identified by GEO2R, and functional analysis was employed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Protein–protein interaction (PPI) and hub genes were identified via the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. Hub genes were further validated in The Cancer Genome Atlas (TCGA) database. Subsequently, survival analysis was performed using the Kapla–Meier curve and Cox progression analysis. Based on univariate and multivariate Cox progression analysis, a gene signature was established to predict overall survival. Receiver operating characteristic curve was used to evaluate the prognostic value of the model. Results A total of 116 up-regulated genes and 84 down-regulated genes were identified. These DEGs were mainly enriched in the two pathways: cell cycle and p53 signaling way. According to the degree of protein nodes in the PPI network, 10 hub genes were identified. The mRNA expression levels of the 10 hub genes in LUSC were also significantly up-regulated in the TCGA database. Furthermore, a novel seven-gene signature (FLRT3, PPP2R2C, MMP3, MMP12, CAPN8, FILIP1 and SPP1) from the DEGs was constructed and acted as a significant and independent prognostic signature for LUSC. Conclusions The 10 hub genes might be tightly correlated with LUSC progression. The seven-gene signature might be an independent biomarker with a significant predictive value in LUSC overall survival.https://peerj.com/articles/9086.pdfLung squamous cell carcinomaDifferentially expressed genesHub genesPrognosisProgressionBioinformatical analysis |
| spellingShingle | Xiaohan Ma Huijun Ren Ruoyu Peng Yi Li Liang Ming Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma PeerJ Lung squamous cell carcinoma Differentially expressed genes Hub genes Prognosis Progression Bioinformatical analysis |
| title | Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma |
| title_full | Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma |
| title_fullStr | Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma |
| title_full_unstemmed | Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma |
| title_short | Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma |
| title_sort | identification of key genes associated with progression and prognosis for lung squamous cell carcinoma |
| topic | Lung squamous cell carcinoma Differentially expressed genes Hub genes Prognosis Progression Bioinformatical analysis |
| url | https://peerj.com/articles/9086.pdf |
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