A novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinoma
BackgroundLung squamous cell carcinoma (LUSC) is a devastating and difficult-to-treat type of lung cancer, and the prognosis of LUSC is the worst. The functional roles of focal adhesion-related genes were explored in LUSC based on data from The Cancer Genome Atlas (TCGA).MethodsRNA sequencing data a...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-01-01
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| Series: | Frontiers in Medicine |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmed.2023.1284490/full |
| _version_ | 1797362425139298304 |
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| author | Gang Hui Yuancai Xie Li Niu Li Niu Jixian Liu |
| author_facet | Gang Hui Yuancai Xie Li Niu Li Niu Jixian Liu |
| author_sort | Gang Hui |
| collection | DOAJ |
| description | BackgroundLung squamous cell carcinoma (LUSC) is a devastating and difficult-to-treat type of lung cancer, and the prognosis of LUSC is the worst. The functional roles of focal adhesion-related genes were explored in LUSC based on data from The Cancer Genome Atlas (TCGA).MethodsRNA sequencing data and clinical characteristics of LUSC patients in TCGA-LUSC were obtained from the TCGA database. Through systematic analysis, we screened the prognostic genes and determined the focal adhesion-related pathways closely associated with LUSC.ResultsWe identified 444 prognostic genes and focal adhesion-related pathways intimately associated with LUSC. According to the focal adhesion-related genes, TCGA-LUSC patients were well divided into two groups: the low-risk group (G1) and the high-risk group (G2). A differential expression analysis identified 44 differentially expressed genes (DEGs) upregulated in the low-risk G1 group and 379 DEGs upregulated in the high-risk G2 group. The upregulated DEGs in the G1 group were primarily related to tyrosine metabolism, steroid hormone biosynthesis, retinol metabolism, platinum drug resistance, pentose and glucuronate interconversions, and metabolism of xenobiotics by cytochrome P450, while the downregulated DEGs in the G1 group were primarily related to ECM-receptor interaction, focal adhesion, proteoglycans in cancer, small cell lung cancer, cytokine-cytokine receptor interaction, and TGF-beta signaling pathway. The immune activity of the G1 group was lower than that of the G2 group, and the half-maximal inhibitory concentration (IC50) of five chemotherapy drugs (i.e., gemcitabine, methotrexate, vinorelbine, paclitaxel, and cisplatin) was significantly different between the G1 and G2 groups. Furthermore, a 10-gene prognostic model was constructed to predict the prognosis for LUSC patients: ITGA3, VAV2, FLNC, FLT4, HGF, MYL2, ITGB1, PDGFRA, CCND2, and PPP1CB.ConclusionThe status of focal adhesion-related genes has a close relationship with tumor classification and immunity in LUSC patients. A novel focal adhesion-related signature had good prognostic and predictive performance for LUSC. Our findings may provide new insight into the diagnosis and treatment of LUSC. |
| first_indexed | 2024-03-08T16:06:49Z |
| format | Article |
| id | doaj.art-da4e8fcb180844e89cbb6d033c093c7c |
| institution | Directory Open Access Journal |
| issn | 2296-858X |
| language | English |
| last_indexed | 2024-03-08T16:06:49Z |
| publishDate | 2024-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Medicine |
| spelling | doaj.art-da4e8fcb180844e89cbb6d033c093c7c2024-01-08T05:28:47ZengFrontiers Media S.A.Frontiers in Medicine2296-858X2024-01-011010.3389/fmed.2023.12844901284490A novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinomaGang Hui0Yuancai Xie1Li Niu2Li Niu3Jixian Liu4Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, ChinaDepartment of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, ChinaShenzhen Cheerland Biotechnology Co., Ltd., Southern University of Science and Technology, Shenzhen, ChinaCheerLand Clinical Laboratory Co., Ltd., Peking University Medical Industrial Park, Beijing, ChinaDepartment of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, ChinaBackgroundLung squamous cell carcinoma (LUSC) is a devastating and difficult-to-treat type of lung cancer, and the prognosis of LUSC is the worst. The functional roles of focal adhesion-related genes were explored in LUSC based on data from The Cancer Genome Atlas (TCGA).MethodsRNA sequencing data and clinical characteristics of LUSC patients in TCGA-LUSC were obtained from the TCGA database. Through systematic analysis, we screened the prognostic genes and determined the focal adhesion-related pathways closely associated with LUSC.ResultsWe identified 444 prognostic genes and focal adhesion-related pathways intimately associated with LUSC. According to the focal adhesion-related genes, TCGA-LUSC patients were well divided into two groups: the low-risk group (G1) and the high-risk group (G2). A differential expression analysis identified 44 differentially expressed genes (DEGs) upregulated in the low-risk G1 group and 379 DEGs upregulated in the high-risk G2 group. The upregulated DEGs in the G1 group were primarily related to tyrosine metabolism, steroid hormone biosynthesis, retinol metabolism, platinum drug resistance, pentose and glucuronate interconversions, and metabolism of xenobiotics by cytochrome P450, while the downregulated DEGs in the G1 group were primarily related to ECM-receptor interaction, focal adhesion, proteoglycans in cancer, small cell lung cancer, cytokine-cytokine receptor interaction, and TGF-beta signaling pathway. The immune activity of the G1 group was lower than that of the G2 group, and the half-maximal inhibitory concentration (IC50) of five chemotherapy drugs (i.e., gemcitabine, methotrexate, vinorelbine, paclitaxel, and cisplatin) was significantly different between the G1 and G2 groups. Furthermore, a 10-gene prognostic model was constructed to predict the prognosis for LUSC patients: ITGA3, VAV2, FLNC, FLT4, HGF, MYL2, ITGB1, PDGFRA, CCND2, and PPP1CB.ConclusionThe status of focal adhesion-related genes has a close relationship with tumor classification and immunity in LUSC patients. A novel focal adhesion-related signature had good prognostic and predictive performance for LUSC. Our findings may provide new insight into the diagnosis and treatment of LUSC.https://www.frontiersin.org/articles/10.3389/fmed.2023.1284490/fulllung squamous cell carcinoma (LUSC)prognosisfocal adhesionfocal adhesion-related signaturenovel gene signaturebiomarkers |
| spellingShingle | Gang Hui Yuancai Xie Li Niu Li Niu Jixian Liu A novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinoma Frontiers in Medicine lung squamous cell carcinoma (LUSC) prognosis focal adhesion focal adhesion-related signature novel gene signature biomarkers |
| title | A novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinoma |
| title_full | A novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinoma |
| title_fullStr | A novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinoma |
| title_full_unstemmed | A novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinoma |
| title_short | A novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinoma |
| title_sort | novel gene signature related to focal adhesions for distinguishing and predicting the prognosis of lung squamous cell carcinoma |
| topic | lung squamous cell carcinoma (LUSC) prognosis focal adhesion focal adhesion-related signature novel gene signature biomarkers |
| url | https://www.frontiersin.org/articles/10.3389/fmed.2023.1284490/full |
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