Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning
Lung cancer remains the leading cause of cancer death globally, with lung adenocarcinoma (LUAD) being its most prevalent subtype. Due to the heterogeneity of LUAD, patients given the same treatment regimen may have different responses and clinical outcomes. Therefore, identifying new subtypes of LUA...
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Frontiers Media S.A.
2021-11-01
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| Series: | Frontiers in Cell and Developmental Biology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcell.2021.756340/full |
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| author | Le-Ping Liu Lu Lu Qiang-Qiang Zhao Qin-Jie Kou Zhen-Zhen Jiang Rong Gui Yan-Wei Luo Qin-Yu Zhao Qin-Yu Zhao |
| author_facet | Le-Ping Liu Lu Lu Qiang-Qiang Zhao Qin-Jie Kou Zhen-Zhen Jiang Rong Gui Yan-Wei Luo Qin-Yu Zhao Qin-Yu Zhao |
| author_sort | Le-Ping Liu |
| collection | DOAJ |
| description | Lung cancer remains the leading cause of cancer death globally, with lung adenocarcinoma (LUAD) being its most prevalent subtype. Due to the heterogeneity of LUAD, patients given the same treatment regimen may have different responses and clinical outcomes. Therefore, identifying new subtypes of LUAD is important for predicting prognosis and providing personalized treatment for patients. Pyroptosis-related genes play an essential role in anticancer, but there is limited research investigating pyroptosis in LUAD. In this study, 33 pyroptosis gene expression profiles and clinical information were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. By bioinformatics and machine learning analyses, we identified novel subtypes of LUAD based on 10 pyroptosis-related genes and further validated them in the GEO dataset, with machine learning models performing up to an AUC of 1 for classifying in GEO. A web-based tool was established for clinicians to use our clustering model (http://www.aimedicallab.com/tool/aiml-subphe-luad.html). LUAD patients were clustered into 3 subtypes (A, B, and C), and survival analysis showed that B had the best survival outcome and C had the worst survival outcome. The relationships between pyroptosis gene expression and clinical characteristics were further analyzed in the three molecular subtypes. Immune profiling revealed significant differences in immune cell infiltration among the three molecular subtypes. GO enrichment and KEGG pathway analyses were performed based on the differential genes of the three subtypes, indicating that differentially expressed genes (DEGs) were involved in multiple cellular and biological functions, including RNA catabolic process, mRNA catabolic process, and pathways of neurodegeneration-multiple diseases. Finally, we developed an 8-gene prognostic model that accurately predicted 1-, 3-, and 5-year overall survival. In conclusion, pyroptosis-related genes may play a critical role in LUAD, and provide new insights into the underlying mechanisms of LUAD. |
| first_indexed | 2024-12-14T15:03:20Z |
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| institution | Directory Open Access Journal |
| issn | 2296-634X |
| language | English |
| last_indexed | 2024-12-14T15:03:20Z |
| publishDate | 2021-11-01 |
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| spelling | doaj.art-d7fe9f7bfa4148fa9a8f0cd7b7b6e77a2022-12-21T22:56:46ZengFrontiers Media S.A.Frontiers in Cell and Developmental Biology2296-634X2021-11-01910.3389/fcell.2021.756340756340Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine LearningLe-Ping Liu0Lu Lu1Qiang-Qiang Zhao2Qin-Jie Kou3Zhen-Zhen Jiang4Rong Gui5Yan-Wei Luo6Qin-Yu Zhao7Qin-Yu Zhao8Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, ChinaCollege of Engineering and Computer Science, The Australian National University, Canberra, ACT, AustraliaLung cancer remains the leading cause of cancer death globally, with lung adenocarcinoma (LUAD) being its most prevalent subtype. Due to the heterogeneity of LUAD, patients given the same treatment regimen may have different responses and clinical outcomes. Therefore, identifying new subtypes of LUAD is important for predicting prognosis and providing personalized treatment for patients. Pyroptosis-related genes play an essential role in anticancer, but there is limited research investigating pyroptosis in LUAD. In this study, 33 pyroptosis gene expression profiles and clinical information were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. By bioinformatics and machine learning analyses, we identified novel subtypes of LUAD based on 10 pyroptosis-related genes and further validated them in the GEO dataset, with machine learning models performing up to an AUC of 1 for classifying in GEO. A web-based tool was established for clinicians to use our clustering model (http://www.aimedicallab.com/tool/aiml-subphe-luad.html). LUAD patients were clustered into 3 subtypes (A, B, and C), and survival analysis showed that B had the best survival outcome and C had the worst survival outcome. The relationships between pyroptosis gene expression and clinical characteristics were further analyzed in the three molecular subtypes. Immune profiling revealed significant differences in immune cell infiltration among the three molecular subtypes. GO enrichment and KEGG pathway analyses were performed based on the differential genes of the three subtypes, indicating that differentially expressed genes (DEGs) were involved in multiple cellular and biological functions, including RNA catabolic process, mRNA catabolic process, and pathways of neurodegeneration-multiple diseases. Finally, we developed an 8-gene prognostic model that accurately predicted 1-, 3-, and 5-year overall survival. In conclusion, pyroptosis-related genes may play a critical role in LUAD, and provide new insights into the underlying mechanisms of LUAD.https://www.frontiersin.org/articles/10.3389/fcell.2021.756340/fulllung adenocarcinomapyroptosissubtypemachine learningprognostic |
| spellingShingle | Le-Ping Liu Lu Lu Qiang-Qiang Zhao Qin-Jie Kou Zhen-Zhen Jiang Rong Gui Yan-Wei Luo Qin-Yu Zhao Qin-Yu Zhao Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning Frontiers in Cell and Developmental Biology lung adenocarcinoma pyroptosis subtype machine learning prognostic |
| title | Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning |
| title_full | Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning |
| title_fullStr | Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning |
| title_full_unstemmed | Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning |
| title_short | Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning |
| title_sort | identification and validation of the pyroptosis related molecular subtypes of lung adenocarcinoma by bioinformatics and machine learning |
| topic | lung adenocarcinoma pyroptosis subtype machine learning prognostic |
| url | https://www.frontiersin.org/articles/10.3389/fcell.2021.756340/full |
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