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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Autores principales:	Le-Ping Liu, Lu Lu, Qiang-Qiang Zhao, Qin-Jie Kou, Zhen-Zhen Jiang, Rong Gui, Yan-Wei Luo, Qin-Yu Zhao
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	lung adenocarcinoma pyroptosis subtype machine learning prognostic Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/d7fe9f7bfa4148fa9a8f0cd7b7b6e77a
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spelling	oai:doaj.org-article:d7fe9f7bfa4148fa9a8f0cd7b7b6e77a2021-11-04T05:44:24ZIdentification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning2296-634X10.3389/fcell.2021.756340https://doaj.org/article/d7fe9f7bfa4148fa9a8f0cd7b7b6e77a2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fcell.2021.756340/fullhttps://doaj.org/toc/2296-634XLung 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.Le-Ping LiuLu LuQiang-Qiang ZhaoQin-Jie KouZhen-Zhen JiangRong GuiYan-Wei LuoQin-Yu ZhaoQin-Yu ZhaoFrontiers Media S.A.articlelung adenocarcinomapyroptosissubtypemachine learningprognosticBiology (General)QH301-705.5ENFrontiers in Cell and Developmental Biology, Vol 9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	lung adenocarcinoma pyroptosis subtype machine learning prognostic Biology (General) QH301-705.5
spellingShingle	lung adenocarcinoma pyroptosis subtype machine learning prognostic Biology (General) QH301-705.5 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
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.
format	article
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
title	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_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_sort	identification and validation of the pyroptosis-related molecular subtypes of lung adenocarcinoma by bioinformatics and machine learning
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/d7fe9f7bfa4148fa9a8f0cd7b7b6e77a
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Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning

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