{"title":"食管鳞状细胞癌中泛素化相关差异表达基因的预后价值:综合分析与未来方向。","authors":"Juhui Chen, Yiping Zhang, Zhongmei Lin, Ying Peng, Ankit Madan, Siqian Cai, Zhizhong Lin, Yongshi Shen, Yuanmei Chen, Yuanji Xu, Junxin Wu","doi":"10.21037/jtd-24-1863","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Esophageal squamous cell carcinoma (ESCC) represents a considerable health challenge, primarily due to its poor prognosis and the limited availability of effective therapeutic interventions. Ubiquitination, a vital post-translational modification, is integral to cellular regulation; nonetheless, its role in ESCC has not been thoroughly explored. This study aims to identify ubiquitination-related differentially expressed genes (URDEGs) that possess prognostic significance in the context of ESCC.</p><p><strong>Methods: </strong>We conducted a comprehensive analysis using The Cancer Genome Atlas ESCC (TCGA-ESCC) dataset, GSE20347, and an in-house ESCC dataset to identify URDEGs. The limma R package was used to determine the intersection of ubiquitination-related genes (URGs) with common differentially expressed genes (Co-DEGs) for differential expression analysis. To evaluate prognostic value, Kaplan-Meier survival analysis was conducted, while functional enrichment was examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Validation was performed using real-time quantitative polymerase chain reaction.</p><p><strong>Results: </strong>Eighty-five URDEGs were identified, with five key genes (<i>BUB1B, CHEK1, DNMT1, IRAK1</i>, and <i>PRKDC</i>) showing significant prognostic value. Analysis revealed that these genes play key roles in essential processes such as the cell cycle and immune response, and their varied expression in ESCC tissues supports their use as targets for therapy.</p><p><strong>Conclusions: </strong>The results of our study highlight the prognostic significance of URDEGs in ESCC, suggesting that they may serve as useful biomarkers and therapeutic targets. Future research should focus on clinical validation and the development of targeted therapies to improve the outcomes of patients with ESCC.</p>","PeriodicalId":17542,"journal":{"name":"Journal of thoracic disease","volume":"16 11","pages":"7866-7884"},"PeriodicalIF":2.1000,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11635202/pdf/","citationCount":"0","resultStr":"{\"title\":\"Prognostic value of ubiquitination-related differentially expressed genes in esophageal squamous cell carcinoma: a comprehensive analysis and future directions.\",\"authors\":\"Juhui Chen, Yiping Zhang, Zhongmei Lin, Ying Peng, Ankit Madan, Siqian Cai, Zhizhong Lin, Yongshi Shen, Yuanmei Chen, Yuanji Xu, Junxin Wu\",\"doi\":\"10.21037/jtd-24-1863\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Esophageal squamous cell carcinoma (ESCC) represents a considerable health challenge, primarily due to its poor prognosis and the limited availability of effective therapeutic interventions. Ubiquitination, a vital post-translational modification, is integral to cellular regulation; nonetheless, its role in ESCC has not been thoroughly explored. This study aims to identify ubiquitination-related differentially expressed genes (URDEGs) that possess prognostic significance in the context of ESCC.</p><p><strong>Methods: </strong>We conducted a comprehensive analysis using The Cancer Genome Atlas ESCC (TCGA-ESCC) dataset, GSE20347, and an in-house ESCC dataset to identify URDEGs. The limma R package was used to determine the intersection of ubiquitination-related genes (URGs) with common differentially expressed genes (Co-DEGs) for differential expression analysis. To evaluate prognostic value, Kaplan-Meier survival analysis was conducted, while functional enrichment was examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Validation was performed using real-time quantitative polymerase chain reaction.</p><p><strong>Results: </strong>Eighty-five URDEGs were identified, with five key genes (<i>BUB1B, CHEK1, DNMT1, IRAK1</i>, and <i>PRKDC</i>) showing significant prognostic value. Analysis revealed that these genes play key roles in essential processes such as the cell cycle and immune response, and their varied expression in ESCC tissues supports their use as targets for therapy.</p><p><strong>Conclusions: </strong>The results of our study highlight the prognostic significance of URDEGs in ESCC, suggesting that they may serve as useful biomarkers and therapeutic targets. Future research should focus on clinical validation and the development of targeted therapies to improve the outcomes of patients with ESCC.</p>\",\"PeriodicalId\":17542,\"journal\":{\"name\":\"Journal of thoracic disease\",\"volume\":\"16 11\",\"pages\":\"7866-7884\"},\"PeriodicalIF\":2.1000,\"publicationDate\":\"2024-11-30\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11635202/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of thoracic disease\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.21037/jtd-24-1863\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/11/29 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q3\",\"JCRName\":\"RESPIRATORY SYSTEM\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of thoracic disease","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.21037/jtd-24-1863","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/11/29 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"RESPIRATORY SYSTEM","Score":null,"Total":0}
Prognostic value of ubiquitination-related differentially expressed genes in esophageal squamous cell carcinoma: a comprehensive analysis and future directions.
Background: Esophageal squamous cell carcinoma (ESCC) represents a considerable health challenge, primarily due to its poor prognosis and the limited availability of effective therapeutic interventions. Ubiquitination, a vital post-translational modification, is integral to cellular regulation; nonetheless, its role in ESCC has not been thoroughly explored. This study aims to identify ubiquitination-related differentially expressed genes (URDEGs) that possess prognostic significance in the context of ESCC.
Methods: We conducted a comprehensive analysis using The Cancer Genome Atlas ESCC (TCGA-ESCC) dataset, GSE20347, and an in-house ESCC dataset to identify URDEGs. The limma R package was used to determine the intersection of ubiquitination-related genes (URGs) with common differentially expressed genes (Co-DEGs) for differential expression analysis. To evaluate prognostic value, Kaplan-Meier survival analysis was conducted, while functional enrichment was examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Validation was performed using real-time quantitative polymerase chain reaction.
Results: Eighty-five URDEGs were identified, with five key genes (BUB1B, CHEK1, DNMT1, IRAK1, and PRKDC) showing significant prognostic value. Analysis revealed that these genes play key roles in essential processes such as the cell cycle and immune response, and their varied expression in ESCC tissues supports their use as targets for therapy.
Conclusions: The results of our study highlight the prognostic significance of URDEGs in ESCC, suggesting that they may serve as useful biomarkers and therapeutic targets. Future research should focus on clinical validation and the development of targeted therapies to improve the outcomes of patients with ESCC.
期刊介绍:
The Journal of Thoracic Disease (JTD, J Thorac Dis, pISSN: 2072-1439; eISSN: 2077-6624) was founded in Dec 2009, and indexed in PubMed in Dec 2011 and Science Citation Index SCI in Feb 2013. It is published quarterly (Dec 2009- Dec 2011), bimonthly (Jan 2012 - Dec 2013), monthly (Jan. 2014-) and openly distributed worldwide. JTD received its impact factor of 2.365 for the year 2016. JTD publishes manuscripts that describe new findings and provide current, practical information on the diagnosis and treatment of conditions related to thoracic disease. All the submission and reviewing are conducted electronically so that rapid review is assured.