{"title":"利用生物信息学和实验验证鉴定和分析缺氧缺血性脑损伤中的氧化应激相关基因。","authors":"Ni Jin, Sha Sha, Yanghao Ruan, Ying Ouyang","doi":"10.1002/iid3.70000","DOIUrl":null,"url":null,"abstract":"<div>\n \n \n <section>\n \n <h3> Background</h3>\n \n <p>Oxidative stress (OS) plays a major role in the progress of hypoxic-ischemic brain damage (HIBD). This study aimed to investigate OS-related genes and their underlying molecular mechanisms in neonatal HIBD.</p>\n </section>\n \n <section>\n \n <h3> Methods</h3>\n \n <p>Microarray data sets were acquired from the Gene Expression Omnibus (GEO) database to screen the differentially expressed genes (DEGs) between control samples and HIBD samples. OS-related genes were drawn from GeneCards and OS-DEGs in HIBD were obtained by intersecting with the DEGs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were conducted to determine the underlying mechanisms and functions of OS-DEGs in HIBD. Moreover, the hub genes were screened using the protein−protein interaction network and identified in the GSE144456 data set. CIBERSORT was then performed to evaluate the expression of immunocytes in each sample and perform a correlation analysis of the optimal OS-DEGs and immunocytes. Finally, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and immunohistochemistry were performed to validate the expression levels of the optimal OS-DEGs.</p>\n </section>\n \n <section>\n \n <h3> Results</h3>\n \n <p>In total, 93 OS-DEGs were identified. GO, KEGG, and GSEA enrichment analyses indicated that these genes were predominantly enriched in OS and inflammation. Four OS-related biomarker genes (Jun, Fos, Tlr2, and Atf3) were identified and verified. CIBERSORT analysis revealed the dysregulation of six types of immune cells in the HIBD group. Moreover, 47 drugs that might target four OS-related biomarker genes were screened. Eventually, RT-qPCR and immunohistochemistry results for rat samples further validated the expression levels of Fos, Tlr2, and Atf3.</p>\n </section>\n \n <section>\n \n <h3> Conclusions</h3>\n \n <p>Fos, Tlr2 and Atf3 are potential OS-related biomarkers of HIBD progression. The mechanisms of OS are associated with those of neonatal HIBD.</p>\n </section>\n </div>","PeriodicalId":13289,"journal":{"name":"Immunity, Inflammation and Disease","volume":null,"pages":null},"PeriodicalIF":3.1000,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/iid3.70000","citationCount":"0","resultStr":"{\"title\":\"Identification and analysis of oxidative stress-related genes in hypoxic-ischemic brain damage using bioinformatics and experimental verification\",\"authors\":\"Ni Jin, Sha Sha, Yanghao Ruan, Ying Ouyang\",\"doi\":\"10.1002/iid3.70000\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div>\\n \\n \\n <section>\\n \\n <h3> Background</h3>\\n \\n <p>Oxidative stress (OS) plays a major role in the progress of hypoxic-ischemic brain damage (HIBD). This study aimed to investigate OS-related genes and their underlying molecular mechanisms in neonatal HIBD.</p>\\n </section>\\n \\n <section>\\n \\n <h3> Methods</h3>\\n \\n <p>Microarray data sets were acquired from the Gene Expression Omnibus (GEO) database to screen the differentially expressed genes (DEGs) between control samples and HIBD samples. OS-related genes were drawn from GeneCards and OS-DEGs in HIBD were obtained by intersecting with the DEGs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were conducted to determine the underlying mechanisms and functions of OS-DEGs in HIBD. Moreover, the hub genes were screened using the protein−protein interaction network and identified in the GSE144456 data set. CIBERSORT was then performed to evaluate the expression of immunocytes in each sample and perform a correlation analysis of the optimal OS-DEGs and immunocytes. Finally, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and immunohistochemistry were performed to validate the expression levels of the optimal OS-DEGs.</p>\\n </section>\\n \\n <section>\\n \\n <h3> Results</h3>\\n \\n <p>In total, 93 OS-DEGs were identified. GO, KEGG, and GSEA enrichment analyses indicated that these genes were predominantly enriched in OS and inflammation. Four OS-related biomarker genes (Jun, Fos, Tlr2, and Atf3) were identified and verified. CIBERSORT analysis revealed the dysregulation of six types of immune cells in the HIBD group. Moreover, 47 drugs that might target four OS-related biomarker genes were screened. Eventually, RT-qPCR and immunohistochemistry results for rat samples further validated the expression levels of Fos, Tlr2, and Atf3.</p>\\n </section>\\n \\n <section>\\n \\n <h3> Conclusions</h3>\\n \\n <p>Fos, Tlr2 and Atf3 are potential OS-related biomarkers of HIBD progression. The mechanisms of OS are associated with those of neonatal HIBD.</p>\\n </section>\\n </div>\",\"PeriodicalId\":13289,\"journal\":{\"name\":\"Immunity, Inflammation and Disease\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.1000,\"publicationDate\":\"2024-08-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/iid3.70000\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Immunity, Inflammation and Disease\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/iid3.70000\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"IMMUNOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Immunity, Inflammation and Disease","FirstCategoryId":"3","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/iid3.70000","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"IMMUNOLOGY","Score":null,"Total":0}
Identification and analysis of oxidative stress-related genes in hypoxic-ischemic brain damage using bioinformatics and experimental verification
Background
Oxidative stress (OS) plays a major role in the progress of hypoxic-ischemic brain damage (HIBD). This study aimed to investigate OS-related genes and their underlying molecular mechanisms in neonatal HIBD.
Methods
Microarray data sets were acquired from the Gene Expression Omnibus (GEO) database to screen the differentially expressed genes (DEGs) between control samples and HIBD samples. OS-related genes were drawn from GeneCards and OS-DEGs in HIBD were obtained by intersecting with the DEGs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were conducted to determine the underlying mechanisms and functions of OS-DEGs in HIBD. Moreover, the hub genes were screened using the protein−protein interaction network and identified in the GSE144456 data set. CIBERSORT was then performed to evaluate the expression of immunocytes in each sample and perform a correlation analysis of the optimal OS-DEGs and immunocytes. Finally, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and immunohistochemistry were performed to validate the expression levels of the optimal OS-DEGs.
Results
In total, 93 OS-DEGs were identified. GO, KEGG, and GSEA enrichment analyses indicated that these genes were predominantly enriched in OS and inflammation. Four OS-related biomarker genes (Jun, Fos, Tlr2, and Atf3) were identified and verified. CIBERSORT analysis revealed the dysregulation of six types of immune cells in the HIBD group. Moreover, 47 drugs that might target four OS-related biomarker genes were screened. Eventually, RT-qPCR and immunohistochemistry results for rat samples further validated the expression levels of Fos, Tlr2, and Atf3.
Conclusions
Fos, Tlr2 and Atf3 are potential OS-related biomarkers of HIBD progression. The mechanisms of OS are associated with those of neonatal HIBD.
期刊介绍：
Immunity, Inflammation and Disease is a peer-reviewed, open access, interdisciplinary journal providing rapid publication of research across the broad field of immunology. Immunity, Inflammation and Disease gives rapid consideration to papers in all areas of clinical and basic research. The journal is indexed in Medline and the Science Citation Index Expanded (part of Web of Science), among others. It welcomes original work that enhances the understanding of immunology in areas including:
• cellular and molecular immunology
• clinical immunology
• allergy
• immunochemistry
• immunogenetics
• immune signalling
• immune development
• imaging
• mathematical modelling
• autoimmunity
• transplantation immunology
• cancer immunology
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