{"title":"支气管肺发育不良的氧化应激相关生物标记物的鉴定与验证","authors":"Zhenzhuang Zou, Yunrong Li, Jiaying Liu, Bo Huang","doi":"10.1007/s12033-024-01281-9","DOIUrl":null,"url":null,"abstract":"<p>The objective of this study was to identify and characterize oxidative stress (OS)-related biomarkers in bronchopulmonary dysplasia (BPD) through a combination of bioinformatics analyses and wet experiments. The study utilized the Gene Expression Omnibus database to obtain the mRNA expression profile dataset GSE32472. Differential expression analysis and functional enrichment analysis were employed to investigate the role of OS-related genes in BPD. Gene Ontology Function Enrichment Analysis and Gene Set Enrichment Analysis were conducted to understand the mechanisms behind the signature. Protein–protein interaction analysis to identify hub genes in BPD, and predictions were made for microRNAs (miRNAs), transcription factors (TFs), and potential medications targeting these genes. CIBERSORT was utilized to investigate the correlation between hub genes and the infiltration of immune cells. Hub genes were ultimately determined and confirmed using expression analysis, correlation analysis, receiver operating characteristic (ROC) analysis, and quantitative real-time PCR (qRT-PCR). A novel OS-related gene signature (<i>ARG1</i>, <i>CSF3R</i>, <i>IL1R1</i>, <i>IL1R2</i>, <i>MMP</i>9, <i>RETN</i>, <i>S100A12</i>, and <i>SOCS3</i>) was constructed for the prediction of BPD. We identified 18 miRNAs, 14 TFs, and 30 potential medications targeting these genes. ROC analysis further validated that these genes could diagnose BPD with high specificity and sensitivity. The qRT-PCR revealed that <i>IL1R1</i> and <i>ARG1</i> were highly expressed in the lung tissue of the model group, while the expressions of <i>RETN</i>, <i>SOCS3</i>, <i>IL1R2</i>, and <i>MMP</i>9 were decreased. This study demonstrated that <i>ARG1</i>, <i>CSF3R</i>, <i>IL1R1</i>, <i>IL1R2</i>, <i>MMP9</i>, <i>RETN</i>, <i>S100A12</i>, and <i>SOCS3</i> may serve as potential diagnostic biomarkers in BPD. Furthermore, a significant association between <i>IL1R1</i> and the pathogenesis of BPD is observed.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.4000,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Identification and Validation of Oxidative Stress-Related Biomarkers for Bronchopulmonary Dysplasia\",\"authors\":\"Zhenzhuang Zou, Yunrong Li, Jiaying Liu, Bo Huang\",\"doi\":\"10.1007/s12033-024-01281-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>The objective of this study was to identify and characterize oxidative stress (OS)-related biomarkers in bronchopulmonary dysplasia (BPD) through a combination of bioinformatics analyses and wet experiments. The study utilized the Gene Expression Omnibus database to obtain the mRNA expression profile dataset GSE32472. Differential expression analysis and functional enrichment analysis were employed to investigate the role of OS-related genes in BPD. Gene Ontology Function Enrichment Analysis and Gene Set Enrichment Analysis were conducted to understand the mechanisms behind the signature. Protein–protein interaction analysis to identify hub genes in BPD, and predictions were made for microRNAs (miRNAs), transcription factors (TFs), and potential medications targeting these genes. CIBERSORT was utilized to investigate the correlation between hub genes and the infiltration of immune cells. Hub genes were ultimately determined and confirmed using expression analysis, correlation analysis, receiver operating characteristic (ROC) analysis, and quantitative real-time PCR (qRT-PCR). A novel OS-related gene signature (<i>ARG1</i>, <i>CSF3R</i>, <i>IL1R1</i>, <i>IL1R2</i>, <i>MMP</i>9, <i>RETN</i>, <i>S100A12</i>, and <i>SOCS3</i>) was constructed for the prediction of BPD. We identified 18 miRNAs, 14 TFs, and 30 potential medications targeting these genes. ROC analysis further validated that these genes could diagnose BPD with high specificity and sensitivity. The qRT-PCR revealed that <i>IL1R1</i> and <i>ARG1</i> were highly expressed in the lung tissue of the model group, while the expressions of <i>RETN</i>, <i>SOCS3</i>, <i>IL1R2</i>, and <i>MMP</i>9 were decreased. This study demonstrated that <i>ARG1</i>, <i>CSF3R</i>, <i>IL1R1</i>, <i>IL1R2</i>, <i>MMP9</i>, <i>RETN</i>, <i>S100A12</i>, and <i>SOCS3</i> may serve as potential diagnostic biomarkers in BPD. Furthermore, a significant association between <i>IL1R1</i> and the pathogenesis of BPD is observed.</p>\",\"PeriodicalId\":18865,\"journal\":{\"name\":\"Molecular Biotechnology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.4000,\"publicationDate\":\"2024-09-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular Biotechnology\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1007/s12033-024-01281-9\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Biotechnology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1007/s12033-024-01281-9","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Identification and Validation of Oxidative Stress-Related Biomarkers for Bronchopulmonary Dysplasia
The objective of this study was to identify and characterize oxidative stress (OS)-related biomarkers in bronchopulmonary dysplasia (BPD) through a combination of bioinformatics analyses and wet experiments. The study utilized the Gene Expression Omnibus database to obtain the mRNA expression profile dataset GSE32472. Differential expression analysis and functional enrichment analysis were employed to investigate the role of OS-related genes in BPD. Gene Ontology Function Enrichment Analysis and Gene Set Enrichment Analysis were conducted to understand the mechanisms behind the signature. Protein–protein interaction analysis to identify hub genes in BPD, and predictions were made for microRNAs (miRNAs), transcription factors (TFs), and potential medications targeting these genes. CIBERSORT was utilized to investigate the correlation between hub genes and the infiltration of immune cells. Hub genes were ultimately determined and confirmed using expression analysis, correlation analysis, receiver operating characteristic (ROC) analysis, and quantitative real-time PCR (qRT-PCR). A novel OS-related gene signature (ARG1, CSF3R, IL1R1, IL1R2, MMP9, RETN, S100A12, and SOCS3) was constructed for the prediction of BPD. We identified 18 miRNAs, 14 TFs, and 30 potential medications targeting these genes. ROC analysis further validated that these genes could diagnose BPD with high specificity and sensitivity. The qRT-PCR revealed that IL1R1 and ARG1 were highly expressed in the lung tissue of the model group, while the expressions of RETN, SOCS3, IL1R2, and MMP9 were decreased. This study demonstrated that ARG1, CSF3R, IL1R1, IL1R2, MMP9, RETN, S100A12, and SOCS3 may serve as potential diagnostic biomarkers in BPD. Furthermore, a significant association between IL1R1 and the pathogenesis of BPD is observed.
期刊介绍:
Molecular Biotechnology publishes original research papers on the application of molecular biology to both basic and applied research in the field of biotechnology. Particular areas of interest include the following: stability and expression of cloned gene products, cell transformation, gene cloning systems and the production of recombinant proteins, protein purification and analysis, transgenic species, developmental biology, mutation analysis, the applications of DNA fingerprinting, RNA interference, and PCR technology, microarray technology, proteomics, mass spectrometry, bioinformatics, plant molecular biology, microbial genetics, gene probes and the diagnosis of disease, pharmaceutical and health care products, therapeutic agents, vaccines, gene targeting, gene therapy, stem cell technology and tissue engineering, antisense technology, protein engineering and enzyme technology, monoclonal antibodies, glycobiology and glycomics, and agricultural biotechnology.