{"title":"人肺上皮细胞抗新型冠状病毒SARS-CoV-2的基因组学研究","authors":"S. Wang, Y. Yang, X. Xie, J. Li, Rui Zhang","doi":"10.7652/jdyxb202105003","DOIUrl":null,"url":null,"abstract":"Objective: Based on the high-throughput sequencing data of the whole genome, genomics and bioinformatics analyses were made to analyze the gene expression changes in the epithelial cells of the lung tissue from patients with coronavirus disease 2019(COVID-19), and explore the effects of the new coronavirus SARS-CoV-2 on human lungs. This study can provide a theoretical basis for the exploration of SARS-CoV-2 on the pathogenesis of lung tissue. Methods: The public data set GSE160435 was retrieved. The data were analyzed by Network analyst, Cytoscape 3. 7. 2, String 11. 0, and other software. The differentially expressed genes were screened, gene function (Gene Ontology, GO)and signal pathway KEGG(Kyoto Encyclopedia of Genes and Genomes)enrichment analysis were carried out. We established the Protein-protein Interactions Network(PPI), PPI of lung tissue-specific DEGs, DEG microRNA regulatory network, Transcription Factor(TF)-DEG regulatory network, and environmental chemicals DEGs regulatory network. Results: We found 324 DEGs in the lung epithelial cells of patients with COVID-19, of which 112(34. 57%) were upregulated and 212(65.43%)were downregulated. Enrichment analysis showed that DEGs were mainly involved in biological processes such as virus-related defense response, mainly involved in protein digestion and absorption, antihuman papillomavirus infection and other signaling pathways. Specific PPI network closely related to DEGs and lung tissue showed that PDGFRB and KIT were core proteins;hsa-mir-340 had targeted interaction with DEGs. It indicated that HOXB4, ISG15 and other related genes were regulated by transcription factors;DEGs interacted with environmental chemicals such as nickel and estradiol. Conclusion: The gene expression pattern of lung epithelial cells in lung tissue of COVID-19 patients has changed significantly. Proteins or genes such as PDGFRB, MMP9 and KIT may play a vital role in the defense immunity of lung tissue. Micro-RNA, TF, signaling pathway molecules, environmental chemicals, and lung tissue-specific genes also play a role in the above-mentioned process. This study provides new ideas for exploring the pathogenic mechanism of SARS-CoV-2 on lung tissue and formulating clinical prevention, diagnosis and treatment measures.","PeriodicalId":35774,"journal":{"name":"Hsi-An Chiao Tung Ta Hsueh/Journal of Xi''an Jiaotong University","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genomics study of human lung epithelial cells against new coronavirus SARS-CoV-2 infection\",\"authors\":\"S. Wang, Y. Yang, X. Xie, J. Li, Rui Zhang\",\"doi\":\"10.7652/jdyxb202105003\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Objective: Based on the high-throughput sequencing data of the whole genome, genomics and bioinformatics analyses were made to analyze the gene expression changes in the epithelial cells of the lung tissue from patients with coronavirus disease 2019(COVID-19), and explore the effects of the new coronavirus SARS-CoV-2 on human lungs. This study can provide a theoretical basis for the exploration of SARS-CoV-2 on the pathogenesis of lung tissue. Methods: The public data set GSE160435 was retrieved. The data were analyzed by Network analyst, Cytoscape 3. 7. 2, String 11. 0, and other software. The differentially expressed genes were screened, gene function (Gene Ontology, GO)and signal pathway KEGG(Kyoto Encyclopedia of Genes and Genomes)enrichment analysis were carried out. We established the Protein-protein Interactions Network(PPI), PPI of lung tissue-specific DEGs, DEG microRNA regulatory network, Transcription Factor(TF)-DEG regulatory network, and environmental chemicals DEGs regulatory network. Results: We found 324 DEGs in the lung epithelial cells of patients with COVID-19, of which 112(34. 57%) were upregulated and 212(65.43%)were downregulated. Enrichment analysis showed that DEGs were mainly involved in biological processes such as virus-related defense response, mainly involved in protein digestion and absorption, antihuman papillomavirus infection and other signaling pathways. Specific PPI network closely related to DEGs and lung tissue showed that PDGFRB and KIT were core proteins;hsa-mir-340 had targeted interaction with DEGs. It indicated that HOXB4, ISG15 and other related genes were regulated by transcription factors;DEGs interacted with environmental chemicals such as nickel and estradiol. Conclusion: The gene expression pattern of lung epithelial cells in lung tissue of COVID-19 patients has changed significantly. Proteins or genes such as PDGFRB, MMP9 and KIT may play a vital role in the defense immunity of lung tissue. Micro-RNA, TF, signaling pathway molecules, environmental chemicals, and lung tissue-specific genes also play a role in the above-mentioned process. This study provides new ideas for exploring the pathogenic mechanism of SARS-CoV-2 on lung tissue and formulating clinical prevention, diagnosis and treatment measures.\",\"PeriodicalId\":35774,\"journal\":{\"name\":\"Hsi-An Chiao Tung Ta Hsueh/Journal of Xi''an Jiaotong University\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2021-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Hsi-An Chiao Tung Ta Hsueh/Journal of Xi''an Jiaotong University\",\"FirstCategoryId\":\"1089\",\"ListUrlMain\":\"https://doi.org/10.7652/jdyxb202105003\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"Engineering\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Hsi-An Chiao Tung Ta Hsueh/Journal of Xi''an Jiaotong University","FirstCategoryId":"1089","ListUrlMain":"https://doi.org/10.7652/jdyxb202105003","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Engineering","Score":null,"Total":0}
引用次数: 0
摘要
目的:基于全基因组高通量测序数据,通过基因组学和生物信息学分析分析2019冠状病毒病(COVID-19)患者肺组织上皮细胞基因表达变化,探讨新型冠状病毒SARS-CoV-2对人体肺部的影响。本研究可为探索SARS-CoV-2对肺组织的发病机制提供理论依据。方法:检索公共数据集GSE160435。数据由网络分析软件Cytoscape 3进行分析。7. 2、字符串0,等软件。筛选差异表达基因,进行基因功能(gene Ontology, GO)和信号通路KEGG(Kyoto Encyclopedia of genes and Genomes)富集分析。我们建立了蛋白-蛋白相互作用网络(PPI)、肺组织特异性DEG的PPI、DEG microRNA调控网络、转录因子(TF)-DEG调控网络和环境化学物DEG调控网络。结果:在新冠肺炎患者肺上皮细胞中检测到324个deg,其中112个(34个)。57%)表达上调,65.43%(212)表达下调。富集分析表明,deg主要参与病毒相关防御反应等生物学过程,主要参与蛋白质消化吸收、抗人乳头瘤病毒感染等信号通路。与DEGs和肺组织密切相关的特异性PPI网络显示PDGFRB和KIT是核心蛋白;hsa-mir-340与DEGs有靶向相互作用。表明HOXB4、ISG15等相关基因受转录因子调控;DEGs与镍、雌二醇等环境化学物质相互作用。结论:新冠肺炎患者肺组织中肺上皮细胞基因表达谱发生了显著变化。PDGFRB、MMP9、KIT等蛋白或基因可能在肺组织的防御免疫中发挥重要作用。微rna、TF、信号通路分子、环境化学物质、肺组织特异性基因等也在上述过程中发挥作用。本研究为探索SARS-CoV-2对肺组织的致病机制,制定临床预防、诊断和治疗措施提供了新的思路。
Genomics study of human lung epithelial cells against new coronavirus SARS-CoV-2 infection
Objective: Based on the high-throughput sequencing data of the whole genome, genomics and bioinformatics analyses were made to analyze the gene expression changes in the epithelial cells of the lung tissue from patients with coronavirus disease 2019(COVID-19), and explore the effects of the new coronavirus SARS-CoV-2 on human lungs. This study can provide a theoretical basis for the exploration of SARS-CoV-2 on the pathogenesis of lung tissue. Methods: The public data set GSE160435 was retrieved. The data were analyzed by Network analyst, Cytoscape 3. 7. 2, String 11. 0, and other software. The differentially expressed genes were screened, gene function (Gene Ontology, GO)and signal pathway KEGG(Kyoto Encyclopedia of Genes and Genomes)enrichment analysis were carried out. We established the Protein-protein Interactions Network(PPI), PPI of lung tissue-specific DEGs, DEG microRNA regulatory network, Transcription Factor(TF)-DEG regulatory network, and environmental chemicals DEGs regulatory network. Results: We found 324 DEGs in the lung epithelial cells of patients with COVID-19, of which 112(34. 57%) were upregulated and 212(65.43%)were downregulated. Enrichment analysis showed that DEGs were mainly involved in biological processes such as virus-related defense response, mainly involved in protein digestion and absorption, antihuman papillomavirus infection and other signaling pathways. Specific PPI network closely related to DEGs and lung tissue showed that PDGFRB and KIT were core proteins;hsa-mir-340 had targeted interaction with DEGs. It indicated that HOXB4, ISG15 and other related genes were regulated by transcription factors;DEGs interacted with environmental chemicals such as nickel and estradiol. Conclusion: The gene expression pattern of lung epithelial cells in lung tissue of COVID-19 patients has changed significantly. Proteins or genes such as PDGFRB, MMP9 and KIT may play a vital role in the defense immunity of lung tissue. Micro-RNA, TF, signaling pathway molecules, environmental chemicals, and lung tissue-specific genes also play a role in the above-mentioned process. This study provides new ideas for exploring the pathogenic mechanism of SARS-CoV-2 on lung tissue and formulating clinical prevention, diagnosis and treatment measures.