tetano
Editor, Senior Moderator
Hum Genomics
. 2021 Mar 16;15(1):18.
doi: 10.1186/s40246-021-00316-5.
Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids
Ke-Ying Fang[SUP] #[/SUP][SUP] 1 2 [/SUP], Wen-Chao Cao[SUP] #[/SUP][SUP] 1 2 [/SUP], Tian-Ao Xie[SUP] #[/SUP][SUP] 1 2 [/SUP], Jie Lv[SUP] 1 2 [/SUP], Jia-Xin Chen[SUP] 1 2 [/SUP], Xun-Jie Cao[SUP] 1 2 [/SUP], Zhong-Wei Li[SUP] 1 2 [/SUP], Shu-Ting Deng[SUP] 1 2 [/SUP], Xu-Guang Guo[SUP] 3 4 5 6 [/SUP]
Affiliations
Abstract
Background: In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people's health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Methods: We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (DEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein-protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in.
Results: In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients.
Conclusions: In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVID-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-2 infection. And we also suggested that further study of these hub genes may be beneficial to treatment, prognostic prediction of COVID-19.
Keywords: 3D structure model; Bioinformatics analysis; Human bronchial organoids; Immune response; Novel coronavirus infection.
. 2021 Mar 16;15(1):18.
doi: 10.1186/s40246-021-00316-5.
Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids
Ke-Ying Fang[SUP] #[/SUP][SUP] 1 2 [/SUP], Wen-Chao Cao[SUP] #[/SUP][SUP] 1 2 [/SUP], Tian-Ao Xie[SUP] #[/SUP][SUP] 1 2 [/SUP], Jie Lv[SUP] 1 2 [/SUP], Jia-Xin Chen[SUP] 1 2 [/SUP], Xun-Jie Cao[SUP] 1 2 [/SUP], Zhong-Wei Li[SUP] 1 2 [/SUP], Shu-Ting Deng[SUP] 1 2 [/SUP], Xu-Guang Guo[SUP] 3 4 5 6 [/SUP]
Affiliations
- PMID: 33726831
- DOI: 10.1186/s40246-021-00316-5
Abstract
Background: In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people's health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Methods: We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (DEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein-protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in.
Results: In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients.
Conclusions: In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVID-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-2 infection. And we also suggested that further study of these hub genes may be beneficial to treatment, prognostic prediction of COVID-19.
Keywords: 3D structure model; Bioinformatics analysis; Human bronchial organoids; Immune response; Novel coronavirus infection.