tetano
Editor, Senior Moderator
Front Immunol
. 2022 Aug 31;13:975848.
doi: 10.3389/fimmu.2022.975848. eCollection 2022.
Discovering common pathogenetic processes between COVID-19 and sepsis by bioinformatics and system biology approach
Lu Lu[SUP] 1 [/SUP], Le-Ping Liu[SUP] 1 2 [/SUP], Rong Gui[SUP] 1 [/SUP], Hang Dong[SUP] 1 [/SUP], Yan-Rong Su[SUP] 3 [/SUP], Xiong-Hui Zhou[SUP] 1 [/SUP], Feng-Xia Liu[SUP] 1 [/SUP]
Affiliations
Abstract
Corona Virus Disease 2019 (COVID-19), an acute respiratory infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has spread rapidly worldwide, resulting in a pandemic with a high mortality rate. In clinical practice, we have noted that many critically ill or critically ill patients with COVID-19 present with typical sepsis-related clinical manifestations, including multiple organ dysfunction syndrome, coagulopathy, and septic shock. In addition, it has been demonstrated that severe COVID-19 has some pathological similarities with sepsis, such as cytokine storm, hypercoagulable state after blood balance is disrupted and neutrophil dysfunction. Considering the parallels between COVID-19 and non-SARS-CoV-2 induced sepsis (hereafter referred to as sepsis), the aim of this study was to analyze the underlying molecular mechanisms between these two diseases by bioinformatics and a systems biology approach, providing new insights into the pathogenesis of COVID-19 and the development of new treatments. Specifically, the gene expression profiles of COVID-19 and sepsis patients were obtained from the Gene Expression Omnibus (GEO) database and compared to extract common differentially expressed genes (DEGs). Subsequently, common DEGs were used to investigate the genetic links between COVID-19 and sepsis. Based on enrichment analysis of common DEGs, many pathways closely related to inflammatory response were observed, such as Cytokine-cytokine receptor interaction pathway and NF-kappa B signaling pathway. In addition, protein-protein interaction networks and gene regulatory networks of common DEGs were constructed, and the analysis results showed that ITGAM may be a potential key biomarker base on regulatory analysis. Furthermore, a disease diagnostic model and risk prediction nomogram for COVID-19 were constructed using machine learning methods. Finally, potential therapeutic agents, including progesterone and emetine, were screened through drug-protein interaction networks and molecular docking simulations. We hope to provide new strategies for future research and treatment related to COVID-19 by elucidating the pathogenesis and genetic mechanisms between COVID-19 and sepsis.
Keywords: COVID-19; differentially expressed gene (DEG); drug molecule; functional enrichment; gene ontology; hub gene; protein–protein interaction (PPI); sepsis.
. 2022 Aug 31;13:975848.
doi: 10.3389/fimmu.2022.975848. eCollection 2022.
Discovering common pathogenetic processes between COVID-19 and sepsis by bioinformatics and system biology approach
Lu Lu[SUP] 1 [/SUP], Le-Ping Liu[SUP] 1 2 [/SUP], Rong Gui[SUP] 1 [/SUP], Hang Dong[SUP] 1 [/SUP], Yan-Rong Su[SUP] 3 [/SUP], Xiong-Hui Zhou[SUP] 1 [/SUP], Feng-Xia Liu[SUP] 1 [/SUP]
Affiliations
- PMID: 36119022
- PMCID: PMC9471316
- DOI: 10.3389/fimmu.2022.975848
Abstract
Corona Virus Disease 2019 (COVID-19), an acute respiratory infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has spread rapidly worldwide, resulting in a pandemic with a high mortality rate. In clinical practice, we have noted that many critically ill or critically ill patients with COVID-19 present with typical sepsis-related clinical manifestations, including multiple organ dysfunction syndrome, coagulopathy, and septic shock. In addition, it has been demonstrated that severe COVID-19 has some pathological similarities with sepsis, such as cytokine storm, hypercoagulable state after blood balance is disrupted and neutrophil dysfunction. Considering the parallels between COVID-19 and non-SARS-CoV-2 induced sepsis (hereafter referred to as sepsis), the aim of this study was to analyze the underlying molecular mechanisms between these two diseases by bioinformatics and a systems biology approach, providing new insights into the pathogenesis of COVID-19 and the development of new treatments. Specifically, the gene expression profiles of COVID-19 and sepsis patients were obtained from the Gene Expression Omnibus (GEO) database and compared to extract common differentially expressed genes (DEGs). Subsequently, common DEGs were used to investigate the genetic links between COVID-19 and sepsis. Based on enrichment analysis of common DEGs, many pathways closely related to inflammatory response were observed, such as Cytokine-cytokine receptor interaction pathway and NF-kappa B signaling pathway. In addition, protein-protein interaction networks and gene regulatory networks of common DEGs were constructed, and the analysis results showed that ITGAM may be a potential key biomarker base on regulatory analysis. Furthermore, a disease diagnostic model and risk prediction nomogram for COVID-19 were constructed using machine learning methods. Finally, potential therapeutic agents, including progesterone and emetine, were screened through drug-protein interaction networks and molecular docking simulations. We hope to provide new strategies for future research and treatment related to COVID-19 by elucidating the pathogenesis and genetic mechanisms between COVID-19 and sepsis.
Keywords: COVID-19; differentially expressed gene (DEG); drug molecule; functional enrichment; gene ontology; hub gene; protein–protein interaction (PPI); sepsis.