tetano
Editor, Senior Moderator
Front Immunol
. 2023 Feb 3;14:1024041.
doi: 10.3389/fimmu.2023.1024041. eCollection 2023.
Comprehensive analysis to identify the influences of SARS-CoV-2 infections to inflammatory bowel disease
Chengyan Zhang[SUP] 1 2 [/SUP], Zeyu Ma[SUP] 1 2 [/SUP], Xi Nan[SUP] 1 2 [/SUP], Wenhui Wang[SUP] 1 2 [/SUP], Xianchang Zeng[SUP] 1 2 [/SUP], Jinming Chen[SUP] 3 [/SUP], Zhijian Cai[SUP] 2 4 [/SUP], Jianli Wang[SUP] 1 2 5 6 [/SUP]
Affiliations
Abstract
Background: Coronavirus disease 2019 (COVID-19) and inflammatory bowel disease (IBD) are both caused by a disordered immune response and have direct and profound impacts on health care services. In this study, we implemented transcriptomic and single-cell analysis to detect common molecular and cellular intersections between COVID-19 and IBD that help understand the linkage of COVID-19 to the IBD patients.
Methods: Four RNA-sequencing datasets (GSE147507, GSE126124, GSE9686 and GSE36807) from Gene Expression Omnibus (GEO) database are extracted to detect mutual differentially expressed genes (DEGs) for IBD patients with the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to find shared pathways, candidate drugs, hub genes and regulatory networks. Two single-cell RNA sequencing (scRNA-eq) datasets (GSE150728, PRJCA003980) are used to analyze the immune characteristics of hub genes and the proportion of immune cell types, so as to find common immune responses between COVID-19 and IBD.
Results: A total of 121 common DEGs were identified among four RNA-seq datasets, and were all involved in the functional enrichment analysis related to inflammation and immune response. Transcription factors-DEGs interactions, miRNAs-DEGs coregulatory networks, and protein-drug interactions were identified based on these datasets. Protein-protein interactions (PPIs) was built and 59 hub genes were identified. Moreover, scRNA-seq of peripheral blood monocyte cells (PBMCs) from COVID-19 patients revealed a significant increase in the proportion of CD14[SUP]+[/SUP] monocytes, in which 38 of 59 hub genes were highly enriched. These genes, encoding inflammatory cytokines, were also highly expressed in inflammatory macrophages (IMacrophage) of intestinal tissues of IBD patients.
Conclusions: We conclude that COVID-19 may promote the progression of IBD through cytokine storms. The candidate drugs and DEGs-regulated networks may suggest effective therapeutic methods for both COVID-19 and IBD.
Keywords: COVID-19; IBD; differentially expressed genes; hub genes; inflammation-related genes; single cell atlas.
. 2023 Feb 3;14:1024041.
doi: 10.3389/fimmu.2023.1024041. eCollection 2023.
Comprehensive analysis to identify the influences of SARS-CoV-2 infections to inflammatory bowel disease
Chengyan Zhang[SUP] 1 2 [/SUP], Zeyu Ma[SUP] 1 2 [/SUP], Xi Nan[SUP] 1 2 [/SUP], Wenhui Wang[SUP] 1 2 [/SUP], Xianchang Zeng[SUP] 1 2 [/SUP], Jinming Chen[SUP] 3 [/SUP], Zhijian Cai[SUP] 2 4 [/SUP], Jianli Wang[SUP] 1 2 5 6 [/SUP]
Affiliations
- PMID: 36817436
- PMCID: PMC9936160
- DOI: 10.3389/fimmu.2023.1024041
Abstract
Background: Coronavirus disease 2019 (COVID-19) and inflammatory bowel disease (IBD) are both caused by a disordered immune response and have direct and profound impacts on health care services. In this study, we implemented transcriptomic and single-cell analysis to detect common molecular and cellular intersections between COVID-19 and IBD that help understand the linkage of COVID-19 to the IBD patients.
Methods: Four RNA-sequencing datasets (GSE147507, GSE126124, GSE9686 and GSE36807) from Gene Expression Omnibus (GEO) database are extracted to detect mutual differentially expressed genes (DEGs) for IBD patients with the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to find shared pathways, candidate drugs, hub genes and regulatory networks. Two single-cell RNA sequencing (scRNA-eq) datasets (GSE150728, PRJCA003980) are used to analyze the immune characteristics of hub genes and the proportion of immune cell types, so as to find common immune responses between COVID-19 and IBD.
Results: A total of 121 common DEGs were identified among four RNA-seq datasets, and were all involved in the functional enrichment analysis related to inflammation and immune response. Transcription factors-DEGs interactions, miRNAs-DEGs coregulatory networks, and protein-drug interactions were identified based on these datasets. Protein-protein interactions (PPIs) was built and 59 hub genes were identified. Moreover, scRNA-seq of peripheral blood monocyte cells (PBMCs) from COVID-19 patients revealed a significant increase in the proportion of CD14[SUP]+[/SUP] monocytes, in which 38 of 59 hub genes were highly enriched. These genes, encoding inflammatory cytokines, were also highly expressed in inflammatory macrophages (IMacrophage) of intestinal tissues of IBD patients.
Conclusions: We conclude that COVID-19 may promote the progression of IBD through cytokine storms. The candidate drugs and DEGs-regulated networks may suggest effective therapeutic methods for both COVID-19 and IBD.
Keywords: COVID-19; IBD; differentially expressed genes; hub genes; inflammation-related genes; single cell atlas.