tetano
Editor, Senior Moderator
BMC Infect Dis
. 2024 Oct 3;24(1):1099.
doi: 10.1186/s12879-024-10000-3. Identification and evaluation of candidate COVID-19 critical genes and medicinal drugs related to plasma cells
Zhe Liu[SUP] 1 2 [/SUP], Olutomilayo Olayemi Petinrin[SUP] 2 [/SUP], Nanjun Chen[SUP] 2 [/SUP], Muhammad Toseef[SUP] 2 [/SUP], Fang Liu[SUP] 3 [/SUP], Zhongxu Zhu[SUP] 4 [/SUP], Furong Qi[SUP] 5 [/SUP], Ka-Chun Wong[SUP] 6 7 [/SUP]
Affiliations
The ongoing COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents one of the most significant global health crises in recent history. Despite extensive research into the immune mechanisms and therapeutic options for COVID-19, there remains a paucity of studies focusing on plasma cells. In this study, we utilized the DESeq2 package to identify differentially expressed genes (DEGs) between COVID-19 patients and controls using datasets GSE157103 and GSE152641. We employed the xCell algorithm to perform immune infiltration analyses, revealing notably elevated levels of plasma cells in COVID-19 patients compared to healthy individuals. Subsequently, we applied the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm to identify COVID-19 related plasma cell module genes. Further, positive cluster biomarker genes for plasma cells were extracted from single-cell RNA sequencing data (GSE171524), leading to the identification of 122 shared genes implicated in critical biological processes such as cell cycle regulation and viral infection pathways. We constructed a robust protein-protein interaction (PPI) network comprising 89 genes using Cytoscape, and identified 20 hub genes through cytoHubba. These genes were validated in external datasets (GSE152418 and GSE179627). Additionally, we identified three potential small molecules (GSK-1070916, BRD-K89997465, and idarubicin) that target key hub genes in the network, suggesting a novel therapeutic approach. These compounds were characterized by their ability to down-regulate AURKB, KIF11, and TOP2A effectively, as evidenced by their low free binding energies determined through computational analyses using cMAP and AutoDock. This study marks the first comprehensive exploration of plasma cells' role in COVID-19, offering new insights and potential therapeutic targets. It underscores the importance of a systematic approach to understanding and treating COVID-19, expanding the current body of knowledge and providing a foundation for future research.
Keywords: COVID-19; Hub genes; Plasma cells; ScRNA-seq; WGCNA.
. 2024 Oct 3;24(1):1099.
doi: 10.1186/s12879-024-10000-3. Identification and evaluation of candidate COVID-19 critical genes and medicinal drugs related to plasma cells
Zhe Liu[SUP] 1 2 [/SUP], Olutomilayo Olayemi Petinrin[SUP] 2 [/SUP], Nanjun Chen[SUP] 2 [/SUP], Muhammad Toseef[SUP] 2 [/SUP], Fang Liu[SUP] 3 [/SUP], Zhongxu Zhu[SUP] 4 [/SUP], Furong Qi[SUP] 5 [/SUP], Ka-Chun Wong[SUP] 6 7 [/SUP]
Affiliations
- PMID: 39363208
- PMCID: PMC11451256
- DOI: 10.1186/s12879-024-10000-3
The ongoing COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents one of the most significant global health crises in recent history. Despite extensive research into the immune mechanisms and therapeutic options for COVID-19, there remains a paucity of studies focusing on plasma cells. In this study, we utilized the DESeq2 package to identify differentially expressed genes (DEGs) between COVID-19 patients and controls using datasets GSE157103 and GSE152641. We employed the xCell algorithm to perform immune infiltration analyses, revealing notably elevated levels of plasma cells in COVID-19 patients compared to healthy individuals. Subsequently, we applied the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm to identify COVID-19 related plasma cell module genes. Further, positive cluster biomarker genes for plasma cells were extracted from single-cell RNA sequencing data (GSE171524), leading to the identification of 122 shared genes implicated in critical biological processes such as cell cycle regulation and viral infection pathways. We constructed a robust protein-protein interaction (PPI) network comprising 89 genes using Cytoscape, and identified 20 hub genes through cytoHubba. These genes were validated in external datasets (GSE152418 and GSE179627). Additionally, we identified three potential small molecules (GSK-1070916, BRD-K89997465, and idarubicin) that target key hub genes in the network, suggesting a novel therapeutic approach. These compounds were characterized by their ability to down-regulate AURKB, KIF11, and TOP2A effectively, as evidenced by their low free binding energies determined through computational analyses using cMAP and AutoDock. This study marks the first comprehensive exploration of plasma cells' role in COVID-19, offering new insights and potential therapeutic targets. It underscores the importance of a systematic approach to understanding and treating COVID-19, expanding the current body of knowledge and providing a foundation for future research.
Keywords: COVID-19; Hub genes; Plasma cells; ScRNA-seq; WGCNA.