Network-Based Data Analysis Reveals Ion Channel-Related Gene Features in COVID-19: A Bioinformatic Approach

Abstract

Coronavirus disease 2019 (COVID-19) seriously threatens human health and has been disseminated worldwide. Although there are several treatments for COVID-19, its control is currently suboptimal. Therefore, the development of novel strategies to treat COVID-19 is necessary. Ion channels are located on the membranes of all excitable cells and many intracellular organelles and are key components involved in various biological processes. They are a target of interest when searching for drug targets. This study aimed to reveal the relevant molecular features of ion channel genes in COVID-19 based on bioinformatic analyses. The RNA-sequencing data of patients with COVID-19 and healthy subjects (GSE152418 and GSE171110 datasets) were obtained from the Gene Expression Omnibus (GEO) database. Ion channel genes were selected from the Hugo Gene Nomenclature Committee (HGNC) database. The RStudio software was used to process the data based on the corresponding R language package to identify ion channel-associated differentially expressed genes (DEGs). Based on the DEGs, Gene Ontology (GO) functional and pathway enrichment analyses were performed using the Enrichr web tool. The STRING database was used to generate a protein–protein interaction (PPI) network, and the Cytoscape software was used to screen for hub genes in the PPI network based on the cytoHubba plug-in. Transcription factors (TF)–DEG, DEG–microRNA (miRNA) and DEG–disease association networks were constructed using the NetworkAnalyst web tool. Finally, the screened hub genes as drug targets were subjected to enrichment analysis based on the DSigDB using the Enrichr web tool to identify potential therapeutic agents for COVID-19. A total of 29 ion channel-associated DEGs were identified. GO functional analysis showed that the DEGs were integral components of the plasma membrane and were mainly involved in inorganic cation transmembrane transport and ion channel activity functions. Pathway analysis showed that the DEGs were mainly involved in nicotine addiction, calcium regulation in the cardiac cell and neuronal system pathways. The top 10 hub genes screened based on the PPI network included KCNA2, KCNJ4, CACNA1A, CACNA1E, NALCN, KCNA5, CACNA2D1, TRPC1, TRPM3 and KCNN3. The TF–DEG and DEG–miRNA networks revealed significant TFs (FOXC1, GATA2, HINFP, USF2, JUN and NFKB1) and miRNAs (hsa-mir-146a-5p, hsa-mir-27a-3p, hsa-mir-335-5p, hsa-let-7b-5p and hsa-mir-129–2-3p). Gene-disease association network analysis revealed that the DEGs were closely associated with intellectual disability and cerebellar ataxia. Drug-target enrichment analysis showed that the relevant drugs targeting the hub genes CACNA2D1, CACNA1A, CACNA1E, KCNA2 and KCNA5 were gabapentin, gabapentin enacarbil, pregabalin, guanidine hydrochloride and 4-aminopyridine. The results of this study provide a valuable basis for exploring the mechanisms of ion channel genes in COVID-19 and clues for developing therapeutic strategies for COVID-19.

Discovering common pathogenetic processes between SARS-CoV-2 infection and polycystic ovary syndrome based on an integrated bioinformatics approach and experiment validation

“…Among them, has-miR-335-5p and has-miR-146a-5p were demonstrated to be involved in the DEGs-miRNA network regulation in COVID-19 52 . In particular, our previous study displayed that miR-335-5p may function as a mediator in the etiopathogenesis of PCOS and has the potential as both a novel diagnostic biomarker and therapeutic target for PCOS 11 .…”

1-L Transcription of SARS-CoV-2 Spike Protein S1 Subunit

“…Knockout of NALCN causes lethal disruption of the respiratory rhythm in mice, while NALCN or UNC79 mutations in humans cause progressive mental, motor and visual deterioration, and early death [155]. NALCN is a hub gene that is upregulated in COVID-19 [156].…”

“…Promoted UNC79 is a very large HEAT-repeat protein important for the localization and function of NALCN-channelosome [154]. NALCN is one of 10 upregulated hub genes in COVID-19 [156]. LRPPRC interacts with 4E-SE-containing mRNAs and exports them to the cytoplasm.…”