Insights into the SARS-CoV-2-Mediated Alteration in the Stress Granule Protein Regulatory Networks in Humans

Prasad, Kartikay; Alasmari, Abdullah F.; Ali, Nemat; Khan, Rehan; Alghamdi, Adel; Kumar, Vijay

doi:10.3390/pathogens10111459

Cited by 15 publications

(11 citation statements)

References 83 publications

(110 reference statements)

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“…Prasad et al. ( 79 ) identified that mir-615-3p as potential candidates for the treatment of COVID-19 and associated manifestations. The obtained results showed that induction of interleukin-8 by SARS-CoV-2 Spike protein in bronchial epithelial IB3-1 cells was mediated by a miR-93-5p agomiR ( 80 ).…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics and System Biology Approach to Identify the Influences of COVID-19 on Rheumatoid Arthritis

Tang

Zhang

et al. 2022

Front. Immunol.

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BackgroundSevere coronavirus disease 2019 (COVID -19) has led to a rapid increase in mortality worldwide. Rheumatoid arthritis (RA) was a high-risk factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, whereas the molecular mechanisms underlying RA and CVOID-19 are not well understood. The objectives of this study were to analyze potential molecular mechanisms and identify potential drugs for the treatment of COVID-19 and RA using bioinformatics and a systems biology approach.MethodsTwo Differentially expressed genes (DEGs) sets extracted from GSE171110 and GSE1775544 datasets were intersected to generate common DEGs, which were used for functional enrichment, pathway analysis, and candidate drugs analysis.ResultsA total of 103 common DEGs were identified in the two datasets between RA and COVID-19. A protein-protein interaction (PPI) was constructed using various combinatorial statistical methods and bioinformatics tools. Subsequently, hub genes and essential modules were identified from the PPI network. In addition, we performed functional analysis and pathway analysis under ontological conditions and found that there was common association between RA and progression of COVID-19 infection. Finally, transcription factor-gene interactions, protein-drug interactions, and DEGs-miRNAs coregulatory networks with common DEGs were also identified in the datasets.ConclusionWe successfully identified the top 10 hub genes that could serve as novel targeted therapy for COVID-19 and screened out some potential drugs useful for COVID-19 patients with RA.

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Section: Discussionmentioning

confidence: 99%

Bioinformatics and System Biology Approach to Identify the Influences of COVID-19 on Rheumatoid Arthritis

Tang

Zhang

et al. 2022

Front. Immunol.

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“…In the serum of lactating mothers with type 1 diabetes, hsa-mir-26a-5p was upregulated and was shown to be significantly associated with inflammatory responses and cytokine-and chemokinemediated signaling pathways (78). Hsa-mir-124-3p and hsamir-20a-5p were also considered as potential therapeutic targets for COVID-19 in previous bioinformatics analysis (79)(80)(81)(82). Although many previous studies have suggested that these TFs and miRNAs may have important therapeutic effects, these analytical results require further experiments to confirm their validity and authenticity.…”

Section: Discussionmentioning

confidence: 99%

Discovering common pathogenetic processes between COVID-19 and sepsis by bioinformatics and system biology approach

Liu

Gui

et al. 2022

Front. Immunol.

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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.

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“…Hsa-miR-124-3p was considered a potential candidate for treating COVID-19 ( Prasad et al, 2021 ) and regulating ACE2 networks ( Wicik et al, 2020 ). Then, hsa-miR-191-5p showed an inhibitory effect on HIV-1 replication ( Zheng et al, 2021 ); it is associated with cervical lesions and can serve as a non-invasive biomarker ( Ning et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis Reveals Hub Genes Regulating Autophagy in Patients With Severe COVID-19

et al. 2022

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Background: The COVID-19 pandemic has currently developed into a worldwide threat to humankind. Importantly, patients with severe COVID-19 are believed to have a higher mortality risk than those with mild conditions. However, despite the urgent need to develop novel therapeutic strategies, the biological features and pathogenic mechanisms of severe COVID-19 are poorly understood.Methods: Here, peripheral blood mononuclear cells (PBMCs) from four patients with severe COVID-19, four patients with mild COVID-19, and four healthy controls were examined by RNA sequencing (RNA-Seq). We conducted gene expression analysis and Venn diagrams to detect specific differentially expressed genes (DEGs) in patients with severe disease compared with those with mild conditions. Gene Ontology (GO) enrichment analysis was performed to identify the significant biological processes, and protein–protein interaction networks were constructed to extract hub genes. These hub genes were then subjected to regulatory signatures and protein–chemical interaction analysis for certain regulatory checkpoints and identification of potent chemical agents. Finally, to demonstrate the cell type-specific expression of these genes, we performed single-cell RNA-Seq analyses using an online platform.Results: A total of 144 DEGs were specifically expressed in severe COVID-19, and GO enrichment analysis revealed a significant association of these specific DEGs with autophagy. Hub genes such as MVB12A, CHMP6, STAM, and VPS37B were then found to be most significantly involved in the biological processes of autophagy at the transcriptome level. In addition, six transcription factors, including SRF, YY1, CREB1, PPARG, NFIC, and GATA2, as well as miRNAs, namely, hsa-mir-1-3p, and potent chemical agents such as copper sulfate and cobalt chloride, may cooperate in regulating the autophagy hub genes. Furthermore, classical monocytes may play a central role in severe COVID-19.Conclusion: We suggest that autophagy plays a crucial role in severe COVID-19. This study might facilitate a more profound knowledge of the biological characteristics and progression of COVID-19 and the development of novel therapeutic approaches to achieve a breakthrough in the current COVID-19 pandemic.

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Insights into the SARS-CoV-2-Mediated Alteration in the Stress Granule Protein Regulatory Networks in Humans

Cited by 15 publications

References 83 publications

Bioinformatics and System Biology Approach to Identify the Influences of COVID-19 on Rheumatoid Arthritis

Bioinformatics and System Biology Approach to Identify the Influences of COVID-19 on Rheumatoid Arthritis

Discovering common pathogenetic processes between COVID-19 and sepsis by bioinformatics and system biology approach

Transcriptome Analysis Reveals Hub Genes Regulating Autophagy in Patients With Severe COVID-19

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