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. 2023 Dec 15:13:1280223.
doi: 10.3389/fcimb.2023.1280223. eCollection 2023.

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

Tengda Huang #  1 , Jinyi He #  1 , Xinyi Zhou  1 , Hongyuan Pan  1 , Fang He  2 , Ao Du  1 , Bingxuan Yu  1 , Nan Jiang  1 , Xiaoquan Li  1 , Kefei Yuan  1 , Zhen Wang  1
Affiliations

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

Tengda Huang et al. Front Cell Infect Microbiol. .

Abstract

Introduction: The coronavirus disease 2019 (COVID-19) pandemic, stemming from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has persistently threatened the global health system. Meanwhile, tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis) still continues to be endemic in various regions of the world. There is a certain degree of similarity between the clinical features of COVID-19 and TB, but the underlying common pathogenetic processes between COVID-19 and TB are not well understood.

Methods: To elucidate the common pathogenetic processes between COVID-19 and TB, we implemented bioinformatics and systematic research to obtain shared pathways and molecular biomarkers. Here, the RNA-seq datasets (GSE196822 and GSE126614) are used to extract shared differentially expressed genes (DEGs) of COVID-19 and TB. The common DEGs were used to identify common pathways, hub genes, transcriptional regulatory networks, and potential drugs.

Results: A total of 96 common DEGs were selected for subsequent analyses. Functional enrichment analyses showed that viral genome replication and immune-related pathways collectively contributed to the development and progression of TB and COVID-19. Based on the protein-protein interaction (PPI) network analysis, we identified 10 hub genes, including IFI44L, ISG15, MX1, IFI44, OASL, RSAD2, GBP1, OAS1, IFI6, and HERC5. Subsequently, the transcription factor (TF)-gene interaction and microRNA (miRNA)-gene coregulatory network identified 61 TFs and 29 miRNAs. Notably, we identified 10 potential drugs to treat TB and COVID-19, namely suloctidil, prenylamine, acetohexamide, terfenadine, prochlorperazine, 3'-azido-3'-deoxythymidine, chlorophyllin, etoposide, clioquinol, and propofol.

Conclusion: This research provides novel strategies and valuable references for the treatment of tuberculosis and COVID-19.

Keywords: SARS-CoV-2; differentially expressed genes; drug molecule; hub gene; protein-protein interaction (PPI); tuberculosis.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
A schematic illustration of the overall general workflow of this study.
Figure 2
Figure 2
The study incorporates TB (GSE126614) and COVID-19 (GSE196822). The Venn diagram revealed 96 common DEGs for TB and COVID-19.
Figure 3
Figure 3
The bar chart of the GO assessment of the shared DEGs between TB and COVID-19. (A) Biological processes, (B) Cellular components, and (C) Molecular function.
Figure 4
Figure 4
The bar graphs of the pathway enrichment of the shared DEGs between TB and COVID-19. (A) Bioplanet, (B) KEGG, and (C) WikiPathways.
Figure 5
Figure 5
PPI network of the mutual DEGs between COVID-19 and TB. The nodes and the edges of the figure represent DEGs and the interactions between the nodes, respectively. The PPI network contains 176 edges and 49 nodes.
Figure 6
Figure 6
The PPI network from all the shared DEGs is constructed by the Cytohubba plugin in Cytosacpe. Red nodes present the selected top 10 hub genes. The network has 22 nodes and 142 edges.
Figure 7
Figure 7
DEG-TF interaction network created by the NetworkAnalyst. The orange nodes represent gene symbols interacting with TFs, while the herringbone nodes represent TFs.
Figure 8
Figure 8
The regulatory interaction network of DEG-miRNAs. MiRNAs are presented by the square node, and gene symbols interacting with miRNAs are in an oval shape.
See this image and copyright information in PMC

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