The Pathogenetic Influence of Smoking on SARS-CoV-2 Infection: Integrative Transcriptome and Regulomics Analysis of Lung Epithelial Cells

Overview

Journal Comput Biol Med

Publisher Elsevier

Specialties Biology
General Medicine
Medical Informatics

Date 2023 Apr 21

PMID 37084641

Authors

Md Ali Hossain

Tania Akter Asa

Md Rabiul Auwul

Md Aktaruzzaman

Md Mahfizur Rahman

M Zahidur Rahman

Mohammad Ali Moni

Affiliations

Soon will be listed here.

Abstract

Corona virus disease (COVID-19) has been emerged as pandemic infectious disease. The recent epidemiological data suggest that the smokers are more vulnerable to infection with COVID-19; however, the influence of smoking (SMK) on the COVID-19 infected patients and the mortality is not known yet. In this study, we aimed to discern the influence of SMK on COVID-19 infected patients utilizing the transcriptomics data of COVID-19 infected lung epithelial cells and transcriptomics data smoking matched with controls from lung epithelial cells. The bioinformatics based analysis revealed the molecular insights into the level of transcriptional changes and pathways which are important to identify the impact of smoking on COVID-19 infection and prevalence. We compared differentially expressed genes (DEGs) between COVID-19 and SMK and 59 DEGs were identified as consistently dysregulated at transcriptomics levels. The correlation network analyses were constructed for these common genes using WGCNA R package to see the relationship among these genes. Integration of DEGs with network analysis (protein-protein interaction) showed the presence of 9 hub proteins as key so called "candidate hub proteins" overlapped between COVID-19 patients and SMK. The Gene Ontology and pathways analysis demonstrated the enrichment of inflammatory pathway such as IL-17 signaling pathway, Interleukin-6 signaling, TNF signaling pathway and MAPK1/MAPK3 signaling pathways that might be the therapeutic targets in COVID-19 for smoking persons. The identified genes, pathways, hubs genes, and their regulators might be considered for establishment of key genes and drug targets for SMK and COVID-19.

Citing Articles

Identification of Biomarkers and Molecular Pathways Implicated in Smoking and COVID-19 Associated Lung Cancer Using Bioinformatics and Machine Learning Approaches.

Hossain M, Rahman M, Bhuiyan T, Moni M Int J Environ Res Public Health. 2024; 21(11).

PMID: 39595659 PMC: 11593889. DOI: 10.3390/ijerph21111392.

References

Auwul M, Rahman M, Gov E, Shahjaman M, Moni M . Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19. Brief Bioinform. 2021; 22(5). PMC: 8083354. DOI: 10.1093/bib/bbab120. View

Zhang C, Wu Z, Li J, Zhao H, Wang G . Cytokine release syndrome in severe COVID-19: interleukin-6 receptor antagonist tocilizumab may be the key to reduce mortality. Int J Antimicrob Agents. 2020; 55(5):105954. PMC: 7118634. DOI: 10.1016/j.ijantimicag.2020.105954. View

Strzelak A, Ratajczak A, Adamiec A, Feleszko W . Tobacco Smoke Induces and Alters Immune Responses in the Lung Triggering Inflammation, Allergy, Asthma and Other Lung Diseases: A Mechanistic Review. Int J Environ Res Public Health. 2018; 15(5). PMC: 5982072. DOI: 10.3390/ijerph15051033. View

Shirvaliloo M . The unfavorable clinical outcome of COVID-19 in smokers is mediated by H3K4me3, H3K9me3 and H3K27me3 histone marks. Epigenomics. 2022; 14(3):153-162. PMC: 8763212. DOI: 10.2217/epi-2021-0476. View

Poudel R, Daniels L, DeFilippis A, Hamburg N, Khan Y, Keith R . Smoking is associated with increased risk of cardiovascular events, disease severity, and mortality among patients hospitalized for SARS-CoV-2 infections. PLoS One. 2022; 17(7):e0270763. PMC: 9286231. DOI: 10.1371/journal.pone.0270763. View

Wang T, Yegambaram M, Gross C, Sun X, Lu Q, Wang H . RAC1 nitration at Y IS involved in the endothelial barrier disruption associated with lipopolysaccharide-mediated acute lung injury. Redox Biol. 2020; 38:101794. PMC: 7664366. DOI: 10.1016/j.redox.2020.101794. View

Jin L, Zuo X, Su W, Zhao X, Yuan M, Han L . Pathway-based analysis tools for complex diseases: a review. Genomics Proteomics Bioinformatics. 2014; 12(5):210-20. PMC: 4411419. DOI: 10.1016/j.gpb.2014.10.002. View

Hazra S, Chaudhuri A, Tiwary B, Chakrabarti N . Integrated network-based multiple computational analyses for identification of co-expressed candidate genes associated with neurological manifestations of COVID-19. Sci Rep. 2022; 12(1):17141. PMC: 9558001. DOI: 10.1038/s41598-022-21109-3. View

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon J, van der Lee R . JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 2017; 46(D1):D260-D266. PMC: 5753243. DOI: 10.1093/nar/gkx1126. View

10.

Langfelder P, Horvath S . WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008; 9:559. PMC: 2631488. DOI: 10.1186/1471-2105-9-559. View

11.

Blanco-Melo D, Nilsson-Payant B, Liu W, Uhl S, Hoagland D, Moller R . Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell. 2020; 181(5):1036-1045.e9. PMC: 7227586. DOI: 10.1016/j.cell.2020.04.026. View

12.

Baker J, Krishnan N, Abroms L, Berg C . The Impact of Tobacco Use on COVID-19 Outcomes: A Systematic Review. J Smok Cessat. 2022; 2022():5474397. PMC: 8777389. DOI: 10.1155/2022/5474397. View

13.

Pacha O, Sallman M, Evans S . COVID-19: a case for inhibiting IL-17?. Nat Rev Immunol. 2020; 20(6):345-346. PMC: 7194244. DOI: 10.1038/s41577-020-0328-z. View

14.

Ismail N, Hassan N, Abd Hamid M, Yusoff U, Khamal N, Omar M . ASSOCIATION OF SMOKING AND SEVERITY OF COVID-19 INFECTION AMONG 5,889 PATIENTS IN MALAYSIA: A MULTI-CENTER OBSERVATIONAL STUDY. Int J Infect Dis. 2022; 116:189-196. PMC: 8743378. DOI: 10.1016/j.ijid.2022.01.011. View

15.

Selvaraj G, Kaliamurthi S, Peslherbe G, Wei D . Identifying potential drug targets and candidate drugs for COVID-19: biological networks and structural modeling approaches. F1000Res. 2021; 10:127. PMC: 8080978. DOI: 10.12688/f1000research.50850.3. View

16.

Wang D, Hu B, Hu C, Zhu F, Liu X, Zhang J . Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. JAMA. 2020; 323(11):1061-1069. PMC: 7042881. DOI: 10.1001/jama.2020.1585. View

17.

Meng P, Zhao H, Huang W, Zhang Y, Zhong W, Zhang M . Three GLI2 mutations combined potentially underlie non-syndromic cleft lip with or without cleft palate in a Chinese pedigree. Mol Genet Genomic Med. 2019; 7(9):e714. PMC: 6732289. DOI: 10.1002/mgg3.714. View

18.

Weisberg E, Parent A, Yang P, Sattler M, Liu Q, Liu Q . Repurposing of Kinase Inhibitors for Treatment of COVID-19. Pharm Res. 2020; 37(9):167. PMC: 7417114. DOI: 10.1007/s11095-020-02851-7. View

19.

Rao S, Baranova A, Cao H, Chen J, Zhang X, Zhang F . Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption. Brief Bioinform. 2021; 22(6). DOI: 10.1093/bib/bbab284. View

20.

Lee K, Lee C, Woo J, Jeong J, Jang A, Yoo C . Cigarette Smoke Extract Enhances IL-17A-Induced IL-8 Production via Up-Regulation of IL-17R in Human Bronchial Epithelial Cells. Mol Cells. 2018; 41(4):282-289. PMC: 5935094. DOI: 10.14348/molcells.2018.2123. View