An experimental in silico study on COVID-19: Response of neutrophil-related genes to antibiotics

Abstract

Background and aims: All components of the immune system are involved in alleviating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Further research is required to provide detailed insights into COVID-19-related immune compartments and pathways. In addition, a significant percentage of hospitalized COVID-19 patients suspect bacterial infections and antimicrobial resistance occurs following antibiotics treatment. The aim of this study was to evaluate the possible effects of antibiotics on the response of neutrophil-related genes in SARS-CoV-2 patients by an experimental in silico study.

Methods: The two data sets GSE1739 and GSE21802 including 10 SARS positive patients and 35 influenza A (H1N1) patients were analyzed, respectively. Differentially expressed genes (DEGs) between these two data sets were determined by GEO2R analysis and the Venn diagram online tool. After determining the hub genes involved in immune responses, the expression of these genes in 30 COVID-19 patients and 30 healthy individuals was analyzed by real-time polymerase chain reaction (PCR). All patients received antibiotics, including levofloxacin, colistin, meropenem, and ceftazidime.

Results: GEO2R analysis detected 240 and 120 DEGs in GSE21802 and GSE1739, respectively. Twenty DEGs were considered as enriched hub genes involved in immune processes such as neutrophil degranulation, neutrophil activation, and antimicrobial humoral response. The central nodes were attributed to the genes of neutrophil elastase (ELANE), arginase 1 (ARG-1), lipocalin 2 (LCN2), and defensin 4 (DEFA4). Compared to the healthy subjects, the expression of LCN2 and DEFA4 were significantly reduced in COVID-19 patients. However, no significant differences were observed in the ELANE and AGR-1 levels between COVID-19 subjects and the control group.

Conclusions: Activation and degranulation of neutrophils were observed mainly in SARS, and H1N1 infection processes and antibiotics administration could affect neutrophil activity during viral infection. It can be suggested that antibiotics can decrease inflammation by restoring the expression of neutrophil-related genes in COVID-19 patients.

Keywords: ARG‐1; DEFA4; ELANE; LCN2; SARS‐CoV‐2; neutrophil‐mediated immunity.

Figure 1

Authentication common differentially expressed genes (DEGs) between severe acute respiratory syndrome (SARS)‐positive and influenza A H1N1‐positive patients with │logFC│ > 1 and p < 0.05 using Venn diagram software. The green box corresponds to 20 DEGs commons between the two mentioned data sets

Figure 2

Heat map of expression of 20 hubs in (A) severe acute respiratory syndrome (SARS)‐positive and (B) influenza A H1N1‐positive samples

Figure 3

ClueGO analysis of LCN2, DEFA4, ELANE, and ARG‐1. Node sizes vary according to p value (≤0.05). Larger nodes represent a more significant p value

Figure 4

Protein–protein interaction (PPI) network analysis of hubs. Edge tags are based on scores of PPI

Figure 5

Quantitative real‐time polymerase chain reaction (PCR) analysis of LCN2 (A), DEFA4 (B), ELANE (C), and ARG‐1 (D) in COVID‐19 patients and control subjects. The expression levels of selected genes in whole blood samples of 30 COVID‐19 patients and 30 control subjects were evaluated. p Values are calculated by parametric t test (p value: 0 ≤ 0001, 0 ≤ 0001, 0.2, and 0.08, respectively). Glyceraldehyde‐3‐phosphate dehydrogenase was utilized as an internal reference to normalize mRNA levels