Identification of host genomic biomarkers from multiple transcriptomics datasets for diagnosis and therapies of SARS-CoV-2 infections

• Published in: PloS one 2023-03, Vol.18 (3), p.e0281981-e0281981
• Main Authors: Sarker, Bandhan, Rahaman, Md Matiur, Islam, Md Ariful, Alamin, Muhammad Habibulla, Husain, Md Maidul, Ferdousi, Farzana, Ahsan, Md Asif, Mollah, Md Nurul Haque
• Format: Article
• Language: English
• Subjects: Analysis; Aurora Kinase A - genetics; Bioinformatics; Biological activity; Biological markers; Biology and life sciences; Biomarkers; Coronaviruses; COVID-19; COVID-19 - diagnosis; COVID-19 - genetics; COVID-19 Testing; Datasets; Diagnosis; Digoxin; DNA microarrays; Drug development; Drugs; ESR1 protein; Gelatinase A; Gene expression; Gene Regulatory Networks; Genes; Genomics; Global economy; Hesperidin; Humans; Infections; Literature reviews; Medical diagnosis; Medicine and Health Sciences; MicroRNAs - genetics; Molecular docking; Molecular Docking Simulation; Mutation; Myc protein; Naltrindole; Network analysis; Nucleotide sequence; Oleanolic acid; Pandemics; Physical Sciences; Post-transcription; Proscillaridin; Proteins; Receptors; Ribonucleic acid; RNA; SARS-CoV-2 - genetics; SARS-CoV-2 - metabolism; Severe acute respiratory syndrome coronavirus 2; Stat4 protein; Transcriptome; Transcriptomics; Vaccination; Viral diseases; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0281981

The pandemic of COVID-19 is a severe threat to human life and the global economy. Despite the success of vaccination efforts in reducing the spread of the virus, the situation remains largely uncontrolled due to the random mutation in the RNA sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which demands different variants of effective drugs. Disease-causing gene-mediated proteins are usually used as receptors to explore effective drug molecules. In this study, we analyzed two different RNA-Seq and one microarray gene expression profile datasets by integrating EdgeR, LIMMA, weighted gene co-expression network and robust rank aggregation approaches, which revealed SARS-CoV-2 infection causing eight hub-genes (HubGs) including HubGs; REL, AURKA, AURKB, FBXL3, OAS1, STAT4, MMP2 and IL6 as the host genomic biomarkers. Gene Ontology and pathway enrichment analyses of HubGs significantly enriched some crucial biological processes, molecular functions, cellular components and signaling pathways that are associated with the mechanisms of SARS-CoV-2 infections. Regulatory network analysis identified top-ranked 5 TFs (SRF, PBX1, MEIS1, ESR1 and MYC) and 5 miRNAs (hsa-miR-106b-5p, hsa-miR-20b-5p, hsa-miR-93-5p, hsa-miR-106a-5p and hsa-miR-20a-5p) as the key transcriptional and post-transcriptional regulators of HubGs. Then, we conducted a molecular docking analysis to determine potential drug candidates that could interact with HubGs-mediated receptors. This analysis resulted in the identification of top-ranked ten drug agents, including Nilotinib, Tegobuvir, Digoxin, Proscillaridin, Olysio, Simeprevir, Hesperidin, Oleanolic Acid, Naltrindole and Danoprevir. Finally, we investigated the binding stability of the top-ranked three drug molecules Nilotinib, Tegobuvir and Proscillaridin with the three top-ranked proposed receptors (AURKA, AURKB, OAS1) by using 100 ns MD-based MM-PBSA simulations and observed their stable performance. Therefore, the findings of this study might be useful resources for diagnosis and therapies of SARS-CoV-2 infections.