Unveiling the Biomarkers of Cancer and COVID-19 and Their Regulations in Different Organs by Integrating RNA-Seq Expression and Protein-Protein Interactions

Abstract

Cancer and COVID-19 have killed millions of people worldwide. COVID-19 is even more dangerous to people with comorbidities such as cancer. Thus, it is imperative to identify the key human genes or biomarkers that can be targeted to develop novel prognosis and therapeutic strategies. The transcriptomic data provided by the next-generation sequencing technique makes this identification very convenient. Hence, mRNA (messenger ribonucleic acid) expression data of 2265 cancer and 282 normal patients were considered, while for COVID-19 assessment, 784 and 425 COVID-19 and normal patients were taken, respectively. Initially, volcano plots were used to identify the up- and down-regulated genes for both cancer and COVID-19. Thereafter, protein-protein interaction (PPI) networks were prepared by combining all the up- and down-regulated genes for each of cancer and COVID-19. Subsequently, such networks were analyzed to identify the top 10 genes with the highest degree of connection to provide the biomarkers. Interestingly, these genes were all up-regulated for cancer, while they were down-regulated for COVID-19. This study had also identified common genes between cancer and COVID-19, all of which were up-regulated in both the diseases. This analysis revealed that FN1 was highly up-regulated in different organs for cancer, while EEF2 was dysregulated in most organs affected by COVID-19. Then, functional enrichment analysis was performed to identify significant biological processes. Finally, the drugs for cancer and COVID-19 biomarkers and the common genes between them were identified using the Enrichr online web tool. These drugs include lucanthone, etoposide, and methotrexate, targeting the biomarkers for cancer, while paclitaxel is an important drug for COVID-19.