Identification of Hub Genes and Pathways in Zika Virus Infection Using RNA-Seq Data: A Network-Based Computational Approach

Zika virus (ZIKV), a single-strand RNA flavivirus, is transmitted primarily through Aedes aegypti. The recent outbreaks in America and unexpected association between ZIKV infection and birth defects have triggered the global attention. This vouches to understand the molecular mechanisms of ZIKV infection to develop effective drug therapy. A systems-level understanding of biological process affected by ZIKV infection in fetal brain sample led us to identify the candidate genes for pharmaceutical intervention and potential biomarkers for diagnosis. To identify the key genes, transcriptomics data (RNA-Seq) with GSE93385 of ZIKV (Strain: MR766) infected human fetal neural stem cell are analyzed. In total, 1,084 differentially expressed genes (DEGs) are identified, that is, 471 upregulated and 613 downregulated genes. Further analysis such as the gene ontology term suggested that the downregulated genes are mostly enriched in defense response to virus, receptor binding, laminin binding, extracellular matrix, endoplasmic reticulum, and for upregulated DEGs: translation initiation, RNA binding, cytosol, and nucleosome are enriched. And through pathway analysis, systemic lupus erythematosus (SLE) is found to be the most enriched pathway. Protein-protein interaction (PPI) network is constructed to find the hub genes using STRING database. The seven key genes namely cyclin-dependent kinase 1 (CDK1), cyclin B1 (CCNB1), histone cluster 1 H2B family member K, (HIST1H2BK) histone cluster 1 H2B family member O (HIST1H2BO), and histone cluster 1 H2B family member B (HIST1H2BB), polo-like kinase 1 (PLK1), and cell division cycle 20 (CDC20) with highest degree are found to be hub genes using Centiscape, a Cytoscape plugin. The modules of PPI network using Molecular Complex Detection plugin are found significant in structural constituent of ribosome, defense response to virus, nucleosome, SLE, extracellular region, and regulation of gene silencing. Thus, identified key hub genes and pathways shed light on molecular mechanism that may contribute to the discovery of novel therapeutic targets and development of new strategies for the intervention of ZIKV disease.