Identification of differentially expressed genes and hub genes of human hosts with tuberculosis through an integrated bioinformatics and cell confirmation strategy

Abstract

Abstract Tuberculosis is a chronic infectious disease caused by M.tuberculosis. The immune defence mechanism of the body against tuberculosis is still unclear. We used four microarray datasets from the Gene Expression Omnibus (GEO) to identify differentially expressed genes (DEGs) between samples from humans infected with M.tuberculosis and healthy controls group. Then, the host hub genes with a relatively high number of connections to other DEGs were identified by Cytoscape. Other bioinformatics methods are also performed, including protein–protein interaction (PPI) network analysis and construction of miRNA–hub gene networks and transcription factors (TF)–hub gene networks. Finally, the expression of hub genes in macrophage infected by M.tuberculosis was verified using the reverse transcription polymerase chain reaction (RT–PCR). A total of 46 DEGs were identified. Gene Ontology (GO) analysis showed that the biological functions of DEGs. Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis showed involvement of the genes in the NOD-like receptor and toll-like receptor signaling pathways. Five highly differentially expressed hub genes (STAT1, TLR7, CXCL8, CCR2, and CCL20) were identified. Finally, based on NetworkAnalyst's database, we constructed miRNA–hub gene networks and TF–hub gene networks.