Genome-wide expression profiling analysis to identify key genes in the anti-HIV mechanism of CD4 and CD8 T cells.

Comprehensive bioinformatics analyses were performed to explore the key biomarkers in response to HIV infection of CD4 and CD8 T cells. The numbers of CD4 and CD8 T cells of HIV infected individuals were analyzed and the GEO database (GSE6740) was screened for differentially expressed genes (DEGs) in HIV infected CD4 and CD8 T cells. Gene Ontology enrichment, KEGG pathway analyses, and protein-protein interaction (PPI) network were performed to identify the key pathway and core proteins in anti-HIV virus process of CD4 and CD8 T cells. Finally, we analyzed the expressions of key proteins in HIV-infected T cells (GSE6740 dataset) and peripheral blood mononuclear cells(PBMCs) (GSE511 dataset). 1) CD4 T cells counts and ratio of CD4 /CD8 T cells decreased while CD8 T cells counts increased in HIV positive individuals; 2) 517 DEGs were found in HIV infected CD4 and CD8 T cells at acute and chronic stage with the criterial of P-value <0.05 and fold change (FC) ≥2; 3) In acute HIV infection, type 1 interferon (IFN-1) pathway might played a critical role in response to HIV infection of T cells. The main biological processes of the DEGs were response to virus and defense response to virus. At chronic stage, ISG15 protein, in conjunction with IFN-1 pathway might play key roles in anti-HIV responses of CD4 T cells; and 4) The expression of ISG15 increased in both T cells and PBMCs after HIV infection. Gene expression profile of CD4 and CD8 T cells changed significantly in HIV infection, in which ISG15 gene may play a central role in activating the natural antiviral process of immune cells.