Gene expression profiling of CD4+ T cell line due to presence of Nef during HIV-1 infection.

We have utilized microarray technology to compare gene expression profile in presence or absence of Nef during HIV-1 infection in T cell-line. We found several genes significantly differentially regulated due to ∆nef HIV-1 infection and WT HIV-1 infection when compared to Uninfected cells and also several genes significantly dergulated due to WT HIV-1 infection as compared to ∆nef HIV-1 infection. We redistributed genes belonging to several gene ontology into broad categories like “signaling”, “apoptosis”, “transcription” and “lipid metabolism”. We selected some lipid metabolism genes to validate the Nef directed differential expression using quantitative real-time RT-PCR. Thus the present work highlights the importance of Nef directed differential gene expression in milieu of other viral proteins present during infection. Gene expression profiling of Uninfected CEMGFP, 0.5 MOI (Multiplicity of Infection) of ∆nef HIV-1 or Wild Type HIV-1 infected CEM-GFP after 72 hours of infection. Three independent infection experiments were set up to be used as replicates.