Differential gene expression in CD8+ cells from HIV-1-infected subjects showing suppression of HIV replication

CD8+ cells from healthy HIV-1-infected individuals suppress human immunodeficiency virus (HIV) replication in infected cells by a non-cytotoxic mechanism. This activity is associated with the production of a soluble CD8+ cell antiviral factor (CAF) that inhibits viral replication at the level of transcription. Strong CD8+ cell non-cytotoxic anti-HIV responses (CNARs) correlate with an asymptomatic state and long-term survival of HIV-infected individuals. This antiviral activity is lost when the infected individual advances to disease. In attempts to define the gene(s) mediating CNAR we have evaluated differential gene expression between CD8+ cells from infected subjects with high CNAR and CD8+ cells from uninfected controls that lack this activity. The expression analysis, using the Affymetrix GeneChip Human Genome U133 Set, indicated that 18% of the genes were differentially expressed (DE) of which 9.2% were up-regulated. A total of 568 genes were up-regulated with a > 2.0-fold difference in expression levels and a > 50% concordance of difference call. Stringent selection criteria narrowed down the list to 52 up-regulated ‘high confidence genes’ (≥ 75% concordance). These genes function in a wide variety of cellular processes and include 13 associated with immunologic activity.