Human immunodeficiency virus type 1 (HIV-1) is the causative virus for acquired immunodeficiency syndrome (AIDS). AIDS is characterized by chronic inflammation and reduction of CD4+ T-cells in the blood. This leads to the patient becoming immunocompromised and much more susceptible to disease in general. Different phenotypes in the progression of AIDS have been observed in patients in either progressing to AIDS faster as a Rapid Progressor (RP), or slower as a Long-Term Non-Progressor (LTNP). Researching elements that result in the LTNP phenotype is of interest as it has the potential to offer alternative treatments and therapies to those suffering from HIV and improve their quality of life. A separate genome wide association study into a population of LTNP patients had associated the R77Q mutation of viral protein R with the LTNP phenotype. Although this association has been controversial, recent work has shown that the R77Q mutation promotes apoptosis in a variety of cell lines compared to unmutated virus. However, the mechanisms behind the increase in apoptosis remain a place for further research. In this thesis, we attempted to elucidate some of the exact changes in gene expression between cells infected with the R77Q mutation and those without in the induction of apoptosis. We observed that apoptosis could be detected approximately 24 hours after infection via Annexin V staining, but there were no significant differences in the expression of genes within the first 24 hours. Furthermore, we observed 289 genes were then differentially expressed at 72 hours post infection. Analysis through SPIA revealed that the c-myc transcription factor pathway was activated in the R77Q infected cells and further analysis of the individual genes suggested less inflammatory signals in R77Q populations as well as an overall increase in antiapoptotic genes in WT infected cells. Exploration into the ANT1, Bax, and B-cl2 genes revealed that B-cl2 was upregulated in WT HIV infections and provided a degree of protection from apoptotic processes. Differences found in the expression of genes between R77Q and WT infected cells support the observation of increased apoptosis in R77Q infections and identify several targets for further research into the LTNP phenotype.

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