Characterizing the role of CD4+ T cell immunoregulatory networks in peripheral blood and lymphoid tissue during HIV-1 clade C infection.

Masters Degree. University of KwaZulu-Natal, Medical School.HIV eradication efforts have been unsuccessful due to virus persistence in cellular and tissue reservoirs. Recent evidence suggests that germinal centers (GCs) within lymph nodes (LN) contain a novel subset of regulatory T cells (TREGs), termed follicular regulatory T (TFR) cells. These cells control the magnitude and specificity of the GC response and like TREGs are essential for the maintenance of self-tolerance and immune homeostasis. However, the exact role of TFR cells in HIV infection and their contribution to viral control is not completely understood, possibly due to their low frequency, heterogeneity and more so, the difficulty in accessing human lymphoid tissue samples to fully study them. Thus, we set out to comprehensively investigate TFR cells in LN and peripheral blood (PB) samples, using a multifaceted approach including flow cytometry, MHC class II tetramers, immunofluorescence microscopy (IF), ELISA, digital droplet PCR and singlecell RNA sequencing (SeqWell), in HIV-1 clade C infection. Furthermore, we aimed to determine the effect of very early treatment on the frequency and function of this cell subset. Overall, our studies contributed various notable findings to the field. Firstly, we were able to develop MHC class II tetramers, specific in our HIV-1 clade C setting, as a more sensitive method of identifying very low cell frequency antigen-specific CD4+ T cells without relying on function. Tetramers eliminate the bias associated with in vitro stimulation required for functional assays and the limitation associated with only detecting subsets of cells capable of secreting a cytokine. Notably, we used class II tetramers to demonstrate that HIV-specific CD4+ T cell responses restricted to DRB1*11-Gag41 are associated with immune control of HIV-1 infection. We next focused on understanding the role of CD4+ regulatory cells during HIV-1 infection. Firstly, we showed that TFR cell frequencies were significantly higher in LN compared to PB samples. Secondly, TFR are a phenotypically and transcriptionally distinct subset compared to regulatory T cells (TREGs) and T Follicular Helper cells (TFH). Thirdly, we were able to detect HIV-specific TFR using our newly synthesized MHC class II tetramers, and showed higher frequencies observed in LNs during untreated HIV infection. Fourthly, as measured by both flow cytometry and IF, most of TFR localized outside of the GC, with very early ART initiators displaying larger proportions of TFR within the GC. Lastly, TFR cells exhibited a potential suppressive functional capacity as they produced IL-10, which is a canonical suppressive cytokine and they were also positively associated with gp41 IgG antibodies titers. Overall, the data presented in this thesis highlights the advantage of MHC class II tetramers in evaluating HIV-specific CD4 + T cell responses in natural infections. More so, the results give important insights into regulatory cells within lymph nodes; their biology, function and their role in the setting of very ART initiation