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There are currently an estimated 33.2 million people living with human immunodeficiency virus (HIV) worldwide. For these individuals, long-term use of combination antiretroviral therapy (cART) is not feasible for a variety of reasons including major adverse complications, multi-drug resistance, poor adherence, and high cost. Hence, development of novel therapeutic strategies that can reduce the life-long dependency on cART is highly desired. In order to develop effective therapeutic strategies such as a therapeutic vaccine, we need to have a greater understanding of the immune correlates of viral control in chronic HIV infection. In this thesis, we used treatment interruption (TI) as a tool to test the efficacy of several therapeutic approaches and immune parameters for their association with effective control of viral replication. / In Chapter 2 we showed that cART intensification and Remune vaccination resulted in reduced viral load (VL) plateau during sequential TIs. Although HIV-specific immune responses measured by interferon-gamma (IFN-gamma) enzyme-linked immunospot assay (ELISPOT) increased in the same time frame, neither their breadth nor magnitude correlated with the decrease in VL plateau. In Chapter 3 the effect of ALVAC-vCP1425 plus Remune vaccination on HIV proteome-wide HIV-specific responses was monitored using a dual color IFN-gamma/interleukin-2 (IL-2) ELISPOT assay. We observed an increase in the magnitude of HIV-specific IFN-gamma/IL-2 responses, as well as in the breadth of Gag-specific IFN-gamma responses in the vaccinated groups compared to placebo groups. A shift towards an increased contribution of Gag-specific responses to total HIV-specific vaccine induced immune response was associated with longer delay to viral rebound during TI. In Chapters 4 and 5, we examined baseline pre-TI immune parameters and their association with viral rebound and CD4 count change during TI in HIV-infected individuals in the chronic phase of infection experiencing virologic failure before TI (Chapter 4) or with different levels of VL control while on therapy prior to TI (Chapter 5). We saw that chronic antigen stimulation from persistent viremia as well as co-infections such as with cytomegalovirus are associated with T-cell senescence, which may result in less favourable clinical outcomes during TI. / Consequently, results from this thesis contribute to further understanding of immune correlates of viral control in chronic HIV infection. New therapeutic vaccines and interventions should induce polyfunctional HIV-specific immune responses, broad Gag-specific immune responses, as well as reducing chronic antigen stimulation to prevent irreversible T-cell exhaustion. Taken together, these insights could potentially lead to the development of novel treatment interventions that could effectively control viral replication off cART.

The peripheral naive CD4 T cell pool is homeostatically regulated through a balance of thymic production, delivery of survival signals and homeostatic proliferation. CD4 recent thymic emigrants (RTEs) have a high T cell receptor excision circle (TREC) content and express high levels of CD31. We report premature thymic involution in RRMS, initiated by reduced numbers of naive CD4 T cells and various naive CD4 T cell subsets in peripheral blood. Further, CXCR4, a receptor involved in emigration from the thymus, and CD127 and Bcl-2 (survival signals) are upregulated in various naive CD4 T cell subsets in RRMS. As a compensatory process, naive CD4 T cells undergo homeostatic proliferation. This proliferation is a form of peripheral positive selection through self-MHC/self-antigen interaction and thus can contribute to the expansion of autoreactive T cells and predispose to development of RRMS.

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Development of a suitable animal model of AIDS is much needed in AIDS research to study infection and pathogenesis as well as to evaluate methods of prevention and treatment of HIV infection. Small animals such as rodents are attractive candidates for AIDS research due to the availability of various inbred and genetically engineered strains, extensive knowledge or their immune system, especially in mice, and the relative ease of breeding and maintaining animal colonies. Transgenic small animal models carrying entire HIV genome or selected genes have been instrumental to understand functions of HIV genes in vivo and their role in HIV pathogenesis. The type of cells in which HIV genes are expressed seems to be an import prerequisite for the study of HIV gene functions in transgenic mice. Mice constitutively expressing the entire HIV-1 genome or HIV-1 nef gene in CD4 + T cells and in the cells of macrophage/dendritic lineage develop an AIDS-like disease very similar to AIDS disease in humans. Similarly, expression of Nef in adult mice, using inducible system, results in the AIDS-like disease. This disease is characterized by thymic atrophy, impaired thymocyte maturation, loss of CD4+ T cells, increased activation and turnover of T cells, which can occur in the absence of lymphypenia, and non-lymphoid organ disease involving the lungs and kidneys. Susceptibility of adult mice to the pathological effects of Nef suggests that the AIDS-like disease in the constitutively expressing Nef Tg mice is not due to developmental defects caused by early expression of Nef. This model highlights the important role of Nef in HIV-1 pathogenesis. The high similarity in the disease in these Tg mice with human AIDS strongly suggest that these mice are a relevant model to study AIDS. This study further evidence that mouse cells can support functions of Nef and these Tg mice represent a unique model to study Nef functions in vivo in the context of the primary immune system. Moreover, the inducible Nef Tg model has given us the ability to control the level and time of expression of Nef which was impossible to do in the previously reported constitutive Nef Tg mouse models. These mice will be useful to study immune reconstitution since Nef expression can be turned off after withdrawal from dox.

Multiple Sclerosis (MS) is a chronic inflammatory and demyelinating disease of the central nervous system. The etiology of MS is unknown but many researchers believe that it is autoimmune mediated. This study investigated naive CD4+ and naive CD8+ T-cell homeostasis in patients with Primary Progressive Multiple Sclerosis and Relapsing Remitting Multiple Sclerosis. The naive T-cell compartment involves a balance between thymic production of naive T-cells, homeostatic proliferation and the delivery of death and survival signals. Naive T-cell production was quantified by measuring signal joint T-cell receptor excision circles (sj-TRECs); episomal byproducts formed during V(D)J T-cell receptor rearrangement. / Homeostatic proliferation was quantified by flow cytometry analysis of % expression of CD31 and Ki-67. CD31 is a marker found on CD4+ recent thymic emigrants (RTE) but not on naive T-cells that have undergone homeostatic proliferation. CD31 can be used as a marker of the proliferation history of naive CD4+ T-cells. Ki-67 is a nuclear and nucleolar antigen found in actively cycling cells. It can be used as a marker of cell proliferation at the moment of isolation. Cell survival was measured by quantifying plasma IL-7 levels and by measuring Bcl-2 expressions. IL-7 plays an important role in maintaining and restoring peripheral naive T-cell homeostasis. It stimulates naive T-cell proliferation and prevents the reduction of Bcl-2, an antiapoptotic protein. / In this study, PPMS patients had significantly reduced naive CD4 + T-cell sj-TRECs compared to healthy controls (p = 0.0007) and compared to RRMS patients (p = 0.0010). RRMS patients had fewer sj-TRECs than healthy controls but this difference was not significant (p = 0.4652). Similarly, in PPMS, naive CD4+ T-cells had significantly lower CD31 expression than healthy controls (p = 0.0017) and RRMS patients (p = 0.0032). This finding indicates increased homeostatic proliferation in naive CD4 + T-cells in PPMS, most probably a response to decreased thymic export as marked by the decreased naive CD4+ T-cell sj-TRECs. % CD31 expression in naive CD4+ T-cells did not differ significantly in RRMS compared to healthy controls (p = 0.7455) which is consistent with their naive CD4+ sj-TREC levels. / Naive CD8+ T-cell sj-TRECs were significantly reduced in PPMS patients compared to healthy controls (p = 0.0212) but not compared to RRMS patients (p = 0.2379). RRMS patients had fewer naive CD8 + T-cell sj-TRECs compared to healthy controls but this difference was not significant (p = 0.1517). PPMS patients expressed increased Bcl-2 levels in their naive CD8+ T-cells. This finding indicates upregulation of survival signals, most probably a consequence of reduced thymic export of naive CD8+ T-cells. / The data from this study indicate that PPMS is different from RRMS in their naive CD4+ T-cell sj-TRECs and naive CD4 + T-cell % CD31 expression but is similar to RRMS in their naive CD8+ T-cell sj-TRECs. This study concludes, therefore, that both PPMS and RRMS patients have altered naive T-cell homeostasis.

Throughout history, human populations have continuously been challenged by new and emerging infectious diseases. For the past 26 years, sub-Saharan Africa and other countries around the world have been dealing with a pandemic caused by a relatively new pathogen called the human immunodeficiency virus (HIV). Although antiretroviral (ARV) therapies effectively reduce morbidity and mortality rates, the long term use in those who have access to treatment inevitably leads to drug-related toxicity and resistance. Even with a strong commitment from governments to expand and finance prevention and treatment programs, transmission rates continue to outpace the benefits of these efforts. Therefore to effectively eradicate the disease, research is focusing on the design of protective and therapeutic vaccines. The first major step in designing these alternative therapies is to define correlates of immune protection. / The research presented in this thesis focuses on characterizing the quantitative and qualitative features of T cell immune responses in individuals who spontaneously control viral replication and exhibit a benign course of disease while remaining off ARV therapy. A comprehensive analysis of HIV-specific IFN-gamma secreting immune responses revealed that neither the breadth nor the magnitude of responses directed against the entire HIV proteome accurately predicts the viral load or rate of CD4 decline. Subsequent analyses showed that the preferential targeting of Gag was associated with reduced rates of CD4 decline and was later confirmed in a cohort of individuals in primary infection whereby the relative breadth and magnitude of Gag p24 was inversely correlated with viral load set point. / The maintenance of polyfunctional immune responses in HIV-infected subjects with a benign course of disease prompted us to develop a method that could comprehensively assess the breadth, magnitude and specificity of three functionally distinct subsets of HIV-specific lymphocytes (single IFN-gamma, single IL-2 and dual IFN-gamma/IL-2 secretors). Survey of immune responses in chronically infected individuals revealed that only the breadth and magnitude of dual IFN-gamma/IL-2 secreting lymphocytes correlated with reduced viral loads and increased CD4 counts suggesting that secretion of IFN-gamma alone was a poor correlate of protection. We also showed that the contribution of polyfunctional lymphocytes to the total response was greater for epitopes restricted by major histocompatibility complex (MHC) class I alleles associated with slow disease progression compared to those restricted by alleles associated with rapid or neutral rates of HIV disease progression. / Taken together, this work supports the view that immune monitoring of infected and vaccinated individuals should include methodologies capable of detecting both IFN-gamma and IL-2 secretion from responding T lymphocytes. The studies presented here have furthered our understanding of what constitutes protection from disease progression emphasizing that both specificity and polyfunctionality are features of effective control of viral replication.

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