HIV-1 chronically infected individuals represent a large disease burden, making the development of a therapeutic vaccine for use in chronic infection a priority. However, therapeutic vaccination has not been successful to date. Most approaches have employed viral vectored vaccines encoding full length viral proteins, which aimed to boost pre-existing CD8+ T cell responses by mimicking natural HIV-1 infection. Simply boosting these pre-existing CD8+ T cell responses which have previously failed to control the virus may be insufficient. Although HIV-1 has a huge capacity to diversify, certain regions are less tolerant of mutations due to structural and functional constraints. We therefore hypothesised that it would be necessary to redirect the immune response to more vulnerable regions of the proteome, such as conserved regions. HIVconsv is a rationally designed conserved region vaccine. Vaccination of 19 chronically HIV-1 infected HAART treated patients with MVA.HIVconsv was safe and well tolerated. There was a significant increase in the magnitude of HIVconsv-specific T cell response following vaccination (p = 0.001), as measured by IFN-γ Elispot assay, but changes observed in vaccinees did not reach statistical significance when compared with placebo recipients (p = 0.48). The capacity of CD8+ T cells to inhibit HIV-1 replication in vitro is highly predictive of virus control in vivo and is thus a possible surrogate of vaccine efficacy. There was a trend towards increased CD8+ T cell mediated inhibition following vaccination with 2x10⁸pfu MVA.HIVconsv (17% inhibition pre- vs 54% inhibition post-vaccination, p = 0.06). However, measurement of the latent HIV-1 reservoir by quantification of total HIV-1 DNA in circulating CD4+ T cells by droplet digital PCR showed no reduction in size upon vaccination, indicating CD8+ T cells induced by vaccination with MVA.HIVconsv were not of sufficient potency to impact the reservoir. In a second cohort of HIV-1 infected individuals, antiviral inhibitory activity was measured in 36 HIV-1-infected STEP and Phambili trial participants. Sustained potent CD8+ T cell antiviral inhibitory responses were rare but were strongly correlated with IFN-γ responses to so-called ‘beneficial’ low entropy regions in HIV-1 Gag and Pol, that had been reported previously to be associated with HIV-1 control, (r = 0.69, p = 0.0001). This correlation was still significant after controlling for protective HLA alleles, whereas responses to conserved elements were only weakly correlated with viral inhibition (r = 0.41, p = 0.04). These data indicate that immunogens that are based on the selection of regions within the viral proteome by conservation score alone may not induce the most effective HIV-1-specific T cell responses and they highlight the importance of systematically selecting specific regions associated with HIV-1 control, together with exclusion of immunodominant decoy epitopes.

Infection with hepatitis C virus (HCV) can cause liver damage known as fibrosis, which often leads to liver disease and hepatocellular carcinoma. The impairment of circulating, bulk (non-specific and specific) CD8+ T cells within HCV-infection, characterized by an altered phenotype and the increased expression of pro-apoptotic genes, is observed when compared to uninfected controls. The relationship between bulk CD8+ T cell function and the extent of liver damage has not been demonstrated. In this study, widespread immune alterations were observed in untreated HCV infection with advanced liver fibrosis. Untreated HCV-infected individuals with advanced fibrosis possessed a significantly decreased proportion of naïve CD8+ T cells and an increased proportion of late effector memory CD8+ T cells compared to uninfected controls. Upon T cell receptor (TCR) stimulation, these individuals also had an increased intracellular IFN-γ expression for four CD8+ T cell subsets, a decreased CD107a expression for central memory CD8+ T cells, and a decreased perforin induction for naïve and central memory CD8+ T cells. These immune alterations did not reverse 24 weeks after viral cure. This study indicates there is a relationship between the differentiation and function of bulk CD8+ T cells and the extent of liver damage within HCV infection.

The aim of this project was to explore the role of the tyrosine kinases JAK1 and JAK3 in cytokine signalling, focusing on interleukin-2 signalling in CD8⁺ effector T lymphocytes. Initial experiments compared the effects of the pan JAK1/JAK3 inhibitor tofacitinib, the selective JAK1 inhibitor GSK186, and the selective JAK3 inhibitor GSK192 on IL-2 control of effector CD8+ cytotoxic T cells (CTL). On the basis of these preliminary data, a detailed analysis of the effect of tofacitinib on effector CD8⁺ T lymphocytes was performed. Phosphorylation events regulated by tofacitinib were identified using mass spectrometry analysis of SILAC (stable isotope labelling with amino acids in cell culture) labelled CTL. Tofacitinib regulated a selective number of phosphorylation sites, with less than 1.2% of the CTL phosphoproteome significantly regulated by tofacitinib treatment following 4hrs tofacitinib treatment. Proteins with downregulated phosphorylation sites were enriched in functions related to the Jak-STAT signalling, regulation of gene expression, and MAPK signalling cascades. Proteins with upregulated phosphorylations were also enriched in functions related to regulation of gene transcription. The proteome of tofacitinib treated CTL was defined by label free mass spectrometry. Approximately 4.5% of the CTL proteome was significantly regulated following 24 hours tofacitinib treatment, suggesting tofacitinib regulates the expression of a selective subset of proteins. Tofacitinib treatment resulted in the downregulation of proteins involved in ribosome biosynthesis, steroid biosynthesis, regulation of transcription and the cell cycle; and the upregulation of proteins with hydrolase activity, and with roles in the lysosome and extracellular exosomes. The phosphoproteomic and proteomic data demonstrates that JAK kinase dependent IL-2 signalling regulates essential processes in CTL by controlling a selective number of phosphorylation events and proteins. Validation of proteins identified as regulated following tofacitinib treatment identified new targets of IL-2 signalling in CTL, including the transcription factor NFIL3. NFIL3 was shown to be upregulated in CD8⁺ T lymphocytes following stimulation with IL-2 and regulated perforin and CD62L expression, suggesting a role in the regulation of CTL effector function.

We have recently demonstrated in a model of influenza A virus (IAV) infection that the absence of specific pulmonary DC subsets, including plasmacytoid DC (pDC) and CD8a+ DC, from the lungs leads to a significant decrease in the number of virus-specific CD8 T cells. Reconstitution of the lungs with physiologic numbers of pDC or CD8a+ DC is able to restore the pulmonary IAV-specific CD8 T cell response to near normal levels via a mechanism that is dependent upon direct DC:T cell interactions, DC-expressed MHC I and the presence of viral antigen. Interestingly, however, this rescue is DC subset specific, as reconstitution with purified alveolar and airway DC or alveolar macrophages was unable to rescue the virus-specific CD8 T cell response. Following IAV infection there is an abundance of IAV antigen and MHC I expressing cells present in the lungs, including infected epithelial cells. Given this fact and the inability of all DC subsets to rescue the virus-specific CD8 T cell response, it suggested that there were additional, undefined requirements for pDC- and CD8a+ DC-mediated rescue of the T cell response in the lungs. Further, although it was known that the reduction in virus-specific CD8 T cells in the lungs was a result of increased T cell apoptosis, it remained unclear what pathways of apoptosis were contributing to the increased cell death, and what mechanism pulmonary DC subsets were utilizing to rescue this defect. Here, we demonstrate that in the absence of lung-resident DC subsets, virus-specific CD8 T cells undergo significantly increased levels of apoptosis via both extrinsic activation induced cell death and intrinsic activated cell-autonomous death pathways. Reconstitution of aDC depleted lungs with pulmonary pDC and CD8a+ DC promotes increased T cell expression of the pro-survival molecule Bcl-2 and hence, increased T cell survival and accumulation in the lungs. Our studies herein demonstrate that pulmonary DC subsets utilize a variety of mechanisms to promote the rescue of virus-specific CD8 T cells in the lungs. Blockade of the costimulatory molecules CD70, and in some cases, 4-1BBL and OX40L, ablates the pulmonary DC mediated rescue of CD8 T cell numbers in the lungs, suggesting that late costimulation is one essential mechanism that pulmonary DC use to regulate CD8 T cell immunity following IAV infection. Further, we demonstrate that the absence of DC following IAV infection results in significantly reduced levels of IL-15 in the lungs and that pulmonary DC-mediated rescue of virus-specific CD8 T cell responses in the lungs requires the trans-presentation of IL-15 via DC-expressed IL-15Ra. In addition to the role of pulmonary DC mediated costimulation and IL-15 trans-presentation, we further demonstrate a previously unrecognized role for viral antigen in regulating the accumulation of both pulmonary DC and virus-specific CD8 T cells in the lungs, suggesting that viral load can dictate the nature of the inflammatory environment in the lungs and thus, regulate the character of the ensuing IAV-specific immune response. Collectively, the results detailed here demonstrate a previously unrecognized role for pulmonary DC in regulating primary IAV-specific CD8 T cell immunity, and hence, promoting enhanced viral clearance and recovery from disease.

In the present studies, the essential role of inducer cells for the induction of soluble anti-viral activity against feline immunodeficiency virus (FIV) was investigated. Induction of suppression of FIV replication was found to not strictly require autologous cells and was probably not FIV specific. Suppression was maximum when the inducer cells and the effector CD8+ T cells were in contact with each other, suggesting a potential role for membrane antigen interactions and/or cytokines in the induction process. Additionally, flow cytometry analysis demonstrated a significant increase in the percentage of CD8+ B7-1+ T cells in the peripheral blood of chronically FIV infected cats as compared with uninfected cats. Examination of the FIV V3-V4 envelope sequences from PBMC, lymph nodes and spleen from six cats chronically infected from three to six years with the molecular clone of FIV-PPR did not demonstrate viral variants specific for the tissues examined, emphasizing the critical role of the initial diversity and virulence of the infecting virus inoculum. Additionally, in vitro CD8+ T cell antiviral activity demonstrated by four of the six cats could have led to the control of virus replication in vivo, resulting in the uniform viral variants observed. Infection of specific pathogen free cats with FIV-TX53, an FIV isolate that belongs to an emerging subtype more closely related to FIV clade B, demonstrated an acute stage infection characterized by lymphoadenopathy and a viral dose dependent decline of CD4+/CD8+ T cell ratios below 1 by 11 weeks post infection. Interestingly, an expansion of CD8 low population of CD8+ T cells was observed in the infected cats. The soluble antiviral activity generated from inducer T cell stimulated CD8+ T cells from FIV-A-PPR infected cats also suppressed in vitro replication of the emerging FIV-TX53 and FIV-TX078 isolates. This is the first report demonstrating that the CD8+ T cell antiviral activity is inter-clade effective among FIV strains. As the success of a FIV vaccine could be hampered by occurrence of highly divergent viral variants in the fields, the exploitation of this innate, soluble anti-FIV activity could contribute to the design of novel, safe and complementary anti-FIV therapeutic strategies.

In the present studies, the essential role of inducer cells for the induction of soluble anti-viral activity against feline immunodeficiency virus (FIV) was investigated. Induction of suppression of FIV replication was found to not strictly require autologous cells and was probably not FIV specific. Suppression was maximum when the inducer cells and the effector CD8+ T cells were in contact with each other, suggesting a potential role for membrane antigen interactions and/or cytokines in the induction process. Additionally, flow cytometry analysis demonstrated a significant increase in the percentage of CD8+ B7-1+ T cells in the peripheral blood of chronically FIV infected cats as compared with uninfected cats. Examination of the FIV V3-V4 envelope sequences from PBMC, lymph nodes and spleen from six cats chronically infected from three to six years with the molecular clone of FIV-PPR did not demonstrate viral variants specific for the tissues examined, emphasizing the critical role of the initial diversity and virulence of the infecting virus inoculum. Additionally, in vitro CD8+ T cell antiviral activity demonstrated by four of the six cats could have led to the control of virus replication in vivo, resulting in the uniform viral variants observed. Infection of specific pathogen free cats with FIV-TX53, an FIV isolate that belongs to an emerging subtype more closely related to FIV clade B, demonstrated an acute stage infection characterized by lymphoadenopathy and a viral dose dependent decline of CD4+/CD8+ T cell ratios below 1 by 11 weeks post infection. Interestingly, an expansion of CD8 low population of CD8+ T cells was observed in the infected cats. The soluble antiviral activity generated from inducer T cell stimulated CD8+ T cells from FIV-A-PPR infected cats also suppressed in vitro replication of the emerging FIV-TX53 and FIV-TX078 isolates. This is the first report demonstrating that the CD8+ T cell antiviral activity is inter-clade effective among FIV strains. As the success of a FIV vaccine could be hampered by occurrence of highly divergent viral variants in the fields, the exploitation of this innate, soluble anti-FIV activity could contribute to the design of novel, safe and complementary anti-FIV therapeutic strategies.

For three decades, CD8+ T cells have been implicated in the control of HIV, ever since early studies revealed that a temporal correlation exists between the emergence of CD8+ T cells and the decline of viral loads in HIV infection. Subsequently, a large body of research focusing on the impact of CD8+ T cell responses on HIV has been produced. The central aim of this thesis was to investigate the relationship between CD8+ T cells and control of HIV, with a focus on the differences in CD8+ T cell responses to consensus HIV epitopes and their naturally occurring variants, as well as CD8+ T cell-mediated infection inhibition in disease progression groups. Previous work has indicated that mutations in HIV epitopes of just one or two amino acids can have a drastic impact on the resulting CD8+ T cell response. Considering the extreme genetic diversity of the virus, understanding how CD8+ T cell responses differ to these common natural variants is essential when trying to elucidate what the best targets for an HIV vaccine would be. It was hypothesized that CD8+ T cell responses to consensus HIV epitopes, as a consequence of them being more common in nature, would be more frequent, polyfunctional, and proliferative than responses to their less common variants, as well as being associated with better disease outcomes. After assessing these functional parameters in response to four consensus HIV epitopes and their natural variants, this hypothesis was rejected, and it was determined that the consensus status of an epitope could not reliably dictate the resulting CD8+ T cell response. Rather, it seems more likely that the particular epitope being presented, combined with the HLA allele presenting it and the particular TCRs binding to it, have a much larger impact on the CD8+ T cell response. In the course of this study, the Gag TL9 T variant epitope was identified as stimulating a CD8+ T cell response that is considered to be beneficial in HIV infection. Responses to this epitope were also associated with higher CD4 counts, which, taken together, suggests that this epitope has potential for further research as an HIV vaccine target. In the spectrum of HIV infection, there is a significant amount of heterogeneity in disease progression, whereby some individuals progress to disease more slowly, and others, more rapidly. The mechanisms by which this differential disease progression occurs are not completely understood. It was hypothesized that CD8+ T cells from individuals who progress to disease more slowly (long term non- progressors) would be able to inhibit p24 production in-vitro to a higher degree than CD8+ T cells from individuals who progress more rapidly or at a normal rate (RP/NP). This hypothesis was confirmed, as CD8+ T cells from LTNP individuals were significantly better at inhibiting both secreted and intracellular p24 levels than CD8+ T cells from RP/NPs in an in vitro viral inhibition assay. Overall, these studies confirm that CD8+ T cells are important in control of HIV, as indicated by an increased capacity to inhibit p24 in LTNP individuals. However, it is also clear from this work that the role that CD8+ T cells play in HIV infection is complex, and the responses to HIV epitopes can vary greatly. / October 2015

The generation of the cytotoxic CD8 T cell response is dependent on the functional outcomes imposed by the intrathymic constraints of differentiation and self-tolerance. Although thymic function can be partly replicated in vitro using OP9-DL1 cell cultures to yield CD8 αβ T cell receptor (TCR)-bearing cells from hematopoietic progenitor cells, a comprehensive and functional assessment of entirely in-vitro generated CD8 T cells derived from bone marrow hematopoietic stem cells (BM-HSCs) has not been established and remains controversial. Here we demonstrate that a phenotypic, molecular, and functional signature of in vitro-derived CD8 T cells is akin to that of ex vivo CD8 T cells. Transfer of in vitro-derived CD8 T cells into syngeneic and immunodeficient host mice showed no graft-versus-host response, while a robust homeostatic proliferation was observed, respectively. These findings, along with a diverse and broad TCR repertoire expressed by the in vitro-derived CD8 T cells, allowed for the successful generation of antigen (Ag)-specific T cells to be obtained from an entirely in vitro-generated CD8 T cell pool, which calls for further tailoring of their use against viral infections or malignancies. Furthermore, I demonstrate that Notch signaling regulates the expression of the cytolytic molecule Granzyme A in CD8+ T cells. This is supported by the inability of Notch-deprived TCR-signaled CD8 T cells to express Granzyme A, while CD8 T cells that received Notch signals readily expressed Granzyme A, suggesting that Notch signaling is a prerequisite for induction of this cytolytic molecule. We further demonstrate that Notch signaling by OP9 cells allows for efficient differentiation of conventional effector CD8 T cells from SAP-/- BM-derived HSCs and restricts differentiation of innate CD8 T cells while allowing for differentiation of IL17-producing CD8 T cells from BM-HSCs isolated from Itk-/-Rlk-/- (DKO) mice. Moreover, we reveal that the process of positive and negative selection in vitro is constrained by peptide-MHC (pMHC) class I expressed by the OP9 cells and disclose that the commitment of DP precursors to the CD8 T cell lineage is facilitated by Notch signaling. Our findings further establish the requirement for Notch receptor-ligand interactions throughout intrathymic T cell differentiation.

The generation of the cytotoxic CD8 T cell response is dependent on the functional outcomes imposed by the intrathymic constraints of differentiation and self-tolerance. Although thymic function can be partly replicated in vitro using OP9-DL1 cell cultures to yield CD8 αβ T cell receptor (TCR)-bearing cells from hematopoietic progenitor cells, a comprehensive and functional assessment of entirely in-vitro generated CD8 T cells derived from bone marrow hematopoietic stem cells (BM-HSCs) has not been established and remains controversial. Here we demonstrate that a phenotypic, molecular, and functional signature of in vitro-derived CD8 T cells is akin to that of ex vivo CD8 T cells. Transfer of in vitro-derived CD8 T cells into syngeneic and immunodeficient host mice showed no graft-versus-host response, while a robust homeostatic proliferation was observed, respectively. These findings, along with a diverse and broad TCR repertoire expressed by the in vitro-derived CD8 T cells, allowed for the successful generation of antigen (Ag)-specific T cells to be obtained from an entirely in vitro-generated CD8 T cell pool, which calls for further tailoring of their use against viral infections or malignancies. Furthermore, I demonstrate that Notch signaling regulates the expression of the cytolytic molecule Granzyme A in CD8+ T cells. This is supported by the inability of Notch-deprived TCR-signaled CD8 T cells to express Granzyme A, while CD8 T cells that received Notch signals readily expressed Granzyme A, suggesting that Notch signaling is a prerequisite for induction of this cytolytic molecule. We further demonstrate that Notch signaling by OP9 cells allows for efficient differentiation of conventional effector CD8 T cells from SAP-/- BM-derived HSCs and restricts differentiation of innate CD8 T cells while allowing for differentiation of IL17-producing CD8 T cells from BM-HSCs isolated from Itk-/-Rlk-/- (DKO) mice. Moreover, we reveal that the process of positive and negative selection in vitro is constrained by peptide-MHC (pMHC) class I expressed by the OP9 cells and disclose that the commitment of DP precursors to the CD8 T cell lineage is facilitated by Notch signaling. Our findings further establish the requirement for Notch receptor-ligand interactions throughout intrathymic T cell differentiation.

The limited success of HIV vaccine candidates to date highlights our need to better characterize protective cell-mediated immunity. Understanding correlates CD8+ T cell protection against HIV infection and progressive disease is essential for informing effective vaccine development, design and evaluation. CD8+ T cell responses with a robust polyfunctional and proliferative component are strongly linked to better disease outcomes. However, the specificity of polyfunctional and proliferative CD8+ T cell responses has not been thoroughly investigated. Additionally, the specificity of memory subsets and their connection to polyfunctionality and proliferation responses has not been adequately assessed. We address these gaps in knowledge and provide a better understanding of the fine specificity of HIV-specific CD8+ T cell responses. We hypothesize that the epitopes recognized by central memory (TCM) and effector memory (TEM) CD8+ T cells, defined by functional attributes, differ in chronic HIV-1 infection. Additionally, we hypothesize that polyfunctional and proliferative responses will better correlate with protection in HIV disease progression. The qualities of CD8+ T cell responses were evaluated using polyfunctional flow cytometry measuring both functional and phenotypic attributes of both TEM and TCM subsets in HIV infected individuals. We evaluated the quality and evolution of CD8+ T cell responses in HIV infected individuals shortly after seroconversion through to the chronic phase of infection, finding that early polyfunctional responses may result in better HIV disease outcomes. Additionally, we show that epitope-specificity differs between short-term cytokine/chemokine secretion and long-term proliferative assays. Importantly, we show that, at a cohort level, particular epitopes preferentially elicit specific qualities of CD8+ T cell responses in preference to others. This research improves our understanding of HIV pathogenesis and indicates that we can identify specific epitopes that can elicit protective responses and that early polyfunctional responses may slow HIV disease progression. Understanding the polyfunctional and proliferative capacities of HIV-specific effector and memory cells at various stages of HIV infection is of critical importance to the design of vaccines intended to elicit protective cell-mediated responses.