abstract: Vaccination remains one of the most effective means for preventing infectious diseases. During viral infection, activated CD8 T cells differentiate into cytotoxic effector cells that directly kill infected cells and produce anti-viral cytokines. Further T cell differentiation results in a population of memory CD8 T cells that have the ability to self-renew and rapidly proliferate into effector cells during secondary infections. However during persistent viral infection, T cell differentiation is disrupted due to sustained antigen stimulation resulting in a loss of T cell effector function. Despite the development of vaccines for a wide range of viral diseases, efficacious vaccines for persistent viral infections have been challenging to design. Immunization against virus T cell epitopes has been proposed as an alternative vaccination strategy for persistent viral infections, such as HIV. However, vaccines that selectively engage T cell responses can result in inappropriate immune responses that increase, rather than prevent, disease. Quantitative models of virus infection and immune response were used to investigate how virus and immune system variables influence pathogenic versus protective T cell responses generated during persistent viral infection. It was determined that an intermediate precursor frequency of virus-specific memory CD8 T cells prior to LCMV infection resulted in maximum T cell mediated pathology. Increased pathology was independent of antigen sensitivity or the diversity of TCR in the CD8 T cell response, but was dependent on CD8 T cell production of TNF and the magnitude of initial virus exposure. The threshold for exhaustion of responding CD8 T cells ultimately influences the precursor frequency that causes enhanced disease.In addition, viral infection can occur in the context of co-infection by heterologous pathogens that modulate immune responses and/or disease. Co-infection of two unrelated viruses in their natural host, Ectromelia virus (ECTV) and Lymphocytic Choriomeningitis virus (LCMV) infection in mice, were studied. ECTV infection can be a lethal infection in mice due in part to the blockade of antiviral cytokines, including Type I Interferons (IFN-I). It was determined that ECTV/LCMV co-infection results in decreased ECTV viral load and amelioration of ECTV-induced disease, presumably due to IFN-I induction by LCMV. However, immune responses to LCMV in ECTV co-infected mice were also lower compared to mice infected with LCMV alone and biased toward effector-memory cell generation. Thus, providing evidence for bi-directional effects of viral co-infection that modulate disease and immunity. Together the results suggest heterogeneity in T cell responses during vaccination with viral vectors may be in part due to heterologous virus infection or vaccine usage and that TNF-blockade may be useful for minimizing pathology while maintaining protection during virus infection. Lastly, quantitative mathematical models of virus and T cell immunity can be useful to generate predictions regarding which molecular and cellular pathways mediate T cell protection versus pathology. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2015

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Lymphocytic choriomeningitis virus (LCMV) infection during pregnancy severely injures the human fetal brain. Neonatal rats inoculated with LCMV are an excellent model of congenital LCMV infection, as they develop neuropathology, including cerebellar injuries, similar to those seen in humans. The goal of this thesis was to determine what underlies brain injury and the differential immune response and to determine the role of T-cells in LCMV induced pathology. First, I examined whether cytokine and chemokine expression after LCMV infection was higher in the cerebellum and olfactory bulbs, which undergo destruction, compared to the hippocampus and septum, which undergo no acute destruction. Second, I used T-cell deficient and T-cell competent animals to evaluate the role of T-lymphocytes in LCMV-induced cerebellar and hippocampus pathology. Finally, I characterized the migration abnormality that develops in the cerebellum after LCMV infection. My results showed that cytokine and chemokine expression is higher in the cerebellum and olfactory bulb than in the hippocampus and septum. Using astrocyte cultures, I determined that astrocytes isolated from the cerebellum have a more robust cytokine response to infection compared to astrocytes from the hippocampus. Furthermore, inoculation of congenitally athymic (rnu/rnu) rats, which are deficient in T-lymphocytes, demonstrated that cerebellar hypoplasia is T-cell independent while cerebellar destruction and abnormal neuron migration is T-cell dependent. In the hippocampus, T-cells protect against loss of dentate granule cells. A study of the migration abnormality determined that LCMV infection disrupts radial glia fibers and extends proliferation of granule cells in a T-cell dependent manner. The findings reported here support a pivotal role of the immune system in regional brain pathology as well as in the disruption of migration.

Transcriptional regulation of CD8+ T cell differentiation during acute and chronic viral infections is an intricate web made up of many of transcription factors. While several transcription factors have been elucidated in this process, there are still many more that remain elusive. In this work, we look into the role of two transcription factors, IRF4 and Runx2, and their role in CD8+ T cell terminal effector cells and memory precursor cells during acute LCMV-Armstrong infection. We found that IRF4 expression was regulated by TCR signal strength during infection, and that IRF4 expression levels directly correlated with the magnitude of the effector cell response. IRF4 was also shown to regulate T-bet and Eomes, two transcription factors critical for CD8+ T cell differentiation into effector and memory cells. From these results, we were interested in the potential role of IRF4 during chronic LCMV-clone 13 infection, where ratios of T-bet and Eomes are critical for viral clearance. We found that haplodeficiency of IRF4 in the T cell compartment lead to an increase in the ratio of Eomes to T-bet in T cells, which in turn affected the proportion of Eomeshi versus T-bethi cells and resulted in a loss in ability to clear viral infection. Irf4+/-Eomes+/- compound heterozygous mice were generated to test if decreasing Eomes expression would rescue the Irf4+/- phenotype. Irf4+/-Eomes+/- mice were phenotypically similar to WT mice in terms of Eomes to T-bet ratios, and were able to clear viral infection, demonstrating a critical role of IRF4 in regulating T-bet and Eomes during chronic viral infection. Next we looked into the role of Runx2 during acute LCMV-Armstrong infection and found that Runx2-deficient pathogen-specific CD8+ T cells had a defect in the total number of memory precursor cells compared to WT controls. We further showed that Runx2 was inversely correlated with TCR signal strength, and that Runx2 expression was repressed by IRF4. From these work, we have introduced two more transcription factors that are critical for CD8+ T cells differentiation during acute and chronic viral infection. Given the sheer number of transcription factors known to regulate these processes, having a full understanding of the transcriptional network will allow us to find the best targets for therapeutic intervention for treatments ranging from vaccine development and autoimmunity to cancer immunotherapy and treatment of chronic viral infections.

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Les lymphocytes T CD8 ont un rôle essentiel dans la protection contre les agents pathogènes intracellulaires et la progression tumorale. Ainsi, la compréhension de la diversité des mécanismes de différenciation des lymphocytes T CD8 naïfs en cellules effectrices, ainsi qu’en cellules mémoires compétentes, est fondamentale pour le développement efficace de vaccins à cellules T. Dans ce travail de thèse, nous avons abordé deux questions centrales : (1)Très tôt après l’activation des cellules T CD8, quels sont les mécanismes par lesquels les cellules T effectrices agissent comme effecteurs pro-inflammatoires en recrutant d’autres cellules? Et quel est leur rôle dans la réponse immunitaire? (2) Quel est le rôle du contexte infectieux dans le programme de différenciation des lymphocytes T CD8 ? Est-il responsable de l’hétérogénéité des cellules répondeuses et a-t-il un rôle dans les différents effets protecteurs des cellules mémoires? Afin de répondre à ces questions, nous avons choisit d’utiliser des cellules T CD8 exprimant un récepteur pour l’antigène transgéniques (TCR-Tg) pour suivre la différentiation in vivo des lymphocytes T CD8. De plus, la méthode de RT-PCR sur des séries de cellules uniques, nous a permis d’analyser la co-expression des ARNm dans ces cellules. Comme l’utilisation à haute fréquence de cellules TCR-Tg a été fortement critiquée, nous avons comparé la différenciation de ces cellules avec celle des cellules endogènes (non transgéniques et rares). Dans ce premier manuscrit nous avons observé un comportement similaire, ce qui a renforcé l'avantage d'utiliser des cellules TCR Tg pour étudier les réponses immunitaires des lymphocytes T CD8. De plus, nous avons conclu que la diversité des réponses immunitaires des lymphocytes T CD8 n’est pas conditionnée par la fréquence de cellules naïves. Dans un deuxième manuscrit, nous avons comparé la réponse des cellules OT1 TCR-Tg (spécifiques de l’antigène OVA) à l'infection bactérienne LM-OVA (Listeria Monocytogènes exprimant OVA) avec la réponse des cellules P14 TCR-Tg (spécifiques de l’épitope GP33) à l’infection par le virus LCMV. Nous avons montré que les cellules OT1, stimulées par l’OVA dans un contexte bactérien (LM-OVA), présentent un profil d’expression génique distinct de celui des cellules P14 stimulées par le GP33 dans un contexte viral (LCMV). Nous avons également co-stimulé les cellules P14 et OT1 dans une même souris suivant le même contexte bactérien avec LM-GP33 et LM-OVA. Dans ce cas, nous n’avons pas observé de différence dans le profil d’expression génique. L’ensemble des résultats démontrent que les stimulations spécifiques des cellules T CD8 par différents agents pathogènes génèrent des cellules T CD8 présentant des caractéristiques différentes qui ne sont pas déterminées par la spécificité du TCR mais plutôt par le contexte infectieux. De plus, nous avons montré que les cellules mémoires endogènes résultant de la stimulation des CD8 en présence de LCMV ont été plus efficaces après une deuxième réponse immunitaire que des cellules mémoires générées après stimulation avec LM-GP33 (bactérie). Nous avons également observé que la protection plus efficace dans le contexte viral est associée à des cellules T CD8 qui présentent un phénotype de cellules T mémoires effectrices (TEM) tandis que les cellules T CD8 générées dans un contexte bactérien ont plutôt un phénotype associé aux cellules T mémoires centrales (TCM). Ces résultats démontrent que différents pathogènes induisent différents profils de différentiation des cellules T CD8 et que malgré l’élimination efficace des différents pathogènes dans une réponse primaire, la qualité des cellules mémoires générées au cours de cette réponse peut être différente. Dans un troisième manuscrit, nous avons étudié les mécanismes de recrutement d’autres cellules par les lymphocytes T CD8 activés à un temps précoce de la réponse immunitaire. (...) / CD8 T cells are essential for the elimination of intracellular pathogens and tumor cells. Understanding how naïve CD8 T cells differentiate into effector cells capable of eliminating pathogens and to generate adequate memory cells during immune responses is fundamental for optimal T cell vaccine design. In this PhD thesis work we addressed two central questions: 1) What are the mechanisms by which early effector T cells could act as pro-inflammatory effectors? And what is their role in the immune response? 2) How heterogeneous are CD8 responses? Could different pathogens modulate CD8 T cell differentiation programs and be responsible for CD8 cell-to-cell heterogeneity? Could they also generate memory cells with different protection capacities? To address these questions related to the diversity of CD8 T cell differentiation during immune responses, we used the single cell RT-PCR technique to detect ex vivo expression of mRNA in each individual cell, and Brefeldin A injected mice to detect ex vivo intracellular proteins. As experimental system to evaluate in vivo cell activation we used T cell receptor transgenic (TCR-Tg) CD8 T cells. Since the use of TCR-Tg cells to study immune responses has been subjected to criticism (due to high frequency of naïve-precursor transfers), in a first Ms. we compared the behavior of TCR-Tg and endogenous (non-transgenic and present at low frequency) cells in the same mouse. We found fully overlapping behavior between these two cell populations, which reinforced the advantage of using TCR-Tg cells to study CD8 immune responses. In addition, we concluded that the frequency of naïve-precursors do not induce diversity on CD8 T cell differentiation patterns. In a second Ms. we evaluated the impact of different pathogens in the diversity of CD8 T cell properties during two different immune responses: OT1 TCR-Tg cells (specific for OVA antigen) in the response to LM-OVA (Listeria Monocytogenes expressing OVA) infection; and P14 TCR-Tg cells (specific for GP33 epitope) in the response to Lymphocytic choriomeningitis vírus (LCMV) infection. We found that OT1 and P14 cells had different properties. As this difference could also be attributed to the different TCR avidity between OT1 and P14 cells, we then compared the behavior of P14 and OT-1 cells in the same mouse, co-injected with LM-OVA and LM-GP33. Since no differences were then detected, these results demonstrated that priming with different pathogens generates CD8 T cells with different characteristics that are not determined by TCR usage, but rather by the infection context. In addition, when looking for the protection capacity of endogenous CD8 memory cells generated in bacterial or viral context, we found that memory cells generated after LCMV priming were more efficient in responding to a second challenge, than memory cells generated after LM-GP33 priming. We also found that this better protection is associated with a T cell effector memory (TEM) phenotype associated with the LCMV infection, in contrast with a T cell central memory (TCM) phenotype generated after LM-OVA infection. These results demonstrate that different pathogens are responsible for diversity of CD8 T cell differentiation patterns and that even when distinct pathogens are efficiently eliminated during the primary immune response the quality of the memory generated may differ. In a third Ms. we studied the mechanisms by which effector CD8 T cells attracted other cell types in the early days of an immune response. We used two experimental systems: the response of OT1 TCR-Tg cells to LM-OVA infection; and the response of anti-HY TCR-Tg cells to male cells (“sterile”-non infectious context). In both cases we found that immediately after activation, CD8 T cells expressed high levels of pro-inflammatory cytokines and chemokines (such as TNFα, XCL1, CCL3 and CCL4). (...)

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La composition des compartiments lymphocytaires T est soumise à de constantes modifications, sous l'effet conjugué de la production de nouvelles spécificités, de la sélection lors d'une rencontre avec un antigène et de la mort cellulaire. Face à ces flux de cellules entre les différents compartiments centraux et périphériques, les mécanismes de la régulation homéostatique assurent le fait que le système immunitaire se maintienne à l'équilibre. A l'image d'un écosystème, on peut alors observer que les lymphocytes T entrent en compétition les uns avec les autres pour des niches de sélection et des ressources en quantité limitée. Durant ce travail de thèse, réalisé chez la souris, nous avons analysé le comportement des lymphocytes T ab CD8+ face à un bouleversement de leur environnement, et nous avons travaillé sur les molécules de classe I du CMH comme modèle de ressource nécessaire à la survie des cellules T ab CD8+.<br />Dans un premier temps, nous avons étudié la sélection centrale et périphérique de cellules T ab CD8+ exprimant deux transgènes codant respectivement pour le TCR aHY, spécifique de l'antigène mâle H-Y, et le TCR P14, spécifique du peptide gp33-41 issu du virus de la chorioméningite lymphocytaire (LCMV). Ce modèle reproduit un phénomène courant dans le système immunitaire, puisqu'on trouve chez l'homme et la souris jusqu'à 30% de cellules exprimant deux TCR différents à leur surface. Nos résultats montrent que l'expression de deux TCR par les cellules T ab CD8+ leur permet d'échapper partiellement à la sélection négative dans le thymus, et de résister à la délétion clonale à la périphérie. Dans un second temps, nous avons étudié l'établissement d'une infection chronique par le LCMV dans des souris n'ayant pour lymphocytes que des cellules T exprimant le TCR P14 (souris MoP14). Nous avons pu observer que cette infection passe par la sélection de variants viraux spécifiquement mutés au niveau de l'épitope gp33-41, mais également par la modification du comportement des cellules T ab CD8+ des animaux. L'ensemble de ces données plaide pour un modèle d'adaptation des lymphocytes T ab CD8+ à leurs conditions environnementales.<br />Enfin, nous avons étendu ce travail à l'étude de l'influence des molécules de classe I du CMH sur la survie et la prolifération homéostatique des lymphocytes T ab CD8+, en utilisant une gamme de souris transgéniques pour le TCR. Nos résultats montrent une variété de comportements en relation avec la réactivité croisée supposée des différents TCR utilisés.

CD8 T cells are essential for the elimination of intracellular pathogens and tumor cells. Understanding how naïve CD8 T cells differentiate into effector cells capable of eliminating pathogens and to generate adequate memory cells during immune responses is fundamental for optimal T cell vaccine design. In this PhD thesis work we addressed two central questions: 1) What are the mechanisms by which early effector T cells could act as pro-inflammatory effectors? And what is their role in the immune response? 2) How heterogeneous are CD8 responses? Could different pathogens modulate CD8 T cell differentiation programs and be responsible for CD8 cell-to-cell heterogeneity? Could they also generate memory cells with different protection capacities? To address these questions related to the diversity of CD8 T cell differentiation during immune responses, we used the single cell RT-PCR technique to detect ex vivo expression of mRNA in each individual cell, and Brefeldin A injected mice to detect ex vivo intracellular proteins. As experimental system to evaluate in vivo cell activation we used T cell receptor transgenic (TCR-Tg) CD8 T cells. Since the use of TCR-Tg cells to study immune responses has been subjected to criticism (due to high frequency of naïve-precursor transfers), in a first Ms. we compared the behavior of TCR-Tg and endogenous (non-transgenic and present at low frequency) cells in the same mouse. We found fully overlapping behavior between these two cell populations, which reinforced the advantage of using TCR-Tg cells to study CD8 immune responses. In addition, we concluded that the frequency of naïve-precursors do not induce diversity on CD8 T cell differentiation patterns. In a second Ms. we evaluated the impact of different pathogens in the diversity of CD8 T cell properties during two different immune responses: OT1 TCR-Tg cells (specific for OVA antigen) in the response to LM-OVA (Listeria Monocytogenes expressing OVA) infection; and P14 TCR-Tg cells (specific for GP33 epitope) in the response to Lymphocytic choriomeningitis vírus (LCMV) infection. We found that OT1 and P14 cells had different properties. As this difference could also be attributed to the different TCR avidity between OT1 and P14 cells, we then compared the behavior of P14 and OT-1 cells in the same mouse, co-injected with LM-OVA and LM-GP33. Since no differences were then detected, these results demonstrated that priming with different pathogens generates CD8 T cells with different characteristics that are not determined by TCR usage, but rather by the infection context. In addition, when looking for the protection capacity of endogenous CD8 memory cells generated in bacterial or viral context, we found that memory cells generated after LCMV priming were more efficient in responding to a second challenge, than memory cells generated after LM-GP33 priming. We also found that this better protection is associated with a T cell effector memory (TEM) phenotype associated with the LCMV infection, in contrast with a T cell central memory (TCM) phenotype generated after LM-OVA infection. These results demonstrate that different pathogens are responsible for diversity of CD8 T cell differentiation patterns and that even when distinct pathogens are efficiently eliminated during the primary immune response the quality of the memory generated may differ. In a third Ms. we studied the mechanisms by which effector CD8 T cells attracted other cell types in the early days of an immune response. We used two experimental systems: the response of OT1 TCR-Tg cells to LM-OVA infection; and the response of anti-HY TCR-Tg cells to male cells ("sterile"-non infectious context). In both cases we found that immediately after activation, CD8 T cells expressed high levels of pro-inflammatory cytokines and chemokines (such as TNFα, XCL1, CCL3 and CCL4). (...)