A highly effective vaccine against malaria is urgently needed, with leading vaccination strategies involving the induction of protective antigen-specific CD8⁺ T-cells via heterologous prime-boost viral vector immunization, targeting primarily the pre- erythrocytic liver stages of the Plasmodium falciparum lifecycle. To date, the greatest immunogenicity has been obtained through a heterologous prime boost regimen, where vaccination with an Adenoviral vector is followed 8 weeks later by a Modified Vaccinia Ankara virus (MVA) boost. Experimental work directed at providing a greater understanding of CD8⁺ T-cell memory responses induced by Ad-MVA vaccinations lead to the development of a novel vaccine strategy aimed at priming CD8⁺ T-cells in the periphery and subsequently targeting them to hepatic tissue with protein loaded poly(lactic- co-glycolic acid) nanoparticles or recombinant viral vectors. Durable Ag-specific CD8+ T- cells exhibiting a phenotype of tissue-resident memory T-cells were generated in the liver, with a ten-fold increase over the conventional heterologous vector regimen. Importantly, in P. berghei sporozoite challenge models of liver-stage malaria, this strategy was found to result in unprecedented levels of sterile protection across multiple clinically relevant antigens and mouse strains. This prime and target immunization strategy for liver-stage malaria may provide a novel general approach for prevention or immunotherapy against other hepato-trophic pathogens.

The receptor tyrosine kinase, RON, is expressed on tissue-resident macrophages. RON functions by activating genes that promote wound repair and resolve inflammation, while repressing genes that perpetuate tissue damage and cell death. Chronic HIV infection is associated with dysregulated inflammation, and we hypothesize that diminished macrophage RON expression contributes to the development of end organ diseases including HIV-associated central nervous system (CNS) inflammation. We utilized CNS tissue from a SIV macaque model to examine the temporal regulation of RON in the brain during infection. Following prolonged SIV infection, RON expression was inversely correlated with the development of CNS disease: RON was highly expressed in animals that did not develop CNS lesions and lower in SIV infected macaques that demonstrated moderate to severe inflammatory lesions. Arginase-1 expression was low during late infection whereas expression of the inflammatory genes, IL-12 p40 and TNF &alpha, was elevated compared to uninfected animals. To validate a role for RON in regulating HIV, we infected human tonsillar tissue-resident macrophages. RON inhibited HIV replication in tissue-resident macrophages. Furthermore, HIV infection diminished RON in tonsil macrophages. We propose a model in which RON expression is decreased, genes that quell inflammation are repressed, and inflammatory mediators are induced to promote tissue inflammation following chronic HIV infection in the brain. The cyclin dependent kinase inhibitor p21 is a factor that, like RON, negatively regulates HIV transcription. Elevated expression of p21 in HIV+ elite controllers, or by ectopic expression in primary CD4+ T cells, resulted in reduced HIV expression. Furthermore, these elite controllers had increased binding of factors that negatively regulate transcription elongation at the HIV long terminal repeat. RON and p21 are examples of cellular factors that limit HIV transcription and contribute to HIV latency. Latently infected cells are not targeted by anti-retroviral therapy and permit rapid rebound of viremia following treatment interruption. Understanding intrinsic mechanisms that establish latency may provide targets for purging these HIV reservoirs or maintaining their transcriptionally silent state.

How CD4 T cells protect against influenza A virus is poorly understood. Here, we address two central questions to better understand how CD4 T cells contribute to immunity during primary and secondary infection. First, we investigate the CD4 T cell-intrinsic requirements for three major transcription factors associated with an antiviral T cell phenotype (termed ‘Th1'): STAT1, STAT4, and T-bet, in directing CD4 T cell responses. We show that STAT4-deficiency does not affect the phenotype or function of wildtype or T-bet-/- CD4 T cells while STAT1-/- cells are virtually undetectable in infected host mice. Depleting NK cells rescues the STAT1-/- cells that phenocopy the compromised Th1 identity of T-bet-/- cells. Finally, we show that cytokine-mediated STAT4 activation enhances infection-induced Th1-polarization and that engaging STAT1 and STAT4 during priming dramatically improves CD4 T cell antiviral capacity. These results are relevant to T cell-based vaccine strategies aiming to promote the most efficient anti-viral T cell responses. Second, we asked the extent to which the recall of influenza-specific lung-resident memory CD4 T cells (TRM) impact the generation of new primary anti-viral T cells. TRM rapidly induce local inflammatory responses that control infection before protective T cells activated in secondary lymphoid organs reach sites of infection. Whether antigen-sensing by TRM can impact T cell priming in secondary lymphoid organs is unclear. We show that activation of influenza-primed lung TRM by antigen delivered into the airways enhances the number and activation status of antigen-bearing dendritic cells in draining lymph nodes. This accelerates the priming of naïve T cells and enhances their recruitment to the lung. Importantly, this TRM-dependent circuit enables productive T cell responses even against levels of airways antigen too low to otherwise activate naïve T cells. This adjuvant-like impact of lung TRM highlights a novel integration of local and regional T cell immunity.

Acute lower respiratory tract infections are a persistent and pervasive public health burden, often caused by Streptococcus pneumoniae. Hospitalization rates due to pneumonia fall dramatically during early childhood, remain low during early adult years, and then increase steadily around middle age. The low-susceptibility period of early adulthood is likely due to frequent respiratory exposures to diverse pneumococcal serotypes resulting in serotype-independent heterotypic immunity. We hypothesize that resolution of repeated respiratory pneumococcal infections establish capsule-independent, lung-resident adaptive immunity that protects against subsequent unrelated pneumococcal pneumonia. In our model of naturally acquired heterotypic immunity, mice are infected with diverse serotypes of pneumococci in the respiratory tract, given time to recover, and then challenged by pulmonary infection with a highly virulent serotype 3 pneumococcus (Sp3). Prior exposures to unrelated pneumococci resulted in multi-log reductions in Sp3 bacterial lung burdens and long-term sterilizing immunity. The enhanced lung defense during pneumonia included more Th17 cells in the lung and significantly elevated IL-17A as well as neutrophils in the airspaces. Depletion of CD4+ cells resulted in less effective antibacterial defense. Upon ex vivo stimulation with pneumococcus lung-resident CD4+ cells produced multiple protective cytokines including IL-17A, IFN-γ, IL-22, IL-2, and TNF-α. In protected lungs, there were increased numbers of CD4+ resident memory T (TRM) cells, confined to the anatomic region of the initial infections. Heterotypic protection was also confined to the site of previous pneumococcal infections. Previously-exposed mice challenged in their contralateral lobes were not protected. RNAseq analysis of heterotypic lungs 24h after Sp3 infection revealed an enrichment of lymphocyte-related pathways including immunoglobulin and other B cell-related genes. B cell-deficient µMT-/- mice exposed to pneumococci had intermediate protection against Sp3 pneumonia, better than naïve mice but less effective than fully immunocompetent peers. Plasma from mice previously exposed to pneumococci was sufficient to protect naïve mice against Sp3 pneumonia. We conclude that mechanisms of naturally-acquired heterotypic protection against pneumococcus involve both lung-resident cell-mediated and humoral immunity and importantly this protection can be compartmentalized within the lung. Advancing our understanding of these mechanisms will guide future vaccine development and treatment strategies for lung disease.

Influenza A virus (IAV) is a major cause of serious respiratory illness worldwide, leading to approximately 5 million severe cases and 500,000 deaths per year. Given the disease severity, associated economic costs, and recent appearance of novel IAV strains, there is a renewed interest in developing novel and efficacious “universal” IAV vaccination strategies as well as therapeutic remedies. Previous studies from our laboratory have concentrated on IAV-specific CD8 T cell-mediated protection against IAV infection as IAV-specific CD8 T cells are needed for efficient clearance of virus. Recent studies highlight that immunizations capable of generating local (i.e., nasal mucosa and lung) tissue-resident memory T and B cells in addition to systemic immunity offer the greatest protection against future IAV encounters. Current IAV vaccines are designed to largely stimulate IAV-specific antibodies, but do not generate the lung-resident memory T and B cells induced during IAV infections. In order to effectively generate lung-resident memory populations, it is believed a local antigen depot is needed as tissue-resident memory formation is enhanced by the presence of local antigen. Recently, polyanhydride nanoparticles have been demonstrated to slowly release their contents at the site of inoculation serving as an antigen depot. However, the ability of an intranasal vaccination with polyanhydride nanoparticles to induce IAV-specific lung-resident immune responses and provide protection against subsequent IAV infection has not been determined. Here, I report on the intranasal administration of a biocompatible polyanhydride nanoparticle-based IAV vaccine (IAV-nanovax). IAV-nanovax is capable of providing protection against subsequent homologous and heterologous IAV infections in both inbred and outbred populations. My findings demonstrate that vaccination with IAV-nanovax promotes the induction of germinal center B cells within the lungs that are associated with both systemic IAV-specific IgG as well as local lung IAV-specific IgG and IgA antibodies. Furthermore, intranasal IAV-nanovax vaccination leads to a significant increase in IAV-specific CD4 and CD8 T cells within the lung vasculature as well as in the lung tissue. Most importantly, my studies demonstrate that IAV-nanovax induced lung-resident IAV-specific CD4 and CD8 T cells express canonical tissue-resident memory markers. This dissertation further explores a novel regulation pathway previously identified by our laboratory where plasmacytoid dendritic cells (pDCs) eliminate IAV-specific CD8 T cells early during high-dose and high-pathogenic IAV infections in a FasL:Fas (pDCs:CD8 T cell) dependent manner. However, recent studies suggest that B cells are the predominate lymphocyte to express FasL in mice. Here, I demonstrate that FasLpos B cells greatly outnumber FasLpos pDC within the lung draining lymph nodes (dLNs) during IAV infections. Interestingly, my results demonstrate the presence of two subsets, CD11cpos and CD11cneg, of FasL-expressing B cells that differentially influence the IAV-specific CD8 T cell response during high-dose IAV infections. While CD11cneg B cells kill IAV-specific CD8 T cells, contributing to lethality during high-dose IAV infections, CD11cpos B cells may instead be protective. In addition to the negative impacts of high-dose IAV infections, I also demonstrate that chronic ethanol (EtOH) consumption detrimentally impacts existing IAV-specific CD8 T cell memory responses. Here, my results reveal that chronic EtOH consumption causes a numerical loss in existing IAV-specific CD8 T cell memory responses. This numerical loss in existing IAV-specific CD8 T cell memory is associated with a reduction in cytotoxic activity within the lungs as well as an increase in morbidity and mortality during a secondary IAV challenge. Together, the results presented herein demonstrate the ability of a novel polyanhydride nanovaccine to induce robust pulmonary IAV-specific T and B cell responses and further our understanding of factors that can negatively impact IAV-specific CD8 T cells as well as protection against IAV infection. Overall these findings highlight the importance of IAV-specific CD8 T cells, as well as CD4 T cells and B cells, in providing protection against IAV infections.

Tuberculosis (TB) is a global health problem, which is proving extremely difficult to control in the absence of an effective vaccine. Bacille Calmette-Guérin (BCG), the only vaccine currently licensed against TB, demonstrates variable efficacy in humans and cattle. A greater understanding of what constitutes a protective host immune response is required in order to aid the development of improved vaccines. Tissue-resident memory T cells (T_RM) are a recently-identified subset of T cells, which may represent an important aspect of protective immunity to TB. This thesis aims to characterise the role of lung T_RM in BCG-induced protection against TB. In a mouse model, intravascular staining allowed discrimination between lung-vascular and lung-parenchymal T cells. Experiments demonstrated that BCG vaccination induced a population of antigen-specific lung-parenchymal CD4⁺ T cells, a putative tissue-resident population. This lung-parenchymal population was significantly increased in frequency following mucosal BCG vaccination, compared to systemic BCG vaccination. This correlated with enhanced protection against Mycobacterium tuberculosis (M.tb) infection in the lungs of mice receiving mucosal BCG, compared to those receiving systemic BCG. Mucosal BCG induced lung-parenchymal CD4⁺ T cells with enhanced proliferative capacity and a PD1⁺KLRG1^- cell-surface phenotype, a memory-like phenotype associated with improved protection against M.tb infection. These cells may represent a BCG-induced lung T_RM population responsible for the enhanced protection observed following mucosal BCG. Overall, this thesis highlights the potential of mucosal vaccination to elicit lung T_RM and identifies this as a possible immunological mechanism underlying enhanced protection against M.tb infection. These cells may constitute an important target for future vaccination strategies.

In the recent years, it has been well established that primary respiratory viral infection-induced lung resident memory CD8 T cells (TRM) characterized by the expression of integrins CD49a and CD103, as well as the early-activation marker CD69, constitute the first line of defense against reinfection. On the other hand, viral vector-based respiratory mucosal (RM) vaccination, as well as parenteral vaccination followed by airway luminal manipulation induce lasting and protective lung T cell immunity towards pulmonary tuberculosis (TB). However, it remains poorly understood whether and how these TB vaccination strategies induce TRM in the lung. As such, within this thesis we will investigate generation of lung CD8 TRM upon different TB vaccination strategies and the underlying mechanisms regulating establishment of such cells. Here using distinct models of replication-deficient adenoviral vector-based TB vaccination, we find that RM vaccination leads to generation of lung CD8 TRM identified by the expression of CD69, CD103, and very late activation Ag 1 (VLA-1). These TRM-associated molecules are acquired by CD8 T cells in distinct tissues. In this regard, VLA-1 is acquired during T cell priming in draining mediastinal lymph nodes (dMLNs) and the others acquired after T cells entered the lung. Once in the lung, Ag-specific CD8 TRM continue to express VLA-1 at high levels through the effector/expansion, contraction, and memory phases of T cell responses. We also reveal that VLA-1 is not required for homing of these cells to the lung, but it negatively regulates them in the contraction phase. Furthermore, VLA-1 has a negligible role in the maintenance of such cells in the lung. Separately, we have observed that while parenteral intramuscular vaccination alone does not induce lung CD8 TRM, subsequent RM inoculation of an Ag-dependent, but not a non-specific inflammatory agonist induces lung CD8 TRM. Such generation of lung CD8 TRM needs CD4 T cell help. These findings not only fill the current knowledge gap, but also hold important implications in developing effective vaccination strategies towards mucosal intracellular infectious diseases such as acquired immunodeficiency syndrome (AIDS), TB and herpes virus infection. / Thesis / Doctor of Philosophy (PhD)

Verstärkte Anstrengungen zur Förderung der T-Zell-basierten Immunität haben eine zwingende Notwendigkeit für unser Verständnis der menschlichen T-Zell-Funktion und –Erhaltung geschaffen. Das Paradigma, dass Gedächtnis-T-Lymphozyten kontinuierlich durch den Körper zirkulieren wurde vor kurzem durch die Entdeckung der Gedächtnis-T-Zellen, die in einer Vielzahl von Geweben, einschließlich des Knochenmarks angesiedelt sind, herausgefordert. Allerdings bleibt der Unterschied zwischen Funktionsweise von zirkulierenden und gewebeansässigen Gedächtnis-T-Zellen nur unzulänglich verstanden. Die Knochenmark ist die Heimat für eine große Anzahl Gedächtnis-T-Zellen. CD4+ Gedächtnis-T-Zellen aus dem Knochenmark beinhalten ein breites Spektrum an Antigenspezifitäten. Interessanterweise wurden CD4+ Gedächtnis-T-Zellen spezifisch für systemische Kindheitsantigene im Knochenmark von älteren Menschen gefunden, auch wenn sie nicht mehr in der Blutzirkulation nachgewiesen werden konnten. Gedächtnis-T-Zellen aus dem Knochenmark sind sesshaft und ruhend und Langzeitgedächtnis gegen systemische Antigene erhalten. Sowohl der Überlebensmechanismus von Gedächtnis-T-Zellen, als auch die Kapazität von gewebsansässigen Gedächtnis-T-Zellen nach einer systemischen Herausforderung mobilisiert zu werden, sind bisher nur unzureichend geklärt. Ich habe gezeigt, dass Gedächtnis-T-Zellen aus dem peripheren Blut und Knochenmark unterschiedliche Überlebensfähigkeiten haben. Weiterhin habe ich die Rolle von Überleben Faktoren in ihrer Erhaltung identifiziert. Zudem habe ich bestimmt, dass Gedächtnis-T-Zellen aus dem Blut und Knochenmark unterschiedliche Zellpopulationen sind, mit unterschiedliche TCRβ Repertoires. Schließlich konnte ich zeigen, dass sesshafte Gedächtnis-T-Zellen, die spezifisch für systemische Antigene sind, schnell in die Blutzirkulation mobilisiert werden. Zusammenfassend bieten diese Studien ein umfassenderes Verständnis der Funktion und des Erhalts des immunologischen Gedächtnisses. / Intensified efforts to promote protective T cell-based immunity in vaccines and immunotherapies have created a compelling need to expand our understanding of human T cell function and maintenance. The paradigm that memory T lymphocytes are continuously circulating through the body in search of their cognate antigen has been recently challenged by the discovery of memory T cells residing in a variety of tissues, including the bone marrow (BM). However, the division of labor and lifestyle of circulating versus tissue resident memory T cells remains poorly understood. The human BM is home to a great number of memory T cells. BM memory CD4+ T cells contain a wide array of antigen specificities. Interestingly, memory CD4+ T cells specific for systemic childhood antigens have been found in the BM of elderly humans, even when they were no longer detectable in peripheral blood (PB) circulation. BM memory T cells are resident, resting and maintain long-term memory to systemic antigens. The survival mechanisms of circulating and BM resident memory T cells; as well as the capacities of tissue resident memory T cells to be mobilized into blood circulation after systemic antigen re-challenge to confer us with immune protection remains to be elucidated. I have shown that PB and BM memory T cells have different survival capacities, as well as identified the role of survival factors in their maintenance. Moreover, using sequencing analysis of the TCRβ repertoire, I have determined that PB and BM memory T cells are separated cell populations. Finally, by tracking the dynamics of antigen-specific memory CD4+ T cells after systemic MMR re-vaccination I could show that TRM CD4+ T cells specific for systemic antigens can be rapidly mobilized into blood circulation and contribute to the immune response. These studies provide a more comprehensive understanding of the function and maintenance of immunological memory in humans.

Les eczémas [eczéma allergique de contact (EAC) et l'eczéma atopique (EA)] sont des dermatoses inflammatoires fréquentes des pays industrialisés. Elles sont induites suite au recrutement et à l'activation dans la peau de lymphocytes T spécifiques d'allergènes, qui sont présents dans notre environnement, et qui sont habituellement très bien tolérés par la majoritédes individus exposés. Ce travail de thèse porte sur un aspect novateur de la physiopathologie des eczémas, à savoir : la contribution des lymphocytes T mémoires résidants (LTrm) dans la peau à la chronicité et à la sévérité de ces maladies.Capitalisant sur des modèles précliniques pertinents ainsi que sur des échantillons cliniques prélevés chez les patients, ce travail a permis d'acquérir de nouvelles connaissances : (i) de nombreux LTrm CD8+ spécifiques colonisent les lésions d'eczéma (ii) ils s'accumulent avecla persistance de l'allergène dans la peau, (iii) ils jouent un rôle majeur dans les récidives de la maladie, mais (iv) ils expriment à leur surface divers récepteurs inhibiteurs, tels que PD-1 ou TIM-3, qui empêchent la survenue de réponses allergiques excessives.Ces travaux apportent donc des informations majeures sur la nature unique des LTrm CD8+ spécifiques d'allergènes et des mécanismes qui contrôlent leur réactivation, afin de préserver l'intégrité de la peau et la survenue de réactions chroniques sévères. Le développement des nouvelles stratégies thérapeutiques ciblant la réactivation des LTrm via leurs récepteursinhibiteurs pourrait permettre de restaurer la tolérance chez les individus allergiques / Allergic contact dermatitis (ACD) and atopic dermatitis (AD), also referred to contact or atopic eczema, are frequent skin inflammatory diseases with increasing prevalence and high socioeconomic impact in Western countries. Eczemas are the prototype of skin delayed-type hypersensitivity reactions. Skin lesions are induced by the recruitment and activation in the skin of effector/memory T cells specific for environmental antigens that are innocuous to healthy non-allergic individuals.The aim of this work was to better understand the pathophysiology of eczemas by a comprehensive analysis of the contribution of skin resident memory T cells (Trm) to the chronicity and severity of these diseases.Capitalizing on relevant preclinical eczema models and on clinical samples collected from allergic patients, this work showed that: (i) numerous allergen-specific CD8+Trm colonize the eczema lesion, (ii) they accumulate in the epidermis in response to the long-term persistence of the allergen in the skin, (iii) they are instrumental for the recurrence of eczema, but (iv) theyexpress several inhibitory check point receptors (ICRs, such as PD-1, TIM-3) at their surface, which keep them in check to prevent the development of severe immunopathology.Thus, our work provides important information for considering the unique nature of hapteninduced CD8+ Trm and the mechanisms that prevent their unwanted reactivation and subsequent development of chronic or severe skin allergy. The development of therapeutic strategies targeting the reactivation of skin Trm in situ via their ICRs should open new avenues to restore tolerance in allergic individuals