<div> <p>Pancreatic ductal adenocarcinoma (PDAC) is a poorly immune responsive, treatment refractory disease, representing the fourth leading cause of cancer deaths in the United States. A lack of significant improvements in patient prognoses over the last few decades highlights the necessity for a more basic understanding of how PDAC develops and progresses. To this end, the research outlined here investigates the contributions of SOX9 and PAR1 in PDAC initiation and tumor immune evasion, respectively. </p> <p>SOX9 is a developmental transcription factor important for proper pancreas development that is restricted to only a small subset of cells in the adult organ. However, SOX9 is aberrantly expressed in precancerous lesions of the pancreas and throughout PDAC development. Using genetically engineered mouse models we demonstrated that PDAC precursor lesions cannot form in the absence of SOX9 and conversely formed at an accelerated rate when SOX9 was ectopically expressed. Surprisingly deletion of SOX9 in primary mouse PDAC cell lines had no impact on tumor growth in subcutaneous allograft experiments, indicating that although SOX9 expression is necessary for PDAC initiation, it is dispensable in many cases for tumor maintenance and growth. Research investigating the transcriptional changes induced by SOX9 prior to lesion formation is ongoing to identify additional downstream factors critical for disease initiation. </p> <p>Previous research has shown that PDAC tumors frequently display low levels of immune infiltration, which is a major limitation for the use of immune-based therapeutics and is generally an unfavorable prognostic factor. We show that in primary mouse tumor cells ablation of the thrombin receptor PAR1 caused a significant increase in the infiltration of tumor targeting CD8a⁺T cells which in turn were found to eliminate PAR1 knockout tumors. When PAR1^KO and PAR1 expressing PDAC tumor cells were co-injected into wild type mice, cells lacking PAR1 were preferentially targeted and eliminated by the immune system, indicating that PAR1 provides cell autonomous protection during an active anti-tumor adaptive immune response. Furthermore, we identified a previously underappreciated association between PAR1-mediated expression of <i>Csf2</i> and <i>Ptgs2</i>, and PDAC tumor immune evasion. Together these findings provide novel insights into the mechanisms and drivers of PDAC initiation and immune evasion.</p> </div> <br>

The innate immune system provides the first line of defense against infection. Pathogens are detected though a variety of Pattern Recognition Receptors (PRRs), which activate downstream signaling cascades. Effector molecules such as cytokines and chemokines are released upon activation and aid in cell recruitment, control of pathogen replication, and coordination of the adaptive immune response. Nucleic acids that are released into the cytosol during viral and bacterial infection are recognized through a special class of PRRs, coined cytosolic nucleic acid sensors. Upon recognition, these receptors induce the production of type I interferons and other cytokines to aid in pathogen clearance. Although many cytosolic nucleic acid sensors have been discovered, it is unclear how they work in concert to mediate these responses. The Interferon Gamma Inducible protein (IFI)16 and its proposed mouse orthologue IFI204 are cytosolic DNA sensors that have been linked to the detection of cytosolic DNA during infection with Herpes Simplex Virus (HSV-1). IFI16 binds dsDNA that has been released into the cytosol during viral infection and engages the adaptor molecule Stimulator of Interferon Genes (STING) leading to TANK binding kinase-1 (TBK1) dependent phosphorylation of interferon regulatory factor 3 (IRF3) and transcription of type I interferons and interferon stimulated genes. In addition to its role as a sensor, in chapter two of this thesis we describe a broader role for IFI16 in the regulation of the type I IFN response to RNA and DNA viruses in anti-viral immunity. In an effort to better understand the role of IFI16 in coordinating type I IFN gene regulation, we generated cell lines with stable knockdown of IFI16 and examined responses to DNA and RNA viruses as well as other inducers of IFN such as cyclic-dinucleotides. As expected, stable knockdown of IFI16 led to a severely attenuated type I IFN response to cytosolic DNA ligands and DNA viruses. In contrast, expression of the NF-κB regulated cytokines such as IL-6 and IL-1β were unaffected in IFI16 knockdown cells, suggesting that the role of IFI16 in sensing these triggers was unique to the type I IFN pathway. Surprisingly, we also found that knockdown of IFI16 led to a severe attenuation of expression of IFN-α and IFN stimulated genes such as RIG-I in response to cyclic GMP-AMP (cGAMP), a second messenger produced in response to cGAS, as well as RNA ligands and viruses. Analysis of IFI16 knockdown cells revealed compromised occupancy of RNA polymerase II on the IFN-α promoter in IFI16 knockdown cells suggesting that transcription of ISGs is dependent on IFI16. Since IFI16 knockdown compromised not only DNA virus driven pathways, we propose additional regulatory roles outside of DNA sensing. Collectively, these results indicate that IFI16 plays a role in the regulation of type I IFN gene transcription and production in response to both RNA and DNA viruses. The role of IFI16/IFI204 has been studied extensively in vitro, however the role of the receptors in vivo has yet to be determined. In chapter three of this thesis, we developed a mouse deficient in IFI204 to explore the role of IFI204 in in vivo immune responses to viruses. We investigated the ability of IFI204 deficient cells to induce type I interferons and other cytokines in response to a panel of DNA and RNA ligands in vitro. IFI204 deficient BMDMs displayed a partial defect in type I interferon induction in response to both DNA and RNA ligands and viruses as compared to WT mice. We also observed that this phenotype is time dependent, since there was no change in type I interferon induction after 12 hours post infection as compared to earlier time points. In contrast to these results, expression of the NF-κB regulated cytokines IL-6 and IL-1β were unaffected in IFI16 knockdown cells. These results suggest that IFI204 plays a partial role in the induction of type I interferons in response to both DNA and RNA ligands. Additionally, IFI204 may work in tandem with other receptors in a sequential manner to amplify the type I interferon response. We also studied the involvement of IFI204 in an in vivo model of HSV-1 infection. IFI204 knockout mice produce less brain and serum IFN-β, IL-6, and IL-1β 72 hours post intraperitoneal infection with HSV-1. Furthermore, IFI204 -/- mice are more susceptible to HSV-1 infection as compared to WT mice. These data indicate that IFI204 mediates the response to HSV-1 in vivo by inducing the production of cytokines that are necessary for the control of viral infection.

La phagocytose est un processus cellulaire par lequel de larges particules sont internalisées dans une vésicule, le phagosome. Lorsque formé, le phagosome acquiert ses propriétés fonctionnelles à travers un processus complexe de maturation nommé la biogénèse du phagolysosome. Cette voie implique une série d’interactions rapides avec les organelles de l’appareil endocytaire permettant la transformation graduelle du phagosome nouvellement formé en phagolysosome à partir duquel la dégradation protéolytique s’effectue. Chez l’amibe Dictyostelium discoideum, la phagocytose est employée pour ingérer les bactéries de son environnement afin de se nourrir alors que les organismes multicellulaires utilisent la phagocytose dans un but immunitaire, où des cellules spécialisées nommées phagocytes internalisent, tuent et dégradent les pathogènes envahissant de l’organisme et constitue la base de l’immunité innée. Chez les vertébrés à mâchoire cependant, la transformation des mécanismes moléculaires du phagosome en une organelle perfectionnée pour l’apprêtement et la présentation de peptides antigéniques place cette organelle au centre de l’immunité innée et de l’immunité acquise. Malgré le rôle crucial auquel participe cette organelle dans la réponse immunitaire, il existe peu de détails sur la composition protéique et l’organisation fonctionnelles du phagosome. Afin d’approfondir notre compréhension des divers aspects qui relient l’immunité innée et l’immunité acquise, il devient essentiel d’élargir nos connaissances sur les fonctions moléculaire qui sont recrutées au phagosome. Le profilage par protéomique à haut débit de phagosomes isolés fut extrêmement utile dans la détermination de la composition moléculaire de cette organelle. Des études provenant de notre laboratoire ont révélé les premières listes protéiques identifiées à partir de phagosomes murins sans toutefois déterminer le ou les rôle(s) de ces protéines lors du processus de la phagocytose (Brunet et al, 2003; Garin et al, 2001). Au cours de la première étude de cette thèse (Stuart et al, 2007), nous avons entrepris la caractérisation fonctionnelle du protéome entier du phagosome de la drosophile en combinant diverses techniques d’analyses à haut débit (protéomique, réseaux d’intéractions protéique et ARN interférent). En utilisant cette stratégie, nous avons identifié 617 protéines phagosomales par spectrométrie de masse à partir desquelles nous avons accru cette liste en construisant des réseaux d’interactions protéine-protéine. La contribution de chaque protéine à l’internalisation de bactéries fut ensuite testée et validée par ARN interférent à haut débit et nous a amené à identifier un nouveau régulateur de la phagocytose, le complexe de l’exocyst. En appliquant ce modèle combinatoire de biologie systémique, nous démontrons la puissance et l’efficacité de cette approche dans l’étude de processus cellulaire complexe tout en créant un cadre à partir duquel il est possible d’approfondir nos connaissances sur les différents mécanismes de la phagocytose. Lors du 2e article de cette thèse (Boulais et al, 2010), nous avons entrepris la caractérisation moléculaire des étapes évolutives ayant contribué au remodelage des propriétés fonctionnelles de la phagocytose au cours de l’évolution. Pour ce faire, nous avons isolé des phagosomes à partir de trois organismes distants (l’amibe Dictyostelium discoideum, la mouche à fruit Drosophila melanogaster et la souris Mus musculus) qui utilisent la phagocytose à des fins différentes. En appliquant une approche protéomique à grande échelle pour identifier et comparer le protéome et phosphoprotéome des phagosomes de ces trois espèces, nous avons identifié un cœur protéique commun à partir duquel les fonctions immunitaires du phagosome se seraient développées. Au cours de ce développement fonctionnel, nos données indiquent que le protéome du phagosome fut largement remodelé lors de deux périodes de duplication de gènes coïncidant avec l’émergence de l’immunité innée et acquise. De plus, notre étude a aussi caractérisée en détail l’acquisition de nouvelles protéines ainsi que le remodelage significatif du phosphoprotéome du phagosome au niveau des constituants du cœur protéique ancien de cette organelle. Nous présentons donc la première étude approfondie des changements qui ont engendré la transformation d’un compartiment phagotrophe à une organelle entièrement apte pour la présentation antigénique. / Phagocytosis is a cellular process by which large particulate material are internalized in a newly formed vesicule, the phagosome. Once formed, the phagosome acquires its functional properties through a complex maturation process called phagolysosome biogenesis. This pathway involves a series of rapid interactions with organelles of the endocytic apparatus, enabling the gradual transformation of newly formed phagosomes into phagolysosomes in which proteolytic degradation occurs. The amoeba Dictyostelium discoideum uses phagocytosis as a predation mechanism for feeding, whereas multicellular organisms utilize this process as an immune mechanism where specialized cells named phagocytes internalize, kill and degrade phatogens found through the host, forming the basis of innate immunity. In jawed verterbrates however, the phagosome links innate and adaptive immunity by processing and presenting antigenic peptides. Despite its crucial role in immunity, little is known about the composition and the functional organization of the phagosome. It is therefore essential to characterize in details the functional properties that are recruited to the phagosome. High-throughput proteomics analysis of isolated phagosomes has been tremendously helpful for the molecular comprehension of this organelle. Studies of our lab notably have revealed the first proteomics identification of mouse phagosomes without determining the roles of these proteins through the complex process of phagocytosis (Brunet et al, 2003; Garin et al, 2001). In the first study of this thesis (Stuart et al, 2007), we characterized the functions of the entire drosophila phagosome proteome by combining high-throughput proteomics, interactive networks and RNAi. By applying this strategy, we’ve identified 617 phagosomal proteins by mass spectrometry from which we’ve expanded this list by building the phagosome interactome. The contribution of each protein to bacterial internalization was tested and validated by RNAi and led to the identification of a new regulator of phagocytosis, the exocyst complex. In generating this 'systems-based model', we show the power of applying this approach to the study of complex cellular processes and organelles and expect that this detailed model of the phagosome will provide a new framework for studying host-pathogen interactions and innate immunity. In the second study of this thesis (Boulais et al, 2010), we characterized some of the key steps that contributed to the remodeling of phagosomes functional properties during evolution. To do so, we isolated this organelle from three distant organisms: the amoeba Dictyostelium discoideum, the fruit fly Drosophila melanogaster, and mouse (Mus musculus) that use phagocytosis for different purposes. By performing and comparing proteomics and phosphoproteomics analyses of isolated phagosomes from the three species, we identified an ancient core of phagosomal proteins around which the immune function of this organelle have likely organized. Our data indicate that a larger proportion of the phagosome proteome, has been acquired through gene duplication at periods coinciding with the emergence of innate and adaptive immunity. Our study also characterizes in detail the acquisition of novel proteins and the significant remodeling of the phagosome phosphoproteome that contributed to modify the core constituents of this organelle in evolution. Our work thus provides the first thorough analysis of the changes that enabled the transformation of the phagosome from a phagotrophic compartment into an organelle fully competent for antigen presentation.

INTRODUÇÃO: Imunodeficiências primárias são um grupo heterogêneo de distúrbios de origem genética que afetam a imunidade e se caracterizam por infecções de repetição. Aproximadamente metade dos casos estão ligados a deficiências humorais e dentre estas podemos destacar a Imunodeficiência Comum Variável (ICV). Uma vez que os pacientes com ICV possuem redução dos níveis de anticorpos, esses pacientes apresentam infecções recidivantes do trato respiratório e aproximadamente 90% tiveram no mínimo um episódio de rinossinusite (RNS). A RNS se instala devido ao desequilíbrio entre o meio ambiente e fatores do hospedeiro e a infecção viral é pelo menos 20 vezes mais frequente do que a infecção bacteriana em indivíduos normais. OBJETIVOS: (1) Identificar os agentes virais da RNS nos pacientes com ICV e em indivíduos controles em um contexto prospectivo; (2) Definir quais citocinas e quimiocinas estão presentes e avaliar a expressão de genes relacionados à imunidade inata e adaptativa antiviral no lavado nasal de pacientes com ICV e nos indivíduos controles. CASUÍSTICA, MATERIAIS E MÉTODOS: Pacientes com ICV e indivíduos controles foram avaliados quando apresentavam sinais e sintomas de uma RNS viral e foi realizado a coleta de lavado nasal para a identificação de vírus respiratórios, além da quantificação da secreção de citocinas e quimiocinas e da avaliação da expressão gênica de genes relacionados à imunidade inata e adaptativa antiviral. A avaliação foi repetida quando todos os indivíduos previamente estudados se encontravam assintomáticos. RESULTADOS: De abril de 2012 a novembro de 2014, foram colhidas 65 amostras de lavado nasal, 43 amostras de 34 indivíduos controles e 22 amostras de 14 pacientes com ICV. Quatro amostras foram positivas para vírus pela técnica da imunofluorescência direta e dezoito amostras foram positivas pelo PCR. Pacientes com ICV tiveram mais infecções, duração maior dos sintomas e maior necessidade de uso de antibióticos que o grupo controle. A avaliação da produção de citocinas e quimiocinas no lavado nasal mostrou aumento da secreção de CXCL10, CCL2, CCL5, CXCL8 IL-6, IL-10, IL-1beta e TNF em ambos os grupos quando esses apresentavam quadro agudo de RNS viral. Foi realizada a expressão de genes pela técnica do PCR Real Time. Os pacientes com ICV apresentaram um aumento de expressão de genes relacionados à imunidade inata e adaptativa anitiviral substancialmente maior frente a um quadro de RNS viral do que os indivíduos controles em situações semelhantes. Quando comparamos os pacientes ICV e os controles ambos sem infecção aguda, observamos que os genes apresentam em sua maioria uma redução de expressão nos pacientes com ICV. DISCUSSÃO: Os vírus detectados respeitaram a sazonalidade em que normalmente são detectados e pacientes com ICV proporcionalmente tiveram mais infecções e uma evolução pior que o grupo controle. Aparentemente não houve diferenças significativas entre os grupos estudados quanto à liberação de citocinas e quimiocinas. Com relação ao estudo da expressão gênica, a maior amplitude de variação observada nos pacientes com ICV pode significar um desajuste de resposta imune levando a um quadro de maior inflamação local com consequente maior dano tecidual e justificando assim a incidência aumentada de complicações, duração aumentada dos sintomas e replicação viral aumentada nesse grupo de pacientes / INTRODUCTION: Primary immunodeficiencies (PIDs) are a heterogeneous group of genetic disorders that affect immunity and are characterized by relapsing, usually severe infections. Approximately half of the cases are linked to humoral deficiencies, being common variable immunodeficiency (CVID) the most frequent. CVID patients have reduced levels of antibodies; therefore, these patients have recurrent infections in the respiratory tract and approximately 90% had at least one episode of rhinosinusitis (RS). RS installs itself due to the imbalance between the environment and host factors and viral infection is at least 20 times as common as the bacterial infection in normal individuals. OBJECTIVES: (1) Identify the viral agents of rhinosinusitis in patients with CVID and in control individuals on a prospective context; (2) define which cytokines and chemokines are present in the nasal wash and evaluate the expression of genes related to innate and adaptive antiviral immunity in nasal wash of CVID patients and in control individuals. CASES, MATERIALS, AND METHODS: patients with CVID and control individuals were examined at Outpatient Facility of Dermatological Manifestations of Primary Immunodeficiencies and when they presented signs and symptoms of a viral RS. Nasal wash was collected in order to identify respiratory viruses; secretion of cytokines and chemokines were quantified and gene expression of genes related to innate and adaptive antiviral immunity were evaluated. This evaluation was repeated when all individuals previously studied were asymptomatic. RESULTS: From April 2012 to November 2014, 65 samples of nasal wash, 43 samples of 34 control individuals and 22 samples of 14 patients with CVID were collected. Four samples were positive for virus by direct immunofluorescence technique and eighteen samples by PCR. The detected viruses behaved according to the season in which they are normally detected and patients with CVID proportionally had more and longer infections and required more antibiotics than the control group. The evaluation of the production of cytokines and chemokines showed an increased secretion of CXCL10, CXCL8 CCL2, CCL5, IL-6, IL-10, IL-1beta and TNF in both groups when they presented acute viral RS. Gene expression was performed by using Real Time PCR. CVID patients showed increased expression of genes related to innate and adaptive antiviral immunity when compared to control individuals presenting acute viral RS. Conversely, when we compared CVID patients and control individuals both without acute infection, we observed a reduction in gene expression in CVID patients. DISCUSSION: The viral rhinosinusitis respected seasonality and CVID patients had proportionally more infections and a worse evolution than the control group. Apparently, there were no significant differences between the groups regarding the release of cytokines and chemokines. The greater magnitude of gene expression variation observed in CVID patients suggests an imbalance of immune response leading to a state of greater local inflammation with consequent greater tissue damage, therefore justifying an increased incidence of complications, increased duration of symptoms and increased viral replication in this group of patients

Embora a fumaça do cigarro configure-se como o principal fator de risco para o desenvolvimento da DPOC, nem todos os fumantes desenvolvem a DPOC clinicamente significativa, sugerindo outros fatores intrínsecos ao indivíduo, como diferenças nas respostas imunológicas envolvidas na patogênese e progressão desta doença. Objetivos: Compreender melhor o papel da resposta imune adaptativa na progressão da DPOC. Métodos: Foram estudados amostras de tecidos pulmonares de 21 indivíduos não fumantes (grupo controle); 22 fumantes não obstrutivos (FNO) e 17 fumantes com DPOC. A densidade de células CD4+ e CD8+, células T regulatórias (Treg) FOXP3+, células B e células positivas para interleucinas IL-10 e IL-17, e citocinas como CCL19, BAFF e TGF-beta foram avaliadas em pequenas e grandes vias aéreas, e em tecidos linfoides associados ou não aos brônquios (BALT e iBALT, respectivamente). Resultados: Observamos um aumento das células T CD4+ e CD8+ em pequenas e grandes vias aéreas, BALT e iBALT em fumantes; no entanto, os valores mais elevados foram detectados em pequenas vias aéreas dos indíviduos DPOC. Além disso, observouse uma diminuição na expressão de TGF-? em pacientes com DPOC em comparação aos grupos de FNO e controle em pequenas e grandes vias aéreas ao passo que uma diminuição na densidade de Treg foi observado apenas em pequenas vias aéreas, com consequente diminuição da densidade de células positivas para IL-10 em pequenas e grandes vias aéreas. Em BALT observou-se uma resposta diferente, com um aumento na densidade de Treg no grupo DPOC, sem diferenças para as análises de IL-10. Houve um aumento da densidade de células positvas para IL-17 em pequenas e grandes vias aéreas e iBALT na DPOC. Conclusões: Observamos que a redução da atividade regulatória do processo inflamatório em pequenas vias aéreas e a progressão da obstrução em fumantes esteve associado à diminuição da densidade de células Treg e da expressão de IL-10 e aumento da expressão de IL-17. Além disso, verificou-se diferenças entre o perfil inflamatório nos compartimentos pulmonares estudados / Although cigarette smoke is configured as the primary risk factor for the development of COPD, not all smokers develop COPD clinically significant, suggesting that there are other factors intrinsic to the individual, such as differences in immune responses involved in the pathogenesis and progression of this disease. Objectives: To better understand the role of the adaptive immune response in the progression of COPD. Methods: Lung tissue samples from 21 nonsmokers were studied (control group); 22 non-obstructive smokers (NOS) and 17 COPD smokers. The density of CD4 + cells and CD8 + regulatory T cells (Treg) FOXP3 + cells, B cells and positive cells for interleukins IL-10 and IL-17, and cytokines as CCL19, BAFF and TGF-beta were evaluated in large and small airways, and lymphoid tissue associated with bronchi or not (BALT and iBALT, respectively). Results: We observed an increase in CD4 + T cells and CD8 + in small and large airways, BALT and iBALT in smokers; however, the highest amounts were detected in the small airways of COPD patients. Furthermore, there was a decrease in TGF-beta expression in COPD patients compared to FNO and control groups in large and small airways while a decrease in Treg density was observed only in small airway and consequent decrease in the density of cells positive for IL-10 in large and small airways. In BALT we observed a different response, with an increase in Treg density in COPD patients without differences in IL-10 analysis. There was an increase in cell density for IL-17 in large and small airways, and iBALT in COPD. Conclusions: We observed that reduction of inflammation regulatory activity in small airways obstruction and progression of smoking was associated with decreased Treg cell density and IL-10 expression and increased IL-17 expression. Furthermore, there are differences between the inflammatory profile in the lung compartments studied

Introdução: Durante o inverno de 2009, o vírus influenza A(H1N1)09pdm surgiu e se espalhou globalmente. A infecção por este vírus pode induzir a síndrome do desconforto respiratório agudo (SDRA) em alguns pacientes. O dano alveolar difuso (DAD), padrão histopatológico principal da SDRA, tem etiologia multifatorial, sendo possível que a imunopatologia seja diferente nas várias apresentações do DAD. Objetivo: Descrever, quantificar e comparar a imunopatologia viral (influenza A (H1N1) pdm09) e não-viral em casos de autópsia com dano alveolar difuso. Métodos: Foram analisados tecidos pulmonares de autopsia de 44 pacientes, sendo divididos em 3 grupos: grupo H1N1 (n=15), caracterizado por DAD secundário à influenza A(H1N1)pdm09; grupo SDRA (n=13), caracterizado por pacientes com DAD exsudativo de causas não-pulmonares; e o grupo de controle (n=16) com indivíduos que faleceram de causas não-pulmonares. Foram utilizadas as técnicas de imunohistoquímica e análise de imagem para quantificar, no parênquima pulmonar e nas pequenas vias aéreas, os marcadores de células imunes. Resultados: Foi observada uma elevada densidade celular de linfócitos T CD4+ e T CD8+, células Natural Killer CD57+, células dendríticas CD83+ e granzima A+ no parênquima pulmonar do grupo H1N1 (p < 0,05) em relação aos outros grupos. Na análise das pequenas vias aéreas, observou-se uma menor densidade célular de mastócitos (triptase), células dendríticas (CD207), e um aumento de IL-17 nos grupos H1N1 e SDRA, além de um aumento do número de granzimas A+ e diminuição de celulas dendríticas (CD83) apenas no grupo H1N1 (p < 0,05). Conclusão: O DAD causado pelo vírus influenza A (H1N1) pdm09 está associado com um fenótipo citotóxico inflamatório diferente do DAD de causas não-virais, com uma resposta parcialmente divergente no parênquima pulmonar em relação às pequenas vias aéreas / Rationale: The pandemic influenza A (H1N1) virus emerged in 2009 and spread globally. This virus infection can induce acute respiratory distress syndrome (ARDS) in some patients. Diffuse alveolar damage (DAD), which is the histological surrogate for ARDS, has a multifactorial etiology. Therefore, it is possible that the immunopathology differs among the various presentations of DAD. Objectives: To compare the lung immunopathology of viral (influenza A(H1N1)pdm09) to non-viral, extrapulmonary etiologies in autopsy cases with DAD. Methods: The lung tissue of 44 patients, was divided into 3 groups: the H1N1 group (n=15) characterized by DAD due to influenza A(H1N1)pdm09 infection; the ARDS group (n=13), characterized by patients with exudative DAD due to non-pulmonary causes; and the control group (n=16), consisting of patients with non-pulmonary causes of death. Measurements and main results: Immunohistochemistry and image analysis were used to quantify, in the lung parenchyma and small airways, several immune cell markers. There was higher expression of CD4+ and CD8+ T lymphocytes, CD83+ dendritic cells, granzyme A+ and natural killer+ cell density in the lung parenchyma of the H1N1 group (p < 0,05). In the small airways, there was a lower cell density of tryptase+ mast cells and dendritic+ cells and an increase of IL-17 in both DAD groups, with an increased number of granzyme A in H1N1 group (p < 0,05). Conclusion: DAD due to viral A(H1N1)pdm09 is associated with a cytotoxic inflammatory phenotype that is different from non-viral causes of DAD, with partially divergent responses in the parenchyma relative to the small airways.

INTRODUÇÃO: Imunodeficiências primárias são um grupo heterogêneo de distúrbios de origem genética que afetam a imunidade e se caracterizam por infecções de repetição. Aproximadamente metade dos casos estão ligados a deficiências humorais e dentre estas podemos destacar a Imunodeficiência Comum Variável (ICV). Uma vez que os pacientes com ICV possuem redução dos níveis de anticorpos, esses pacientes apresentam infecções recidivantes do trato respiratório e aproximadamente 90% tiveram no mínimo um episódio de rinossinusite (RNS). A RNS se instala devido ao desequilíbrio entre o meio ambiente e fatores do hospedeiro e a infecção viral é pelo menos 20 vezes mais frequente do que a infecção bacteriana em indivíduos normais. OBJETIVOS: (1) Identificar os agentes virais da RNS nos pacientes com ICV e em indivíduos controles em um contexto prospectivo; (2) Definir quais citocinas e quimiocinas estão presentes e avaliar a expressão de genes relacionados à imunidade inata e adaptativa antiviral no lavado nasal de pacientes com ICV e nos indivíduos controles. CASUÍSTICA, MATERIAIS E MÉTODOS: Pacientes com ICV e indivíduos controles foram avaliados quando apresentavam sinais e sintomas de uma RNS viral e foi realizado a coleta de lavado nasal para a identificação de vírus respiratórios, além da quantificação da secreção de citocinas e quimiocinas e da avaliação da expressão gênica de genes relacionados à imunidade inata e adaptativa antiviral. A avaliação foi repetida quando todos os indivíduos previamente estudados se encontravam assintomáticos. RESULTADOS: De abril de 2012 a novembro de 2014, foram colhidas 65 amostras de lavado nasal, 43 amostras de 34 indivíduos controles e 22 amostras de 14 pacientes com ICV. Quatro amostras foram positivas para vírus pela técnica da imunofluorescência direta e dezoito amostras foram positivas pelo PCR. Pacientes com ICV tiveram mais infecções, duração maior dos sintomas e maior necessidade de uso de antibióticos que o grupo controle. A avaliação da produção de citocinas e quimiocinas no lavado nasal mostrou aumento da secreção de CXCL10, CCL2, CCL5, CXCL8 IL-6, IL-10, IL-1beta e TNF em ambos os grupos quando esses apresentavam quadro agudo de RNS viral. Foi realizada a expressão de genes pela técnica do PCR Real Time. Os pacientes com ICV apresentaram um aumento de expressão de genes relacionados à imunidade inata e adaptativa anitiviral substancialmente maior frente a um quadro de RNS viral do que os indivíduos controles em situações semelhantes. Quando comparamos os pacientes ICV e os controles ambos sem infecção aguda, observamos que os genes apresentam em sua maioria uma redução de expressão nos pacientes com ICV. DISCUSSÃO: Os vírus detectados respeitaram a sazonalidade em que normalmente são detectados e pacientes com ICV proporcionalmente tiveram mais infecções e uma evolução pior que o grupo controle. Aparentemente não houve diferenças significativas entre os grupos estudados quanto à liberação de citocinas e quimiocinas. Com relação ao estudo da expressão gênica, a maior amplitude de variação observada nos pacientes com ICV pode significar um desajuste de resposta imune levando a um quadro de maior inflamação local com consequente maior dano tecidual e justificando assim a incidência aumentada de complicações, duração aumentada dos sintomas e replicação viral aumentada nesse grupo de pacientes / INTRODUCTION: Primary immunodeficiencies (PIDs) are a heterogeneous group of genetic disorders that affect immunity and are characterized by relapsing, usually severe infections. Approximately half of the cases are linked to humoral deficiencies, being common variable immunodeficiency (CVID) the most frequent. CVID patients have reduced levels of antibodies; therefore, these patients have recurrent infections in the respiratory tract and approximately 90% had at least one episode of rhinosinusitis (RS). RS installs itself due to the imbalance between the environment and host factors and viral infection is at least 20 times as common as the bacterial infection in normal individuals. OBJECTIVES: (1) Identify the viral agents of rhinosinusitis in patients with CVID and in control individuals on a prospective context; (2) define which cytokines and chemokines are present in the nasal wash and evaluate the expression of genes related to innate and adaptive antiviral immunity in nasal wash of CVID patients and in control individuals. CASES, MATERIALS, AND METHODS: patients with CVID and control individuals were examined at Outpatient Facility of Dermatological Manifestations of Primary Immunodeficiencies and when they presented signs and symptoms of a viral RS. Nasal wash was collected in order to identify respiratory viruses; secretion of cytokines and chemokines were quantified and gene expression of genes related to innate and adaptive antiviral immunity were evaluated. This evaluation was repeated when all individuals previously studied were asymptomatic. RESULTS: From April 2012 to November 2014, 65 samples of nasal wash, 43 samples of 34 control individuals and 22 samples of 14 patients with CVID were collected. Four samples were positive for virus by direct immunofluorescence technique and eighteen samples by PCR. The detected viruses behaved according to the season in which they are normally detected and patients with CVID proportionally had more and longer infections and required more antibiotics than the control group. The evaluation of the production of cytokines and chemokines showed an increased secretion of CXCL10, CXCL8 CCL2, CCL5, IL-6, IL-10, IL-1beta and TNF in both groups when they presented acute viral RS. Gene expression was performed by using Real Time PCR. CVID patients showed increased expression of genes related to innate and adaptive antiviral immunity when compared to control individuals presenting acute viral RS. Conversely, when we compared CVID patients and control individuals both without acute infection, we observed a reduction in gene expression in CVID patients. DISCUSSION: The viral rhinosinusitis respected seasonality and CVID patients had proportionally more infections and a worse evolution than the control group. Apparently, there were no significant differences between the groups regarding the release of cytokines and chemokines. The greater magnitude of gene expression variation observed in CVID patients suggests an imbalance of immune response leading to a state of greater local inflammation with consequent greater tissue damage, therefore justifying an increased incidence of complications, increased duration of symptoms and increased viral replication in this group of patients

Le virus de l’hépatite C (VHC) est un problème mondial. La majorité des personnes infectées (70-85%) développent une infection chronique qui cause des complications hépatiques. Le seul régime thérapeutique approuvé pour le VHC est l'interféron alpha (IFN-α). Ce traitement a un taux de réussite de 50-80% selon le génotype de virus et le moment de l'initiation de la thérapie. Les facteurs régissant la réponse au traitement ne sont pas bien définis. Des études antérieures ont suggéré un rôle potentiel de la réponse immunitaire de l'hôte au succès de la thérapie, toutefois, ces résultats sont controversés. Nous avons émis l'hypothèse que la réponse immunitaire de l’hôte sera plus efficace chez les patients qui commencent la thérapie tôt pendant la phase aiguë de l'infection. En revanche, la réponse immunitaire sera épuisée lorsque le traitement est initié pendant la phase chronique. L'objectif principal de ce mémoire est d’étudier les facteurs immunologiques qui régissent la réponse à la thérapie, et de déterminer si la contribution de la réponse immunitaire de l'hôte peut être influencée par la période de l'infection. Nos résultats démontrent l'efficacité de la restauration de la réponse immunitaire spécifique au VHC lorsque la thérapie par l'interféron est initiée tôt. Ceci est démontré par le sauvetage des cellules T efficaces spécifiques au VHC efficace similaires à celles observées chez les individus qui ont résolu spontanément, suggérant ainsi qu'elles jouent un rôle actif dans la réponse au traitement. Toutefois, cette réponse n'a pas été restaurée chez les patients traités au cours de la phase chronique. Ces résultats ont des implications importantes dans la compréhension des mécanismes sous-jacents à la réponse aux traitements actuels et au développement des nouvelles thérapies. / Hepatitis C virus (HCV) is a major public health problem worldwide. Only 15-30% of infected individuals clear the virus spontaneously, while the majority develops chronic infection that causes liver complications. The only approved therapy for HCV is interferon alpha (IFN-α) based. This therapy has a 50-80% success rate depending on the infecting virus genotype and the timing of initiation of therapy. Factors governing the response to therapy are not well defined. Previous studies have suggested a role for the host immune response in the success of therapy. However, these results were controversial. We hypothesized that host immunity has an effective role in the success of IFN-α therapy when initiated early during the acute phase of HCV infection, while late initiation during the chronic phase minimizes this role. The main objective of this thesis was to dissect the immunological factors governing the differential response to IFN-α therapy, and to determine if the contribution of the immune response to success of therapy might be influenced by the period of infection. Our results demonstrate restoration of efficient HCV-specific immune responses when therapy is initiated early during the acute phase. This is demonstrated by the rescue of functional HCV-specific T cells similar to those observed in spontaneously resolved individuals, suggesting that they may play an active role in response to therapy. However, such responses were not restored following late therapy suggesting irreversible damage to the host’s defence system with chronicity. These findings have important implications in understanding the mechanisms underlying response to current treatments and development of novel therapies.

La phagocytose est un processus cellulaire par lequel de larges particules sont internalisées dans une vésicule, le phagosome. Lorsque formé, le phagosome acquiert ses propriétés fonctionnelles à travers un processus complexe de maturation nommé la biogénèse du phagolysosome. Cette voie implique une série d’interactions rapides avec les organelles de l’appareil endocytaire permettant la transformation graduelle du phagosome nouvellement formé en phagolysosome à partir duquel la dégradation protéolytique s’effectue. Chez l’amibe Dictyostelium discoideum, la phagocytose est employée pour ingérer les bactéries de son environnement afin de se nourrir alors que les organismes multicellulaires utilisent la phagocytose dans un but immunitaire, où des cellules spécialisées nommées phagocytes internalisent, tuent et dégradent les pathogènes envahissant de l’organisme et constitue la base de l’immunité innée. Chez les vertébrés à mâchoire cependant, la transformation des mécanismes moléculaires du phagosome en une organelle perfectionnée pour l’apprêtement et la présentation de peptides antigéniques place cette organelle au centre de l’immunité innée et de l’immunité acquise. Malgré le rôle crucial auquel participe cette organelle dans la réponse immunitaire, il existe peu de détails sur la composition protéique et l’organisation fonctionnelles du phagosome. Afin d’approfondir notre compréhension des divers aspects qui relient l’immunité innée et l’immunité acquise, il devient essentiel d’élargir nos connaissances sur les fonctions moléculaire qui sont recrutées au phagosome. Le profilage par protéomique à haut débit de phagosomes isolés fut extrêmement utile dans la détermination de la composition moléculaire de cette organelle. Des études provenant de notre laboratoire ont révélé les premières listes protéiques identifiées à partir de phagosomes murins sans toutefois déterminer le ou les rôle(s) de ces protéines lors du processus de la phagocytose (Brunet et al, 2003; Garin et al, 2001). Au cours de la première étude de cette thèse (Stuart et al, 2007), nous avons entrepris la caractérisation fonctionnelle du protéome entier du phagosome de la drosophile en combinant diverses techniques d’analyses à haut débit (protéomique, réseaux d’intéractions protéique et ARN interférent). En utilisant cette stratégie, nous avons identifié 617 protéines phagosomales par spectrométrie de masse à partir desquelles nous avons accru cette liste en construisant des réseaux d’interactions protéine-protéine. La contribution de chaque protéine à l’internalisation de bactéries fut ensuite testée et validée par ARN interférent à haut débit et nous a amené à identifier un nouveau régulateur de la phagocytose, le complexe de l’exocyst. En appliquant ce modèle combinatoire de biologie systémique, nous démontrons la puissance et l’efficacité de cette approche dans l’étude de processus cellulaire complexe tout en créant un cadre à partir duquel il est possible d’approfondir nos connaissances sur les différents mécanismes de la phagocytose. Lors du 2e article de cette thèse (Boulais et al, 2010), nous avons entrepris la caractérisation moléculaire des étapes évolutives ayant contribué au remodelage des propriétés fonctionnelles de la phagocytose au cours de l’évolution. Pour ce faire, nous avons isolé des phagosomes à partir de trois organismes distants (l’amibe Dictyostelium discoideum, la mouche à fruit Drosophila melanogaster et la souris Mus musculus) qui utilisent la phagocytose à des fins différentes. En appliquant une approche protéomique à grande échelle pour identifier et comparer le protéome et phosphoprotéome des phagosomes de ces trois espèces, nous avons identifié un cœur protéique commun à partir duquel les fonctions immunitaires du phagosome se seraient développées. Au cours de ce développement fonctionnel, nos données indiquent que le protéome du phagosome fut largement remodelé lors de deux périodes de duplication de gènes coïncidant avec l’émergence de l’immunité innée et acquise. De plus, notre étude a aussi caractérisée en détail l’acquisition de nouvelles protéines ainsi que le remodelage significatif du phosphoprotéome du phagosome au niveau des constituants du cœur protéique ancien de cette organelle. Nous présentons donc la première étude approfondie des changements qui ont engendré la transformation d’un compartiment phagotrophe à une organelle entièrement apte pour la présentation antigénique. / Phagocytosis is a cellular process by which large particulate material are internalized in a newly formed vesicule, the phagosome. Once formed, the phagosome acquires its functional properties through a complex maturation process called phagolysosome biogenesis. This pathway involves a series of rapid interactions with organelles of the endocytic apparatus, enabling the gradual transformation of newly formed phagosomes into phagolysosomes in which proteolytic degradation occurs. The amoeba Dictyostelium discoideum uses phagocytosis as a predation mechanism for feeding, whereas multicellular organisms utilize this process as an immune mechanism where specialized cells named phagocytes internalize, kill and degrade phatogens found through the host, forming the basis of innate immunity. In jawed verterbrates however, the phagosome links innate and adaptive immunity by processing and presenting antigenic peptides. Despite its crucial role in immunity, little is known about the composition and the functional organization of the phagosome. It is therefore essential to characterize in details the functional properties that are recruited to the phagosome. High-throughput proteomics analysis of isolated phagosomes has been tremendously helpful for the molecular comprehension of this organelle. Studies of our lab notably have revealed the first proteomics identification of mouse phagosomes without determining the roles of these proteins through the complex process of phagocytosis (Brunet et al, 2003; Garin et al, 2001). In the first study of this thesis (Stuart et al, 2007), we characterized the functions of the entire drosophila phagosome proteome by combining high-throughput proteomics, interactive networks and RNAi. By applying this strategy, we’ve identified 617 phagosomal proteins by mass spectrometry from which we’ve expanded this list by building the phagosome interactome. The contribution of each protein to bacterial internalization was tested and validated by RNAi and led to the identification of a new regulator of phagocytosis, the exocyst complex. In generating this 'systems-based model', we show the power of applying this approach to the study of complex cellular processes and organelles and expect that this detailed model of the phagosome will provide a new framework for studying host-pathogen interactions and innate immunity. In the second study of this thesis (Boulais et al, 2010), we characterized some of the key steps that contributed to the remodeling of phagosomes functional properties during evolution. To do so, we isolated this organelle from three distant organisms: the amoeba Dictyostelium discoideum, the fruit fly Drosophila melanogaster, and mouse (Mus musculus) that use phagocytosis for different purposes. By performing and comparing proteomics and phosphoproteomics analyses of isolated phagosomes from the three species, we identified an ancient core of phagosomal proteins around which the immune function of this organelle have likely organized. Our data indicate that a larger proportion of the phagosome proteome, has been acquired through gene duplication at periods coinciding with the emergence of innate and adaptive immunity. Our study also characterizes in detail the acquisition of novel proteins and the significant remodeling of the phagosome phosphoproteome that contributed to modify the core constituents of this organelle in evolution. Our work thus provides the first thorough analysis of the changes that enabled the transformation of the phagosome from a phagotrophic compartment into an organelle fully competent for antigen presentation.

Malaria, caused by the apicomplexan parasite Plasmodium, is a major cause of morbidity and mortality throughout the world. This study has focused on the role of the spleen in the control of the blood stage of infection. Three aspects have been examined specifically: the effect of infection on the architecture of the spleen, the role of the spleen in parasite clearance and the formation of B cell memory. Firstly, the effect of infection on the splenic microarchitecture was examined. An essential component of the splenic architecture is the marginal zone (MZ), an area of the spleen that separates the reticuloendothelial red pulp of the spleen from the lymphoid white pulp compartment. Two unique populations of macrophages are found in the marginal zone: marginal zone macrophages (MZM) and marginal metallophilic macrophages (MMM). In the current study, parasitised red blood cells (pRBC) as well as normal RBC located to the MZ thirty minutes after intravenous injection and formed close associations with both MMM and MZM. Eight days after infection, at the time of peak parasitemia, a complete loss of both MMM and MZM was observed. Assays to detect cell death revealed that the loss of both MMM and MZM appeared to occur as a result of apoptosis. The apoptosis was not induced by up regulation of the inflammatory cytokines tumour necrosis factor or interferon-γ and could not be blocked by over expression of the apoptosis inhibitor Bcl2. Significantly, MMM were retained in the absence of CD8+ T cells implicating CD8+ T cells in the loss of MMM. Finally, infection of CD95-/- mice demonstrated that CD95/CD95-ligand (Fas/Fas-ligand) interactions were responsible for some of the CD8+ T cell-mediated loss of MMM. These data provide evidence for a novel interaction between MMM and CD8+ T cellsfollowing infection with Plasmodium. Secondly, the role of the spleen in the control of parasitemia and disease was monitored with an emphasis on determining the role of splenic macrophage populations (MMM, MZM and red pulp macrophages [RPM]) in parasite clearance. A clodronate liposome-mediated macrophage depletion technique was used, and caused a complete loss of all three macrophage sub-populations, as well as 50% of splenic dendritic cells, within 24 hours of administration. Each of the macrophage populations, as well as splenic DC, demonstrated different repopulation kinetics following their depletion from the spleen and these kinetics were utilised to examine each cell population in isolation. RPM depleted mice had significantly higher peak parasitemias than the controls. This peak returned to the level observed in undepleted control animals only after the repopulation of RPM was complete, suggesting that RPM play a role in the control of peak parasitemia following infection. Neither MMM nor MZM played a role in the control of parasitemia. The role of non-splenic macrophages and splenic dendritic cells also was investigated and shown to be insignificant in the absence of splenic macrophages. Finally, the role of RPM in mice immune to infection was investigated and their role shown to be dispensable, with immune mice clearing parasitemia efficiently in the absence of RPM. RPM therefore are important for the innate control of infection with P. chabaudi but are dispensible once adaptive immunity is established. Finally, the role of the spleen in the development of parasite-specific B cell memory was examined. Initial studies demonstrated that germinal centre (GC) development was compromised following infection with P. chabaudi, with an involution of B cell follicles noted early in infection. Adoptive transfer of memory B cells from immunised to naïve mice demonstrated that some protection was conferred on recipient mice by parasite-specific memory B cells. But, the memory B cells could not protect the host from developing parasitemia and did not produce significant amounts of parasite-specific immunoglobulin within seven days of challenge infection. Memory B cells could not be detected ten weeks after infection, indicating that the development, or survival, of parasite-specific memory B cells was compromised. The development of bystander memory B cells was not affected by infection. Finally, long-lived plasma cells were shown to develop in response to infection, although re-exposure of the cells to parasites in the form of recrudescent parasitemia resulted in their loss. This study therefore has identified a defect in the development of long-term, B cell-mediated, protection against infection with P. chabaudi. Each of these factors has significant implications for the understanding of how the spleen contributes to the control of infection with Plasmodium and potential applications for the further development of malaria vaccines and treatment regimens.