Since late 1980s, porcine reproductive and respiratory syndrome virus (PRRSV) has emerged as the most economically important swine pathogen affecting pig industries worldwide. Vaccination is the principal means that have been used for prevention of PRRSV infection. However, the currently available vaccines for PRRSV are generally considered as not very effective. One of the major obstacles for developing an effective modified live-attenuated vaccine (MLV) with broad protection is the delayed and insufficient immune responses mounted by PRRSV, and the problem is further exacerbated by the antigenic variations of the constantly-evolving field strains of PRRSV. In order to boost the immune response induced by the MLV vaccine virus, we evaluated the immunogenicity and vaccine efficacy of recombinant PRRSV MLVs expressing porcine IL-15 or IL-18 as adjuvants. The cytokine genes were fused with a GPI modification signal so that they are anchored onto the cell surface upon infection with the recombinant MLV. Both cytokines are successfully expressed on the cell membrane of porcine alveolar macrophage (PAMs) after recombinant MLVs infection in vitro. Subsequently, pigs vaccinated with cytokine-expressing recombinant PRRSV MLVs had an improved antiviral response of cytotoxic lymphocytes including natural killer (NK) cells and T cells, characterized by increased IFN-γ secretion and/or enhanced CD107a expression. The results offer a novel strategy to incorporate cytokine genes into PRRSV genome as potent bio-active adjuvants expressed by the vaccine virus itself. Since we showed that PRRSV VR2385 down-regulated swine leukocyte antigen class I surface expression, naturally the next logical question is which viral protein is responsible for this down-regulation. To answer the question, we cloned and expressed all known PRRSV structural and non-structural proteins and examined which protein(s) is involved in SLA-I downregulation. Our results identified the newly-discovered nonstructural protein Nsp2TF of PRRSV as the main mediator in down-regulating SLA-I expression. We also demonstrated that the Nsp2TF-knockout mutant virus lost its function of negatively modulating SLA-I presentation compared to the wild-type virus. The results suggest that disruption of the Nsp2TF's ability to down-regulate SLA-I expression may improve the existing PRRSV vaccines towards a better CMI response against the virus. / PHD / Porcine reproductive and respiratory syndrome virus (PRRSV) is an important swine pathogen, causing enormous economical losses in the pork industry worldwide. However, the vaccine program is not satisfactory, with the insufficient protection against genetically divergent strains and newly emerged strains. One of the most important reasons is that PRRSV is able to suppress immune responses in the host, but the underlying mechanisms are not well known. Therefore, the first dissertation study is to investigate novel strategies of developing live-attenuated vaccines with improved efficacy against PRRSV. In this study, we successfully generated recombinant PRRSV live vaccines that are able to express immuno-activating cytokines as adjuvants. Subsequently, pigs vaccinated with cytokine-expressing PRRSVs had significantly improved anti-PRRSV immune repsonses when compared to pigs vaccinated with unmodified PRRSV. Those recombinant PRRSVs also provided cross-protection against a heterologous PRRSV challenge. The second part of disseration research is to understand the mechanism of immune modulation by PRRSV. Our results showed that one of PRRSV proteins- Nsp2TF contributes to the PRSV-induced down-regulation of swine leukocyte antigen (SLA) class I expression. Since SLA class I molecules are essential in the activation of the immune response and required for the clearance of viruses, Our study suggested that knocking-out Nsp2TF could be of great value to generate PRRSV vaccines with a better immune response.

Presque toutes les cellules nucléées expriment des peptides associés au CMH I (HLA I chez l’humain)(MAP) qui sont échantillonnés à partir du protéome cellulaire et transportés vers la surface cellulaire pour inspection par les lymphocytes T CD8. En tant que tel, la collection de MAP à la surface des cellules, ou immunopeptidome, informe les lymphocytes T CD8 de l’état cellulaire interne. L’immunosurveillance du cancer repose sur la capacité des lymphocytes T CD8 à reconnaître les MAP anormaux sur les cellules tumorales et à les éliminer tout en épargnant les cellules saines. Par conséquent, l’existence du cancer indique que bien souvent, les lymphocytes T CD8 spécifiques à la tumeur sont impuissants, dysfonctionnels ou incapables d’exercer leur fonction. Les vaccins anticancéreux peuvent actionner la destruction des tumeurs en stimulant la reconnaissance des MAP anormaux. Toutefois, le développement de vaccins anticancéreux efficaces est entravé par le manque de MAP exploitables, ou antigènes tumoraux (TA), exprimés exclusivement sur les cellules tumorales. La recherche et l’identification de TA ont été largement limitées aux MAP dérivés de mutations non synonymes situées dans des exons canoniques codant pour des protéines. Ces régions génomiques ne représentent que 2% du génome humain. Le fait que les MAP puissent potentiellement dériver de la traduction non canonique de toutes les régions génomiques n’a été pleinement compris que récemment. Ici, nous avons utilisé la protéogénomique pour découvrir des TA exploitables dérivés de produits de traduction canoniques et non canoniques partagés au sein ou entre divers types de cancers humains. Premièrement, nous avons utilisé des cellules souches pluripotentes induites (iPSC) pour identifier les MAP associés à la pluripotence (paMAP) étant partagés par les cellules cancéreuses. Les antigènes pluripotents sont exprimés dans les tissus embryonnaires et absents des tissus adultes sains, mais anormalement réexprimés par les cellules cancéreuses. Ainsi, bien qu'ils ne soient pas mutés, les paMAP constituent des cibles idéales et spécifiques au cancer. Nous avons identifié un ensemble de 48 paMAP dérivés de transcrits codants et non codants (48 %) impliqués dans le maintien de la pluripotence et exprimés de manière aberrante dans plusieurs types de cancer. Ainsi, bien qu’elles proviennent de différents types de cellules et de tissus, des tumeurs 4 distinctes convergent vers un programme transcriptionnel associé à la pluripotence. En effet, l’expression des paMAP dans les cancers est corrélée à l’hypométhylation récurrente de leurs gènes sources, la présence d’aberrations génomiques courantes et l’adoption par les tumeurs de stratégies d’évasion immunitaire communes. Enfin, comme plusieurs paMAP sont immunogènes, leur utilisation comme cibles dans des vaccins anticancéreux pourrait entrer en synergie avec les inhibiteurs disponibles des voies d'évasion immunitaire et améliorer le traitement de plusieurs cancers agressifs. Ensuite, nous avons évalué l’ensemble des TA ayant un potentiel thérapeutique dans deux types de tumeurs présentant une charge mutationnelle particulièrement élevée, le mélanome et le cancer du poumon non à petites cellules (NSCLC). Nous avons constaté que les TA mutés (mTSAs) représentent une minorité (1 %) des TA exploitables dans ces deux types de cancer. Cela peut s'expliquer par une faible expression d'ARN de la plupart des mutations non synonymes ainsi que par leur localisation en dehors des régions génomiques les plus efficaces pour la génération de MAP. En revanche, 99 % des TA dérivent de séquences génomiques non mutées spécifiques au cancer (aeTSA), surexprimées dans le cancer (TAA) ou spécifiques à la lignée cellulaire d'origine (LSA, exprimés par les mélanocytes ou par les cellules épithéliales pulmonaires, pour le mélanome et le NSCLC, respectivement). Tout comme les paMAP, environ 50 % des aeTSA identifiés dans le mélanome et le NSCLC proviennent de séquences non canoniques et sont régulés de manière épigénétique. Alors que les mTSA sont exclusivement spécifiques à chaque patient patient, les aeTSA sont partagés entre les échantillons tumoraux. De plus, leur absence dans les tissus normaux, leur abondance et leur capacité à activer les lymphocytes T CD8 en font des cibles idéales pour traiter les mélanomes et les NSCLC. En conclusion, cette thèse fournit un aperçu de la biogenèse de différents types de TA dans diverses cohortes de patients et ouvre la voie au développement d’immunothérapies ciblées et efficaces contre une grande variété de cancers. / Nearly all nucleated cells express MHC I (HLA I in humans)-associated peptides (MAPs) which are sampled from the cellular proteome and transported to the cell surface for inspection by CD8 T cells. As such, the collection of cell-surface MAPs, or the immunopeptidome, informs CD8 T cells on the inner cell state. Cancer immunosurveillance relies on the capacity of CD8 T cells to recognize abnormal MAPs on tumor cells and eliminate them while sparing healthy cells. Hence, the existence of cancer indicates that tumor-specific CD8 T cells are underpowered, dysfunctional or inhibited from exerting their function. Anti-cancer vaccines can boost tumor killing by stimulating the recognition of abnormal MAPs. The development of effective anti-cancer vaccines is limited by the identification of actionable MAPs, or tumor antigens (TAs), expressed exclusively on tumor cells. The TA search space has been largely limited to MAPs derived from non-synonymous mutations in canonical protein-coding exons which represent a mere 2% of the human genome. That MAPs can derive from the non-canonical translation of potentially all genomic regions has only recently been fully appreciated. Herein, we used proteogenomics to discover actionable TAs derived from canonical and non-canonical translation products shared within or across different types of human cancer. First, we used induced pluripotent stem cells (iPSCs) to identify pluripotency-associated MAPs (paMAPs) shared by cancer cells. Pluripotency antigens are restricted to embryonic tissues and absent from healthy adult tissues but abnormally re-expressed by cancer cells, which makes them ideal tumor-specific targets despite being unmutated. We identified a set of 46 paMAPs derived from coding and allegedly non-coding (48%) transcripts involved in pluripotency maintenance and aberrantly expressed in multiple cancer types. Thus, despite originating from different cell types and tissues, distinct tumor types converged towards a pluripotency-associated transcriptional program. Indeed, the expression of paMAPs across cancers correlated with recurrent source gene hypomethylation, genomic aberrations, and immune evasion properties. Several paMAPs were immunogenic, thus their targeting could synergize with available inhibitors of immune evasion pathways to improve the outcome of multiple aggressive cancers. 7 Next, we evaluated the actionable TA landscape of two tumor types with particularly high mutational load, melanoma and non-small cell lung cancer (NSCLC). We found that mutated TAs (mTSAs) represent a minority (1%) of actionable TAs in both cancer types, which can be explained by a low RNA expression of most non-synonymous mutations and their localization outside genomic regions proficient for MAP generation. By contrast, 99% of TAs derived from unmutated genomic sequences specific to cancer (aeTSAs), overexpressed in cancer (TAAs), or specific to the cell lineage of origin (LSAs, expressed by melanocytes or by lung epithelial cells, for melanoma and NSCLC LSAs, respectively). As for paMAPs, around 50% of aeTSAs in melanoma and NSCLC were non-canonical and were epigenetically regulated. Whereas mTSAs were exclusively patient-specific, aeTSAs were shared among tumor samples and exhibited all characteristics of targetable TAs, including tumor-specificity, high abundance, and immunogenicity. Altogether, this thesis provides insights into the biogenesis of different TA types in various patient cohorts and paves the way for the development of effective TA-based immunotherapies against a large variety of cancers.

Class I PI3Ks are a family (α, β, δ and γ) of ubiquitous lipid kinases that can be activated by cell surface receptors to 3-phosphorylate PI(4,5)P2 (phosphatidylinositol(4,5)-bisphosphate) and generate the signalling lipid PI(3,4,5)P3. The PI(3,4,5)P3 signal then activates a diverse collection of effector proteins involved in regulation of cell migration, metabolism and growth. The importance of this network is evidenced by the relatively high frequency with which cancers acquire gain-of-function mutations in this pathway and huge efforts to make PI3K inhibitors to treat cancer. The canonical model describing these events suggests class I PI3Ks are activated at the plasma membrane and generate PI(3,4,5)P3 in the inner leaflet of the plasma membrane where its effectors are activated. The PI(3,4,5)P3 signal can be terminated directly, by the tumour-suppressor and PI(3,4,5)P3-3-phosphatase PTEN, or modified to a distinct PI(3,4)P2 signal, by SHIP-family 5-phosphatases. The PI(3,4)P2 is removed by INPP4-family 4-phosphatases. Published work has shown that PI(3,4,5)P3 signalling can also occur in endosomes and nuclei, however, there is very little data defining the intracellular distribution of endogenous class I PI3Ks that supports these ideas; this is as a result of technical problems such as; their very low abundance, poor antibody-based tools and artefacts generated by overexpression of PI3Ks. Past work has indicated that, in PTEN-null mouse models of prostate tumour progression, either PI3Kβ or PI3Ks α and β, have important roles. Furthermore, the cell types and mechanism involved remained unclear. Recent published work in the host laboratory had indicated that there is an unexpectedly large accumulation of PI(3,4)P2 in PTEN-null cells that might be an important part of its status as a major tumour suppressor. The explanation and prevalence of this observation was unclear but potentially a result of PTEN also acting as a PI(3,4)P2 3-phosphatase in vivo. MEFs were derived from genetically-modified mice expressing endogenous, AviTagged class I PI3K subunits and used in experiments to define the subcellular localisation of class I PI3Ks. We found that following stimulation with PDGF, class IA PI3K subunits were unexpectedly depleted from the adherent basal membrane, in contrast, p85α and p110α, but not p85β and p110β, accumulated transiently in the nucleus. Interestingly, p110β, but none of the other subunits, was constitutively localised in the nucleus. These results support the idea that class I PI3K and PI(3,4,5)P3 signalling occurs in the nucleus. In organoids derived from WT, PI3Kγ-null or PTEN-null mouse prostate, application of PI3K-selective inhibitors revealed that PI3Kα had a dominant role in generating PI(3,4,5)P3 in prostate epithelial cells. The levels of PI(3,4)P2 were also elevated substantially in PTEN-null, compared to WT prostate organoids, use of PI3K-selective inhibitors suggested that it was also generated by PI3Kα. These data were consistent with the idea that PTEN can act as a PI(3,4)P2 3-phosphatase. Surprisingly, raising the pH of the organoids medium dramatically increased accumulation of PI(3,4,5)P3 and PI(3,4)P2, although the cause of this effect was unclear, we hypothesised the pH of the local environment may influence signalling via class I PI3Ks.

L’immunité adaptive et la discrimination entre le soi et le non-soi chez les vertébrés à mâchoire reposent sur la présentation de peptides par les récepteurs d’histocompatibilité majeur de classe I. Les peptides antigéniques, présentés par les molécules du complexe d’histocompatibilité (CMH), sont scrutés par les lymphocytes T CD8 pour une réponse immunitaire appropriée. Le répertoire des peptides du CMH de classe I, aussi appelé immunopeptidome, est généré par la dégradation protéosomale des protéines endogènes, et a un rôle essentiel dans la régulation de l’immunité cellulaire. La composition de l’immunopeptidome dépend du type de cellule et peut présenter des caractéristiques liées à des maladies comme le cancer. Les peptides antigéniques peuvent être utilisés à des fins immunothérapeutiques notamment dans le traitement voire la prévention de certains cancers. La spectrométrie de masse est un outil de choix pour l’identification, le séquençage et la caractérisation de ces peptides. Cependant, la composition en acides aminés, la faible abondance et la diversité de ces peptides compliquent leur détection et leur séquençage. Nous avons développé un programme appelé StatPeaks qui permet de calculer un certains nombres de statistiques relatives à la fragmentation des peptides. À l’aide de ce programme, nous montrons sans équivoque que les peptides du CMH classe I, en mode de fragmentation par dissociation induite par collision (CID), fragmentent très différemment des peptides trypsiques communément utilisés en protéomique. Néanmoins, la fragmentation par décomposition induite par collision à plus haute énergie (HCD) proposée par le spectromètre LTQ-Orbitrap Velos améliore la fragmentation et fournit une haute résolution qui permet d’obtenir une meilleure confiance dans l’identification des peptides du CMH de classe I. Cet avantage permet d’effectuer le séquençage de novo pour identifier les variants polymorphes qui ne sont normalement pas identifiés par les recherches utilisant des bases de données. La comparaison des programmes de séquençage Lutefisk, pepNovo, pNovo, Vonode et Peaks met en évidence que le dernier permet d’identifier un plus grand nombre de peptides du CMH de classe I. Ce programme est intégré dans une chaîne de traitement de recherche d’antigènes mineurs d’histocompatibilité. Enfin, une base de données contenant les informations spectrales de plusieurs centaines de peptides du CMH de classe I accessible par Internet a été développée. / Adaptive immunity and discrimination between self and nonself in jawed vertebrates relies on the presentation of peptides by the major histocompatibility (MHC) class I receptors. Foreign or self peptide antigens presented by the MHC molecules are probed by CD8 T-cell lymphocyte for proper immune response. The repertoire of MHC I peptides collectively referred to as the immunopeptidome is generated through the proteasomal degradation of endogenous proteins and plays an important role in the regulation of cellular immunity. The composition of the immunopeptidome is cell specific and can harbor important hallmark of human diseases including cancer. Antigenic peptides can also be used in immunotherapy to mount an appropriate immune response against cancer cells displaying these peptides. Mass spectrometry is a tool of choice for the identification, sequencing and characterization of these peptides. However, the amino acid composition, the low abundance and diversity of these peptides make their detection and sequencing more challenging. We developed a software, called StatPeaks, that calculates statistics relative to the fragmentation of peptides. Using this software, we demonstrate that under collision induced dissociation (CID) MHC class I peptides fragment in a very different fashion than tryptic peptides, commonly used in proteomics. However, the higher-energy collisional dissociation (HCD) mode available on the LTQ-Orbitrap Velos enhances peptide fragmentation and provides high resolution fragment information that significantly improves the confidence in MHC class I peptide identification. This inherent advantage confers the ability to perform de novo sequencing to identify polymorphic variants that would normally elude conventional database searches. The comparison of de novo peptide sequencing software Lutefisk, pepNovo, pNovo, Vonode and Peaks indicated that the later software enabled higher rates of correct identification for MHC class I peptides. This software was integrated into a data analysis pipeline for the identification minor histocompatibility antigens (MiHAs). A web-based library that stores spectral information of hundreds of synthetic MHC class I peptides was developed in support to the needs of the immunopeptidome discovery program.

Le système ubiquitine-protéasome est le principal mécanisme par lequel les protéines intracellulaires sont dégradées. Le protéasome dit constitutif (PC) est donc essentiel à l’homéostasie mais aussi à la régulation de la majorité des processus cellulaires importants. La découverte d’un deuxième type de protéasome, appelé immunoprotéasome (IP), soulève toutefois de nouvelles questions. Pourquoi existe-t-il plus d’un type de protéasome ? L’IP a-t-il des rôles redondants ou complémentaires avec le PC ? L’IP étant présent principalement dans les cellules immunitaires ou stimulées par des cytokines, plusieurs groupes ont tenté de définir son rôle dans la réponse immunitaire. Or, l’implication de son homologue constitutif dans un éventail de processus non spécifiquement immunitaires nous laisse croire que l’IP pourrait lui aussi avoir un impact beaucoup plus large. L’objectif de cette thèse était donc de caractériser certains rôles cellulaires de l’IP dans les cellules dendritiques. Nous avons d’abord étudié l’impact global de l’IP sur la présentation antigénique de classe I. Ce faisant, nous avons pu déterminer ses deux contributions principales, soit l’augmentation drastique du nombre et de la diversité des peptides présentés sur les complexes majeurs d’histocompatibilité de classe I. Les différences de clivage entre le PC et l’IP pourraient expliquer en partie cette diversité du répertoire peptidique, notamment par l’affinité apparente de l’IP pour les régions protéiques non structurées. Dans un deuxième temps, nous avons dévoilé un nouveau rôle de l’IP sur un processus dépassant le cadre immunitaire : la transcription. Nous avons découvert que l’IP modifie l’abondance des ARNm en agissant principalement au niveau de leur synthèse. L’impact de l’IP sur le transcriptome est majeur et serait dû en partie à une dégradation différente de facteurs de transcription des familles IRF, STAT et NF-kB. Les cellules dendritiques IP-déficientes activent moins efficacement les lymphocytes T CD8+ et nous croyons que cette défaillance est causée (du moins en partie) par la perturbation transcriptomique provoquée par l’absence d’IP. Il importe donc de comprendre les différents rôles moléculaires de l’IP afin de mieux définir sa contribution globale au fonctionnement de la cellule et comprendre l’avantage évolutif, au niveau de l’organisme, procuré par une telle plasticité du système ubiquitine-protéasome. / The ubiquitin-proteasome system is the major mechanism by which intracellular proteins get degraded. Constitutive proteasomes (CPs) are thus essential for cellular homeostasis but also to regulate the majority of important cellular processes. However, the discovery of a second type of proteasome, named immunoproteasome (IP), raises new questions. Why are there more than one type of proteasome? Does the IP perform redundant or complementary roles with the CP? The IP is predominantly expressed in immune or cytokine-stimulated cells and several groups worked at defining its role during the immune response. Yet, the implication of its constitutive homolog in a variety of processes suggests that the IP may also have a much broader impact. The objective was to characterize cellular roles of the IP in dendritic cells. We first studied the global impact of the IP on class I antigen presentation. We discovered that the IP drastically increases the number and the diversity of peptide presented by class I major histocompatibility complexes. Cleavage differences between the CP and the IP are likely part of the explanation for this peptide repertoire diversity, notably due to IP’s apparent affinity for unstructured protein regions. Second, we discovered a new role for the IP in a process unrestricted to the immune system: transcription. We found that the IP affects transcript abundance mostly at the level of mRNA synthesis. The impact of IPs on the transcriptome is major and would be partly based on a different degradation of IRF, STAT and NF-kB transcription factor family members by the two types of proteasomes. IP-deficient dendritic cells are less potent activators of CD8+ T cells and we believe that this defect is at least partly caused by the transcriptome alterations induced by the absence of IPs. It is therefore important to understand the different molecular roles of the IP in order to better define its global contribution to cellular functions and to understand the evolutionary advantage, at the level of the organism, brought by such plasticity of the ubiquitin- proteasome system.

Das Proteasom ist eine ATP- abhängige Protease, die sich aus vielen Untereinheiten zusammensetzt. Es ist für die Generierung der MHC Klasse I- restringierten Peptide verantwortlich, die im Folgenden auf der Zelloberfläche präsentiert werden. Nicht-funktionelle Proteine, die als so genannte defective ribosomal products (DRIP) bezeichnet werden, stellen eine wichtige Quelle für die Generierung von antigenen Peptiden, insbesondere jedoch von viralen Peptiden dar. Generell wird die Lehrmeinung vertreten, dass der Abbau von polyubiquitinierten Proteinen durch das 26S Proteasom zur Generierung von MHC Klasse I- Liganden führt. Allerdings ist weiterhin unklar, ob virale Proteine Ubiquitin- abhängig vom Proteasom abgebaut werden. Demnach sollte im Rahmen dieser Arbeit der Proteasom- abhängige Abbau des mCMV ie pp89 Proteins vor allem hinsichtlich einer Ubiquitinierung untersucht werden. Folglich wurden Konstrukte sowohl für ein rekombinantes pp89 (rek pp89) als auch für ein ODCpp89 Fusionsprotein entworfen. Somit konnten sowohl der in vitro Abbau dieser Proteine als auch die Prozessierung des spezifischen MHC Klasse I H2-Ld Epitops verfolgt werden. Experimente zum Nachweis von Ubiquitin- Protein- Konjugaten wurden in vivo mit stabil transfizierten Mausfibroblasten (B8 Zellen) durchgeführt. Die experimentellen Daten sprechen für einen schnellen in vitro Abbau des rek pp89 durch das 20S Proteasom. Das MHC Klasse I pp89 Epitop bzw. dessen 11mer Precursorpeptid wurden dabei mit hoher Präzision generiert. Spezifische CTL Assays weisen auf die Generierung des korrekten Epitops bzw. des Precursors hin. Nach Verdau des ODCpp89 Fusionsproteins durch 26S Proteasomen in Anwesenheit von Antizym konnten mit diesem Test ebenfalls das 9mer Epitop respektive das 11mer des pp89 nachgewiesen werden. Eine potentielle Ubiquitinierung des pp89 wurde in vivo in Zellkulturen untersucht. Nach Gabe von Proteasomeninhibitoren zu Mausfibroblasten konnte eine starke Akkumulierung von Ubiquitin- Konjugaten beobachtet werden. Allerdings konnte in den verschiedenen Versuchsansätzen kein Nachweis von pp89- Ubiquitin- Konjugaten erbracht werden. Demzufolge ist für die Generierung von viralen Epitopen ein Proteasom- abhängiger, aber Ubiquitin- unabhängiger Abbauweg denkbar. / The proteasome, an ATP-dependent, multisubunit protease, is responsible for the generation of most MHC class I restricted epitopes presented on the cell surface. Non-functional proteins, also known as defectice ribosomal products (DRiP), represent an important source for the generation of antigenic peptides in general and of viral epitopes in particular. It is widely accepted that the degradation of polyubiquitinated proteins by the 26S proteasome is a prerequisite for the generation of MHC class I ligands. However, the ubiquitin dependence for the proteasomal degradation of viral proteins is an issue so far unresolved. Therefore, the aim of this study was to analyze the proteasomal degradation of the mCMV ie pp89 in respect to an anticipated ubiquitinylation. Thus, a recombinant pp89 (recpp89) as well as an ODCpp89 fusion protein were generated. The in vitro processing of these proteins and the generation of a MHC class I H2-Ld epitope by proteasomes was further studied. Murine fibroblast cell lines (B8 cells) were used to analyze any in vivo evidence for potentially existing ubiquitin-protein conjugates. The experiments show that the recpp89 protein is rapidly degraded in vitro by the 20S proteasomes and that the correct MHC class I pp89 epitope or its 11mer precursor are generated with high fidelity. Furthermore, CTL assays, indicating the generation of the specific pp89 epitope or the 11mer precursor, also suggested a 26S proteasome-dependent degradation of the mCMV pp89-ODC fusion protein in the presence of antizyme. Treating cell cultures with proteasome inhibitors resulted in a significant accumulation of ubiquitin-conjugates in vivo. However, higher molecular weight pp89-ubiquitin conjugates were not detectable throughout the entire experimental set-up. Consequently, a proteasome-dependent, but ubiquitin-independent pathway can be postulated for the generation of viral epitopes.

Im Kampf gegen eine Virusinfektion spielen CD8+ T Zellen des adaptiven Immunsystems eine besondere Rolle. Sie patroullieren im Körper und entdecken spezifische Virusepitope, welche mittels MHC Klasse I Molekülen auf der Oberfläche infizierter Zellen präsentiert werden. Wird eine virus-infizierte Zelle erkannt, kann diese schnell und effizient eliminiert. Für die Generierung viraler Peptide, welche auf MHC Klasse I Komplexe geladen werden, ist das Ubiquitin-Proteasom-System von essentieller Bedeutung. Kürzlich wurden weitere Funktionen des Immunoproteasoms aufgedeckt wie zum Beispiel der Schutz gegen oxidativen Stress. Innerhalb der vorliegenden Arbeit konnte die Fähigkeit des Immunoproteasoms gegen eine Akkumulation oxidativ geschädigter Proteine zu schützen mit der Generierung von MHC Klasse I Liganden kombiniert und neu interpretiert werden. Es konnte gezeigt werden, dass während einer Virusinfektion in Nicht-Immunzellen die Produktion reaktiver Sauerstoffspezies durch die alternative NADPH Oxidase Nox4 eine bedeutende Rolle spielt. Die Aktivierung von Nox4 resultiert in der Akkumulation oxidativ geschädigter Proteine. Innerhalb von zwei Stunden nach dem Eintreten von Viruspartikeln in die Zellen wurden strukturelle Virusproteine oxidiert und anschließend ubiquityliert. Die gleichzeitige, virus-induzierte Expression von Immunoproteasomen führte zu einem schnellen und effizienten Abbau ubiquitylierter Virusantigene. Infolgedessen konnten immundominante Virusepitope vermehrt freigesetzt werden. Folglich wurde ein soweit unbekannter Mechanismus gefunden, welcher Substrate für das Proteasom zur Generierung von MHC Klasse I Liganden bereitstellt. Zusammenfassend konnte innerhalb dieser Arbeit gezeigt werden, dass das Immunoproteasom den Schutz vor oxidativen Stress mit der Generierung antigener Peptide verbindet, wodurch eine effektive adaptive Immunantwort etabliert werden kann. / An efficient immune control of virus infection is predominantly mediated by CD8+ T cells which patrol through the body and eliminate infected cells. Infected cells are recognized when they present viral antigenic peptides on their surface via MHC class I molecules. To make antigenic peptides available for loading on MHC class I complexes, the ubiquitin proteasome system plays a crucial role. Moreover, the induction of the i-proteasome is known to support the generation of MHC class I ligands. Recently, new functions of the i-proteasome have been discovered. Evidence is increasing that the i-proteasome is involved in the protection of cells against oxidative stress. Within this thesis the characteristic of the i-proteasome to protect cells against the accumulation of oxidant-damaged proteins could be linked to its role in improving the generation of MHC class I ligands. It could be demonstrated that during a virus infection in non-immune cells the production of reactive oxygen species by the alternative NADPH oxidase Nox4 is of critical importance resulting in the accumulation of potentially toxic oxidant-damaged proteins. Indeed, within two hours of infection structural virus proteins were oxidized and subsequently poly-ubiquitylated. The concomitant formation of i-proteasomes led to a rapid and efficient degradation of ubiquitylated virus antigens thereby improving the liberation of immunodominant viral epitopes. In conclusion, a so far unknown mechanism to fuel proteasomal substrates into the MHC class I antigen presentation pathway has been revealed. A new protein pool consisting of exogenously delivered viral proteins provides proteasomal substrates in the very early phase of a virus infection. Within the scope of this thesis the i-proteasome has been shown to link the protection against oxidative stress, initiated directly by pathogen recognition, with the generation of antigenic peptides. Together, an effective adaptive immune response is triggered.

INTRODUÇÃO: O penfigoide bolhoso é uma doença autoimune, vesicobolhosa com incidência de 0,2 a 1,4 por 100.000 hab. Sua fisiopatologia caracteriza-se pela ação de autoanticorpos na junção dermoepidérmica dos hemidesmossomos, promovendo a formação de bolhas subepidérmicas na pele e mucosas. Estudos vêm sendo publicados demonstrando a associação de penfigoide com alelos do sistema HLA classe II em diferentes populações do mundo, entretanto não há dados sobre a população brasileira, uma das mais heterogêneas do mundo. PACIENTES E MÉTODOS: O grupo de estudo incluiu 17 pacientes brasileiros com diagnóstico confirmado de PB de um hospital na cidade de São Paulo, sudeste do Brasil. O DNA foi extraído a partir de sangue periférico utilizando kits Qiagen (QIAamp DNA Mini Kit®) e a tipagem HLA loci A, B, C, DR e DQ foi realizada por meio de PCR e a amplificação utilizando o oligonucleótido de sequência específica (SSO) contido nos kits LABType®. O grupo controle foi composto por um banco de dados de 297 doadores falecidos da cidade de São Paulo. Este banco de dados é parte do Sistema de Transplantes da Secretaria de Saúde do Governo do Estado de São Paulo. RESULTADOS: Os resultados mostram que os alelos HLA C*17, DQB1*03:01, DQA1*01:03 e DQA1*05:05 estão associados com o aparecimento da doença na população brasileira, com risco relativo de 8,31 (2,46 a 28,16), 3,76 (1,81 a 7,79), 3,57 (1,53 a 8,33) e 4,02 (1,87 a 8,64), respectivamente (p < 0,005). O nível de significância estatística foi ajustado utilizando a correção de Bonferroni, dependendo das frequências fenotípicas avaliadas para HLA de classe I (A, B e C) e classe II (DRB1, DQB1 e DQA1). DISCUSSÃO: Os dados indicam que pacientes brasileiros com PB apresentam a mesma predisposição genética ligada ao HLA-DQB1*03:01 relatado anteriormente em caucasianos e indivíduos iranianos e o estudo apresenta três novos alelos (C *17, DQA1*01:03 e DQA1* 05:05) envolvidos na fisiopatologia da PB. CONCLUSÕES: Os resultados mostram que os alelos HLA C*17, DQB1*03:01, DQA1*01:03 e DQA1*05:05 estão associados com o aparecimento da doença na população brasileira / BACKGROUND: Bullous pemphigoid (BP) is an autoimmune disease with bullous vesicles and an incidence of 0.2 to 1.4 per 100,000 inhabitants. Its pathophysiology is characterized by the action of autoantibodies on hemidesmosomes at the dermalepidermal junction, promoting subepidermal blister formation in the skin and mucous membranes. Many studies have been published demonstrating the association of pemphigoid with HLA class II system alleles in different populations, however there are no data on the Brazilian population, one of the most heterogeneous in the world. PATIENTS AND METHODS: The study group included 17 Brazilian patients with a confirmed diagnosis of BP from a hospital in Sao Paulo city, southeast Brazil. DNA was extracted from peripheral blood using Qiagen kits (QIAamp DNA Mini Kit®) and HLA A, B, C, DR and DQ typing was performed using PCR and amplification using Sequence-Specific Oligonucleotide (SSO) contained in LABType® kits. The control group was composed of a database of 297 deceased donors from the city of São Paulo. This database is part of the Transplants State System of the Government\'s Health Secretary from the State of Sao Paulo. RESULTS: Our findings show that alleles HLA C*17, DQB1*03:01, DQA1*01:03 and DQA1*05:05 are associated with the onset of the disease in the Brazilian population, with relative risks of 8.31 (2.46 to 28.16), 3.76 (1.81 to 7.79), 3.57 (1.53 to 8.33), and 4.02 (1.87 to 8.64), respectively (p < 0.005). The statistical significance level was adjusted using the Bonferroni correction depending on the phenotypic frequencies evaluated for HLA class I (A, B and C) and class II (DRB1, DQB1 and DQA1). DISCUSSION: Our data indicate that Brazilian patients with BP present the same genetic predisposition linked to HLA-DQB1*03:01 previously reported in Caucasian and Iranian individuals and our study introduces three new alleles (C*17, DQA1*01:03 and DQA1*05:05) involved in the pathophysiology of BP. CONCLUSIONS: Our findings show that alleles HLA C*17, DQB1*03:01, DQA1*01:03 and DQA1*05:05 are associated with the onset of the disease in the Brazilian population

INTRODUÇÃO: O penfigoide bolhoso é uma doença autoimune, vesicobolhosa com incidência de 0,2 a 1,4 por 100.000 hab. Sua fisiopatologia caracteriza-se pela ação de autoanticorpos na junção dermoepidérmica dos hemidesmossomos, promovendo a formação de bolhas subepidérmicas na pele e mucosas. Estudos vêm sendo publicados demonstrando a associação de penfigoide com alelos do sistema HLA classe II em diferentes populações do mundo, entretanto não há dados sobre a população brasileira, uma das mais heterogêneas do mundo. PACIENTES E MÉTODOS: O grupo de estudo incluiu 17 pacientes brasileiros com diagnóstico confirmado de PB de um hospital na cidade de São Paulo, sudeste do Brasil. O DNA foi extraído a partir de sangue periférico utilizando kits Qiagen (QIAamp DNA Mini Kit®) e a tipagem HLA loci A, B, C, DR e DQ foi realizada por meio de PCR e a amplificação utilizando o oligonucleótido de sequência específica (SSO) contido nos kits LABType®. O grupo controle foi composto por um banco de dados de 297 doadores falecidos da cidade de São Paulo. Este banco de dados é parte do Sistema de Transplantes da Secretaria de Saúde do Governo do Estado de São Paulo. RESULTADOS: Os resultados mostram que os alelos HLA C*17, DQB1*03:01, DQA1*01:03 e DQA1*05:05 estão associados com o aparecimento da doença na população brasileira, com risco relativo de 8,31 (2,46 a 28,16), 3,76 (1,81 a 7,79), 3,57 (1,53 a 8,33) e 4,02 (1,87 a 8,64), respectivamente (p < 0,005). O nível de significância estatística foi ajustado utilizando a correção de Bonferroni, dependendo das frequências fenotípicas avaliadas para HLA de classe I (A, B e C) e classe II (DRB1, DQB1 e DQA1). DISCUSSÃO: Os dados indicam que pacientes brasileiros com PB apresentam a mesma predisposição genética ligada ao HLA-DQB1*03:01 relatado anteriormente em caucasianos e indivíduos iranianos e o estudo apresenta três novos alelos (C *17, DQA1*01:03 e DQA1* 05:05) envolvidos na fisiopatologia da PB. CONCLUSÕES: Os resultados mostram que os alelos HLA C*17, DQB1*03:01, DQA1*01:03 e DQA1*05:05 estão associados com o aparecimento da doença na população brasileira / BACKGROUND: Bullous pemphigoid (BP) is an autoimmune disease with bullous vesicles and an incidence of 0.2 to 1.4 per 100,000 inhabitants. Its pathophysiology is characterized by the action of autoantibodies on hemidesmosomes at the dermalepidermal junction, promoting subepidermal blister formation in the skin and mucous membranes. Many studies have been published demonstrating the association of pemphigoid with HLA class II system alleles in different populations, however there are no data on the Brazilian population, one of the most heterogeneous in the world. PATIENTS AND METHODS: The study group included 17 Brazilian patients with a confirmed diagnosis of BP from a hospital in Sao Paulo city, southeast Brazil. DNA was extracted from peripheral blood using Qiagen kits (QIAamp DNA Mini Kit®) and HLA A, B, C, DR and DQ typing was performed using PCR and amplification using Sequence-Specific Oligonucleotide (SSO) contained in LABType® kits. The control group was composed of a database of 297 deceased donors from the city of São Paulo. This database is part of the Transplants State System of the Government\'s Health Secretary from the State of Sao Paulo. RESULTS: Our findings show that alleles HLA C*17, DQB1*03:01, DQA1*01:03 and DQA1*05:05 are associated with the onset of the disease in the Brazilian population, with relative risks of 8.31 (2.46 to 28.16), 3.76 (1.81 to 7.79), 3.57 (1.53 to 8.33), and 4.02 (1.87 to 8.64), respectively (p < 0.005). The statistical significance level was adjusted using the Bonferroni correction depending on the phenotypic frequencies evaluated for HLA class I (A, B and C) and class II (DRB1, DQB1 and DQA1). DISCUSSION: Our data indicate that Brazilian patients with BP present the same genetic predisposition linked to HLA-DQB1*03:01 previously reported in Caucasian and Iranian individuals and our study introduces three new alleles (C*17, DQA1*01:03 and DQA1*05:05) involved in the pathophysiology of BP. CONCLUSIONS: Our findings show that alleles HLA C*17, DQB1*03:01, DQA1*01:03 and DQA1*05:05 are associated with the onset of the disease in the Brazilian population

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