In den humanen Leukozyten-Antigenen (HLA) wird die wichtigste genetische Ursache von rheumatoider Arthritis gesehen. Es wurden bisher mehrere Mechanismen beschrieben, wie diese HLA-Moleküle die Entstehung und den Verlauf der Erkrankung beeinflussen. Im Rahmen dieser Arbeit wurde die differentielle Expression von HLA-DRB-Genen in unterschiedlichen Antigen-präsentierenden Zellen als möglicher Mechanismus untersucht. Dabei wurden strukturelle Unterschiede zwischen den Promotoren des krankheitsassoziierten HLA-DR4-Haplotyps und den neutralen Haplotypen DR7 und DR9 eingehender betrachtet. Allen drei Haplotypen ist gemein, daß sie das DRB4-Gen als zweites funktionelles DRB-Gen tragen, wobei das DRB4-Gen entweder den DRB4A oder den -B-Promotor besitzt. Um den Einfluß einzelner Promotorelemente auf die mit dem Luziferase-Assay bestimmten Transkriptionsaktivitäten näher zu untersuchen, wurde mit Hilfe der surface plasmon resonance die Bindung der Transkriptionsfaktoren aus den Zellkernlysaten von der humanen Monozytenzellinie THP-1 und von der humanen B-Lymphom-Zellinie BJAB an die unterschiedlichen S-, X-, Y-, CCAAT- und TATA-Boxen analysiert. Es konnte gezeigt werden, daß die unterschiedliche Expression von DRB4A und DRB4B durch die ubiquitäre TATA-Box vermittelt wird. Dagegen wurde die INF-gamma-Stimulation der HLA-DR-Expression von THP-1- aber auch von BJAB-Zellen durch die für die HLA-DR-Promotoren spezifische X-Box vermittelt. Bei der Analyse von DR4-, DR7- und DR9-positiven Patienten einer bereits gut charakterisierten RA-Kohorte stellte sich heraus, daß der DRB4B-Promotor, welcher im Vergleich zu DRB4A eine höhere transkriptionelle Aktivität besitzt, mit einem schweren Krankheitsverlauf assoziiert ist, so daß eine erhöhte HLA-DR-Expression den Krankheitsverlauf negativ zu beeinflussen scheint. / Disease associated human leukocyte antigen (HLA) genes have been identified in humans where they are assumed to promote the susceptibility and/or progression of rheumatoid arthritis. Several mechanisms have been described how these HLA haplotypes impact on the disease. Among them the differential expression of HLA-DRB molecules in different types of antigen-presenting cells, which was investigated here in detail. The promoters of the disease associated HLA-DR4 to the neutral DR7 and DR9 haplotypes were analyzed for sequence polymorphisms resulting in functional differences. All three haplotypes carry as a second functional DRB gene the DRB4 gene, which is regulated by the DRB4A or -B promoter. To determine the impact of the promoter elements on the transcriptional activities measured by luciferase assay the surface plasmon resonance technology was employed. To this end, nuclear extracts from the monocytic cell line THP-1 and from the B lymphoma cell line BJAB were used to analyze their binding to the various S-, X-, Y-, CCAAT-, and TATA boxes. It could be demonstrated that the differential expression of DRB4A and -B was regulated via the ubiquitous TATA box. By contrast, the INF-gamma stimulation of HLA expression in THP-1 and BJAB was mediated via the unique X box. Analyzing the DR4, DR7 and DR9 positive patients of an RA cohort, the DRB4B promoter, which has a higher transcriptional activity than the DRB4A promoter, is associated with radiographic progression of RA. This data is thus indicative of an impact of elevated HLA-DR expression on the progression of the disease.

Dendritische Zellen (DCs) und Makrophagen sind spezialisierte antigenpräsentierende Zellen, die eigene und fremde Antigene prozessieren und mittels Haupthistokompatibilitätsmoleküle, humane Leukozytenantige (HLA) im Menschen, T-Zellen präsentieren, um Toleranzen zu induzieren oder T-Zell-vermittelte Immunantworten zu initiieren. Abhängig von ihrer Differenzierung haben sie spezifische Phänotypen und Funktionen undunterschiedliche Interaktionen mit Pathogenen, in dieser Arbeit durch Leishmania donovani (LD) repräsentiert, welche in Phagolysosomen der Makrophagen propagieren. Der Einfluss der Differenzierungszustände und von intrazelluläre Infektionen auf die Antigenprozessierung und -präsentation waren weitgehend undefiniert. Um hier Einblick zu gewinnen, haben wir die HLA-I-präsentierten Selbstpeptidome von menschlichen unreifen und reifen DCs, die aus der MUTZ3-Zelllinie generiert wurden, und LD-infizierte bzw. nicht-infizierte aus der THP1-Zelllinie generierte Makrophagen mittels Flüssigchromatographie-Tandem-Massenspektrometrie (LC-MS/MS), sowie die Proteasom-Zusammensetzung per RT-PCR und die HLA-Expression und Aktivierungszustände der Zellen per Durchflusszytometrie analysiert und verglichen. Wir fanden, dass die HLA-I-Selbstpeptidome der Zellen heterogen und individualisiert waren, von Nonapeptiden dominiert wurden und ähnliche HLA-Bindungsaffinitäten und Ankerreste aufwiesen. Sie stammten aus Quellenproteinen aus fast allen subzellulären Lokalisationen und mit unterschiedlichen zellulären Funktionen in ähnlichen Anteilen und schlossen Tumor-assoziierter Antigene (TAAs) ein. Die Persistenz der LD hatte keinen Einfluß auf den Aktivierungszustand der Makrophagen, verursachte aber eine weitgehende Veränderungen des Peptidoms, der HLA-Bindungsaffinitäten und Ankerreste, der Quellproteine einschließlich TAAs und der HLA- und Proteasom-Expression. / Dendritic cells (DCs) and macrophages are specialized antigen presenting cells that process self and foreign antigens and present them to T cells via major histocompatibility complex molecules, human leukocyte antigens (HLA) in humans, for induction of tolerance or initiation of T cell-mediated immune responses. Related to differentiation state, they have specific phenotypes and functions, and varied interactions with pathogens herein exemplified by Leishmania donovani (LD) that parasitize macrophages and propagate within their phagolysosomes. The impact of the differentiation state and intracellular infection on antigen processing and presentation by HLA class I remained undefined. To gain insight, we analyzed and compared the HLA-I self peptidomes of MUTZ3 cell line-derived human immature and mature DCs, and THP1 cell line-derived LD-infected and none-infected macrophages by liquid chromatography-tandem mass spectrometry (LC-MS/MS), as well as proteasome compositions by quantitative RT-PCR, and HLA expression and cell activation states by flow cytometry. We found that the HLA I-presented self-peptidomes of the cells in the different states were heterogeneous and individualized, dominated by nonapeptides with similar HLA binding affinities and anchor residues. They were sampled from source proteins of almost all subcellular locations and from proteins involved in various cellular functions in similar proportion including tumour-associated antigens (TAAs). The persistence of LD within the macrophage, did not affect macrophage activation. However, its impact was observed in self-peptidome heterogeneity, HLA binding affinities, anchor residue preferences, source protein peptide sampling (including TAAs) and HLA and proteasome expression.

Die Expression von Haupthistokompatibilitätsantigenen auf der Zelloberfläche kernhaltiger Zellen ist die Hauptursache für die Detektion durch das Immunsystem und die Rejektion allogener Transplantate. Eine vielversprechende Strategie, die MHC-I-Expression auf der Zelloberfläche zu senken, ist der Einsatz intrazellulär lokalisierter Antikörpern, sogenannter Intrabodies. In der vorliegenden Arbeit wurde erstmals versucht, eine die Expression an MHC-I-Molekülen auf der Zelloberfläche durch den Einsatz von anti-MHC-I-Intrabodies zu verhindern. Ein Hauptproblem in der Transplantation ist der Mangel an geeignetem Spendermaterial. Um diesem Zustand entgegenzuwirken, wird versucht, adäquaten Organersatz durch Tissue Engineering bereitzustellen. Die in vitro-Züchtung autologer epithelialer Zellen zur Generierung transplantierbarer Hautstücke spielt heute bereits eine große Rolle bei der Transplantation artifizieller Gewebe. Ferner werden diverse vollsynthetische Materialien für diesen Zweck hergestellt. Eine Verbesserung in diesen Bereich würde die Generierung von nicht-immunogenen allogenen Keratinozyten darstellen. Im Rahmen dieser Arbeit wurden primäre Rattenkeratinozyten mit anti-MHC-I-Intrabodies transfiziert. Diese Zellen zeigten einen MHC-I-"knock-out"-Phänotyp - eine starke Expression der Intrabodies war jedoch essentiell für die vollständige Zurückhaltung aller MHC-I-Moleküle in der Zelle. Neben der Applikation von Intrabodies in Rattenkeratinozyten konnte die MHC-I-Expression auf der Zelloberfläche von 293-Zellen und primären humanen Keratinozyten ebenfalls durch die Expression von anti-MHC-I-Intrabodies vermindert werden. Im Vergleich mit dem ebenfalls MHC-I-bindenden adenoviralen Protein p19 bewirkten die eingesetzten anti-MHC-I-Intrabodies bei gleich starker Expression eine wesentlich stärkere "Downregulation" der MHC-I-Oberflächenexpression von 293-Zellen. Intrabody-exprimierende Zellen zeigten keine signifikanten morphologischen oder physiologischen Veränderungen gegenüber untransfizierten Zellen: Wachstum, die Expression anderer Oberflächenmoleküle und morphologische Erscheinung waren unverändert. Es konnte lediglich eine verstärkte intrazelluläre Akkumulation von MHC-I-Molekülen detektiert werden. Die funktionelle Bedeutung der MHC-I-"Downregulation" durch Intrabodies konnte durch die stark verminderte zytolytische Aktivität zytotoxischer T-Zellen gegenüber Intrabody-exprimierender Rattenkeratinozyten im Vergleich zu unmodifizierten Zellen gezeigt werden. In der vorliegenden Arbeit ist es erstmals gelungen, Zellen mit einem vollständigen MHC-I-"knock-out"-Phänotyp zu erzeugen - bisherige Modifikationen der MHC-I-Oberflächenexpression durch die Generierung _2-Mikroglobulin- oder TAP-defizienter Mäuse führte zu keinem restlosen Verlust der Klasse-I-Moleküle auf der Zelloberfläche. MHC-I-"downregulierte" Keratinozyten könnten in der Hauttransplantation anstelle der limitiert zur Verfügung stehenden autologen Zellen eingesetzt werden oder in Kombination mit synthetischen Materialien verwendet werden, wo sie durch die Sekretion von heilungsfördernden Faktoren eine Verbesserung des Wundheilungsprozesses bewirken würden. / The expression of major histocompatibility antigens on the surface of eucaryotic cells is the predominant reason for immunologic detection and the rejection of allogeneic transplants. A promising strategy to lower the MHC I expression on the cell surface is the use of intracellular localized antibodies, termed intrabodies. In this work it has been tried for the first time to prevent the expression of MHC class I molecules on the cell surface by intrabody expression. A major problem in transplantation is the shortage of suitable donor material. To overcome this situation tissue engineering has and will continue to enlarge the scope of organ grafting. Today, the in vitro culture of autologous epithelial cells to generate transplantable skin sheets plays an important role in the transplantation of artificial tissues. Furthermore various fully synthetic materials are produced for transplantation. An improvement in this field could be the generation of non-immunogeneic allogeneic keratinocytes. Within this work primary rat keratinocytes have been transfected with anti-MHC-I-Intrabodies. These cells show a MHC I "knockout" phenotype - yet a strong intrabody expression was essential for the complete retention of all MHC I molecules inside the cell. Besides the application of intrabodies in keratinocytes the MHC I expression on the surface of 293 cells and human primary keratinocytes could be reduced by anti-MHC I intrabodies as well. In comparison with the also employed adenoviral protein p19 the applied intrabodies generated at the same expression level a much stronger down-regulation of the MHC I surface expression of 293 cells. Intrabody expressing cells did not show any significant morphologic or physiologic alterations compared to untransfected cells: growth, the expression of other surface molecules and the morphological appearance were unaltered. Merely an enhanced intracellular accumulation of MHC I molecules could be detected. The functional relevance of the MHC I down-regulation by intrabodies could be shown by the strong diminished cytolytic activity of cytotoxic T cells to intrabody expressing rat keratinocytes in comparison to unmodified cells. In this work cells with a completely MHC I knock-out phenotype has been successfully generated for the first time - modifications of the MHC I surface expression by generation of _2-microglobulin or TAP deficient mice did not lead to a complete loss of all MHC I molecules on the cell surface so far. MHC I down-regulated keratinocytes could be employed in skin transplantation instead of the limited available autologous cells or utilized in combination with synthetic materials where they would induce an improvement of the healing process by the secretion of cytokines.

The immune system is essential for keeping the integrity of multicellular organisms. We were able to make a step forward in studying the complex immune reactions in mammals in vivo and/ or in situ using the major histocompatibility complex (MHC) class II/ enhanced green fluorescent protein (EGFP) knock-in mouse model. Due to the EGFP visualization of MHC II expressing cells we were able to observe antigen presenting cells, which are essential for the onset of immune responses, in their natural environment. Thus, we report some original features of the immune system. We have identified MHC II+ cell clusters with unknown, probably unique function, in the intestine. We have also described MHC II+ cell migration to the lactating mammary gland and tested few hypotheses about the role of this phenomenon for the development of the mammary gland, milk secretion or infant immune system establishment. Lastly, we observed residential macrophages in the cornea. The presence of APCs in the cornea is a very contradictory issue due to the fact that cornea is an immunologically privileged tissue and therefore harbors special immune features. key words: antigen presenting cells (APC), major histocompatibility complex class II (MHC II), enhanced green fluorescent protein (EGFP), immune system, knock-in mouse model

A hepatite auto-imune (HAI) é uma doença inflamatória crônica do fígado, de etiologia desconhecida, que acomete preferencialmente mulheres, com destruição progressiva do parênquima hepático e que, sem tratamento imunossupressor, evolui freqüentemente para cirrose. É uma doença rara na infância, com menos de 10% dos pacientes com doença hepática crônica, porém de alta mortalidade. Caracteriza-se pela presença de hipergamaglobulinemia, auto-anticorpos não órgãos-específicos e infiltrado inflamatório portal linfoplasmocitário. Cerca da metade dos pacientes atendidos no Instituto da Criança, apresenta também níveis elevados de IgE, sem causas aparentes como parasitoses ou atopia. A suscetibilidade genética à doença está principalmente associada a genes que codificam as moléculas de histocompatibilidade (HLA). A presença do HLA-DR é importante, mas não suficiente para o desenvolvimento dessa doença rara, fazendo inclusive supor um forte componente externo/ambiental no desencadeamento da doença. Genes recém descritos, localizados na região de classe III do Complexo Principal de Histocompatibilidade (CPH) e ligados ao controle da resposta imune, em especial, alguns próximos à junção com a região de classe I, têm sido investigados como \"loci\" secundários para o desenvolvimento de doenças auto-imunes. A forte associação da HAI com genes na região do MHC, bastante comuns na população, aliada a incidência muito baixa da doença, leva à questão da presença de genes adicionais de suscetibilidade, que, junto com o HLA-DR, seriam responsáveis pela suscetibilidade genética observada. Dessa forma, o HLADRB1* 13, além de um fator por si, também pode ser um marcador da região cromossômica, ou seja, de um haplótipo específico e que, portanto, carrega mais de um gene de suscetibilidade. Estudamos polimorfismos, tipo SNP, de xx genes próximos ao HLA-DRB1, como TNFA, LTA, NFKBIL1 e BAT1, buscando haplótipos de susceptibilidade à doença, em pacientes HAI-1 (n=105) e controles sadios (n=227). O haplótipo ancestral 8.1 que inclui HLA-DRB1*03 e o alelo raro na posição -308 do gene TNFA estava aumentado (p=0.0005). Já o alelo HLA-DRB1*13, presente na maioria dos pacientes, não mostrou haplótipo específico associado. Também avaliamos genes de citocinas envolvidas na produção de IgE, elevado em parte dos pacientes HAI-1. Na comparação com controles, a freqüência dos SNPs IL- 4+33 e IL13+110, localizados em genes vizinhos, apresentou aumento estatisticamente significante nos pacientes, sugerindo haver um grupo gênico adicional no cromossomo 5q31 envolvido na susceptibilidade à HAI / Autoimmune hepatitis (AIH) is an inflammatory chronic liver disease of unknown etiology found predominantly in females, leading when untreated, to cirrhosis. It is a rare disease in the childhood, corresponding to about 10% of patients with chronic hepatitis, but exhibits high mortality. It is characterized by hipergammaglobulinemia, organ nonspecific circulating autoantibodies, and an inflammatory liver-infiltrating lymphocytes and plasma cells. Almost half of patients investigated at Instituto da Criança had increased plasma IgE levels, without any apparent cause such as parasite infestation or atopy. Genetic predisposition to AIH has been mainly linked to genes coding for HLA class II molecules. HLA-DR is important but not sufficient to explain this rare disease, suggesting there is an external/environmental component triggering the disease. Recently, several genes in the class III region of MHC, linked to immune responses, especially near the junction with the MHC class I region have been investigated as secondary loci for autoimmune disease susceptibility. The strong association of AIH with genes in the MHC region, common in the population, but a disease with the very low incidence, suggests additional genes linked with HLA-DR could add to the disease susceptibility. So, HLA-DR*13 besides being a factor by itself, could also be a chromosomal region marker, taking part of a specific haplotype carrying more than one susceptibility gene. We studied single nucleotide polymorphisms (SNP) in genes near HLA-DRB1, like TNFA, LTA, NFKBIL1 and BAT1 searching for disease susceptibility haplotypes, in HAI-1 patients (n=105) compared to healthy controls (n=227). The ancestral haplotype 8.1, which includes HLA-DRB1*03 and the rare TNFA allele at position -308 was increased (p=0.0005). However, HLA-DRB1*13, though present in the majority of the patients, did not show any specific haplotype associated to it. xxii We also analyzed cytokine genes involved in IgE production, which is increased in a part of the AIH type 1 patients. In comparison with controls, the frequency of the SNPs IL-4+33 and IL13+110 was significantly increased, suggesting the existence of an additional gene cluster in chromosome 5q31 involved in the susceptibility to AIH

Japanese encephalitis virus (JEV) is one of the major causes of encephalitis in Asia. JEV causes serious inflammation of the brain, which may lead to permanent brain damage and has a high mortality rate. Almost 3 billion people live in JE endemic areas and JEV causes an estimated 20,000 cases of disease and 6000 deaths per year. JEV is a positive stranded RNA virus belonging to the Flavivirus genus of the family Flaviviridae. The genome of JEV is about 11 kb long and codes for a polyprotein which is cleaved by both host and viral encoded proteases to form 3 structural and 7 non-structural proteins. JEV transmission occurs through a zoonotic cycle involving mosquitoes and vertebrate amplifying hosts, chiefly pigs and ardeid birds. Humans are infected when bitten by an infected mosquito and are dead end hosts. The role of humoral and cell mediated immune responses during JEV infection have been studied by several groups. While the humoral responses play a central role in protection against JEV, the cell mediated immune responses contributing to this end are not fully understood. The MHC molecules have been known to play predominant roles in host responses to viral infections and the consequences of virus infection on the expression of MHC molecules are varied. The expression of MHC-I molecules is known to decrease upon infection with many viruses such as HIV, MCMV, HCMV, Adv, and EBV. In contrast, infection with flavivirus such as West Nile Virus (WNV) has been shown to increase the cell surface expression of both MHC-I and MHC-II molecules. It has been reported previously that WNV infection increases the cell surface expression of adhesion molecules such as ICAM-1, VCAM-1 as well as E-Selectin and these changes were mediated directly by WNV and not by soluble cytokines. In contrast to classical MHC-I molecules, the nonclassical MHC-I molecules do not belong to a single group of structurally and functionally homologous proteins and normally have lower cell surface expression. Earlier studies have shown that the expression of nonclassical MHC-I molecules were induced during infection with JHM strain of mouse hepatitis virus (MHV). However, the functional significance of this induction is unclear. Expression of nonclassical MHC-I molecules upon flaviviral infection is not very well understood. In this thesis, evidence is presented that JEV infection induces the expression of both classical and nonclassical MHC-I molecules on primary mouse brain astrocytes, mouse embryonic fibroblasts (MEFs) and H6 (hepatoma cell). The levels of adhesion molecules as well as molecules involved in antigen processing and presentation were also analyzed and our results clearly demonstrate that JEV infection induces their expression on astrocytes, MEFs and H6. The role of NF-κB and type-I IFNs in the induction of classical and nonclassical MHC-I molecules as well as molecules involved in antigen processing and presentation were also analyzed and our results demonstrated that type-I IFN mediated signaling is responsible for the induction of these molecules during JEV infection. Chapter 1 discusses the innate and adaptive immune system, the role of classical and nonclassical MHC molecules in the initiation of immune response and diverse strategies adapted by different viruses to evade the immune response. It also includes a detailed discussion about the IFN and NF-κB signaling pathways and their modulation by viral infection. Finally, the genome organization, epidemiology, transmission cycle, pathogenesis and pathology, clinical features, humoral as well as cell mediated immune response to JEV infection and the current vaccine status to JEV infection are briefly discussed. Chapter 2 describes the general materials and methods used in this study. It includes the details of the reagents and cell lines used in the experiments. It also discusses the various techniques such as RT-PCR, FACS analysis, EMSA and ELISA. Chapter 3 focusses on the validation of different knockout MEFs used in the study as well as confirming the purity of primary astrocyte cultures established from pub brains. The susceptibility of various cells to JEV infection has also been investigated. Our results confirmed the authenticity of all the cells and the purity of primary astrocyte cultures used in the study. Our results also indicated that all the cells used in the study are susceptible to JEV infection. Chapter 4 discusses the expression of MHC and related genes involved in immune response upon JEV infection of primary mouse brain astrocytes, MEFs and H6. Chapter 4 demonstrates for the first time that JEV infection induces the expression of nonclassical MHC-I or class Ib molecules namely Qa-1, Qb1 and T10 in addition to the induction of classical MHC-I molecules. In contrast to WNV, there was no increase in the cell surface expression of MHC-II molecules upon JEV infection of primary mouse brain astrocytes. JEV infection also induces the expression of adhesion molecules as well as molecules involved in antigen processing and presentation namely Tap1, Tap2, Tapasin, Lmp2, Lmp7 and Lmp10. Chapter 5 demonstrates that JEV infection induces NF-κB activation in astrocytes and MEFs. Studies using MEFs deficient in classical and alternate pathways of NF-κB activation indicate that JEV activates the classical pathway of NF-κB activation and is dependent on canonical lKKβ/IKK2 activity. JEV infection of astrocytes, MEFs and H6 induces the production of type-I IFNs. To determine the mechanism of type-I IFN induction during JEV infection, MEFs deficient in NF-κB signaling and IFN signaling were used. Results indicate that type-I IFN production in MEFs occurs by both NF-κB dependent and independent mechanisms. In contrast, the production of IFN-α was completely abrogated in IFNAR-\- MEFs whereas IFN-β production was greatly reduced. Production of type-I IFNs in IFNGR-\- MEFs is also reduced upon JEV infection but the reason for this is unclear. Chapter 6 demonstrates that JEV induced expression of classical MHC-I molecules occurs by type-I IFN mediated signaling. This result is in contrast to WNV infection, in which both NF-κB and type-I IFNs are involved in the induction of classical MHC-I molecules. Type-I IFNs were also shown to be involved in the induction of nonclassical MHC molecules namely, Qa-1 and Qb1 during JEV infection. In contrast, the expression of T10, another nonclassical MHC molecule occurs independent of type-I IFN signaling. The expression of molecules involved in antigen processing and presentation namely, Tap1, Tap2, Lmp2 and Lmp7 was type-I IFN-mediated, whereas the expression of Tapasin and Lmp10 was mediated by both type-I IFN dependent and independent mechanisms. The expression of VCAM-1 was dependent on NF-κB mediated signaling. Chapter 7 precisely describes the underlying mechanism of induction of MHC and various other related molecules and their significance during JEV infection. In addition, it also includes a working model for the induction of these molecules during JEV infection. In summary, this is the first study in which the mechanism of JEV mediated induction of classical as well as nonclassical MHC molecules has been studied in detail. This study clearly demonstrated that type-I IFNs are involved in the induction of classical and nonclassical MHC-I molecules during JEV infection. The functional significance of this JEV mediated induction of classical MHC-I molecules is unclear, but it has been proposed that this is to escape from the action of NK cells. The absence of MHC-II induction during JEV infection could be important because it may lead to the initiation of an immune response which is different from that induced during other viral infections which induce the expression of MHC-II molecules. In contrast to classical MHC-I molecules, the functional and biological significance of nonclassical MHC-I molecules are poorly studied. Nonclassical MHC-I molecules play an important role in bridging adaptive and innate immune response. So the nonclassical MHC molecules induced during JEV infection may play an important role in the initiation of immune response during JEV infection. The role these nonclassical MHC-I molecules in antigen presentation during JEV infection is not known. These nonclassical antigens are also recognized by NK and γδT cells, thus the expression of nonclassical MHC-I molecules during JEV infection might also confer a protective role.

To be able to make informed descicions regarding the research of new drug molecules (ligands), it is crucial to have access to information regarding the chemical interaction between the drug and its biological target (protein). Computer-based methods have a given role in drug research today and, by using methods such as molecular docking, it is possible to investigate the way in which ligands and proteins interact. Despite the acceleration in computer power experienced in the last decades many problems persist in modelling these complicated interactions. The main objective of this thesis was to investigate and improve molecular modelling methods aimed to estimate protein-ligand binding. In order to do so, we have utilised chemometric tools, e.g. design of experiments (DoE) and principal component analysis (PCA), in the field of molecular modelling. More specifically, molecular docking was investigated as a tool for reproduction of ligand poses in protein 3D structures and for virtual screening. Adjustable parameters in two docking software were varied using DoE and parameter settings were identified which lead to improved results. In an additional study, we explored the nature of ligand-binding cavities in proteins since they are important factors in protein-ligand interactions, especially in the prediction of the function of newly found proteins. We developed a strategy, comprising a new set of descriptors and PCA, to map proteins based on their cavity physicochemical properties. Finally, we applied our developed strategies to design a set of glycopeptides which were used to study autoimmune arthritis. A combination of docking and statistical molecular design, synthesis and biological evaluation led to new binders for two different class II MHC proteins and recognition by a panel of T-cell hybridomas. New and interesting SAR conclusions could be drawn and the results will serve as a basis for selection of peptides to include in in vivo studies.

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease that leads to degradation of cartilage and bone mainly in peripheral joints. In collagen-induced arthritis (CIA), a mouse model for RA, activation of autoimmune CD4+ T cells depends on a molecular recognition system where T-cell receptors (TCRs) recognize a complex between the class II MHC Aq protein and CII259-273, a glycopeptide epitope from type II collagen (CII). Interestingly, vaccination with the Aq/CII259-273 complex can relieve symptoms and cause disease regression in mice. This thesis describes the use of modified glycopeptides to explore interactions important for binding to the Aq protein and recognition by autoimmune T-cell hybridomas obtained from mice with CIA. The CII259-273 glycopeptide was modified by replacement of backbone amides with different amide bond isosteres, as well as substitution of two residues that anchor the glycopeptide in prominent pockets in the Aq binding site. A three-dimensional structure of the Aq/glycopeptide complex was modeled to provide a structural basis for interpretation of the modified glycopeptide’s immunological activities. Overall, it was found that the amide bond isosteres affected Aq binding more than could be explained by the static model of the Aq/glycopeptide complex. Molecular dynamics (MD) simulations, however, revealed that the introduced amide bond isosteres substantially altered the hydrogen-bonding network formed between the N-terminal 259-265 backbone sequence of CII259-273 and Aq. These results indicated that the N-terminal hydrogen-bonding interactions follow a cooperative model, where the strength and presence of individual hydrogen bonds depended on the neighboring interactions. The two important anchor residues Ile260 and Phe263 were investigated using a designed library of CII259-273 based glycopeptides with substitutions by different (non-)natural amino acids at positions 260 and 263. Evaluation of binding to the Aq protein showed that there was scope for improvement in position 263 while Ile was preferred in position 260. The obtained SAR understanding provided a valuable basis for future development of modified glycopeptides with improved Aq binding. Furthermore, the modified glycopeptides elicited varying T-cell responses that generally could be correlated to their ability to bind to Aq. However, in several cases, there was a lack of correlation between Aq binding and T-cell recognition, which indicated that the interactions with the TCRs were determined by other factors, such as presentation of altered epitopes and changes in the kinetics of the TCR’s interaction with the Aq/glycopeptide complex. Several of the modified glycopeptides were also found to bind well to the human RA-associated DR4 protein and elicit strong responses with T-cell hybridomas obtained from transgenic mice expressing DR4 and the human CD4 co-receptor. This encourages future investigations of modified glycopeptides that can be used to further probe the MHC/glycopeptide/TCR recognition system and that also constitute potential therapeutic vaccines for treatment of RA. As a step towards this goal, three modified glycopeptides presented in this thesis have been identified as candidates for vaccination studies using the CIA mouse model.

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.

Diss. (sammanfattning) Umeå : Umeå universitet, 2010.