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Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 131-153).

Antigen presented to CD4+ T cells by major histocompatibility complex class II molecules (MHCII) plays a key role in adaptive immunity. Antigen presentation is initiated by the proteolytic cleavage of pathogenic or self proteins and loading of resultant peptides to MHCII. The loading and exchange of peptides to MHCII is catalyzed by a nonclassical MHCII molecule, HLA-DM (DM). It is well established that DM promotes peptide exchange in vitro and in vivo. However, the mechanism of DM-catalyzed peptide association and dissociation, and how this would affect epitope selection in human responses to infectious disease remain unclear. The work presented in this thesis was directed towards the understanding of mechanism of DM-mediated peptide exchange and its role in epitope selection. In Chapter II, I measured the binding affinity, intrinsic dissociation half-life and DM-mediated dissociation half-life for a large set of peptides derived from vaccinia virus and compared these properties to the peptide-specific CD4+ T cell responses. These data indicated that DM shapes the peptide repertoire during epitope selection by favoring the presentation of peptides with greater DM-mediated kinetic stability, and DM-susceptibility is a strong and independent factor governing peptide immunogenicity. In Chapter III, I computationally simulated peptide binding competition reactions and found that DM influences the IC50 (50% inhibition concentration) of peptides based on their susceptibility to DM, which was confirmed by experimental data. Therefore, I developed a novel fluorescence polarization-based method to measure DM-susceptibility, reported as a IC50 (change in IC50 in the absence and presence of DM). Traditional assays to measure DM-susceptibility based on differential peptide dissociation rates are cumbersome because each test peptide has to be individually labeled and multiple time point samples have to be collected. However, in this method developed here only single probe peptide has to be labeled and only single reading have to be done, which allows for fast and high throughput measure of DM-susceptibility for a large set of peptides. In Chapter IV, we generated a series of peptide and MHCII mutants, and investigated their interactions with DM. We found that peptides with non-optimal P1 pocket residues exhibit low MHCII affinity, low kinetic stability and high DM-susceptibility. These changes were accompanied with conformational alterations detected by surface plasmon resonance, gel filtration, dynamic light scattering, small-angle X-ray light scattering, antibody-binding, and nuclear magnetic resonance assays. Surprisingly, all these kinetic and conformational changes could be reversed by reconstitution with a more optimal P9 pocket residue. Taken together, our data demonstrated that conformation of MHCII-peptide complex constrained by interactions throughout the peptide binding groove is a key determinant of DM-susceptibility. B cells recognizing cognate antigen on the virion can internalize and process the whole virion for antigen presentation to CD4+ T cells specific for an epitope from any of the virion proteins. In turn, the epitope-specific CD4+ T cells provide intermolecular (also known as noncognate or heterotypic) help to B cells to generate antibody responses against any protein from the whole virion. This viral intermolecular help model in which CD4+ T cells provide help to B cells with different protein specificities was established in small size influenza virus, hepatitis B virus and viral particle systems. For large and complex pathogens such as vaccinia virus and bacteria, the CD4+ T cell-B cell interaction model may be complicated because B cells might not be able to internalize the large whole pathogen. Recently, a study in mice observed that CD4+ T cell help is preferentially provided to B cells with the same protein specificity to generate antibody responses against vaccinia virus. However, for larger pathogens such as vaccinia virus and bacteria the CD4+ T cell-B cell interaction model has yet to be tested in humans. In Chapter V, I measured in 90 recently vaccinated and 7 long-term vaccinia-immunized human donors the CD4+ T cell responses and antibody responses against four vaccinia viral proteins (A27L, A33R, B5R and L1R) known to be strongly targeted by cellular and humoral responses. We found that there is no direct linkage between antibody and CD4+ T cell responses against each protein. However, the presence of immune responses against these four proteins is linked together within donors. Taken together, our data indicated that individual viral proteins are not the primary recognition unit and CD4+ T cells provide intermolecular help to B cells to generate robust antibody responses against large and complicated vaccinia virus in humans.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Raymond R. R. Rowland / Open reading frame 2 (ORF2) of porcine circovirus type 2 (PCV2) codes for the 233 amino acid capsid protein (CP). Baculovirus-based vaccines that express only ORF2 are protective against clinical disease following experimental challenge or natural infection. The goal of this study was to identify regions in CP preferentially recognized by sera from experimentally infected and vaccinated pigs, and compare these responses to pigs diagnosed with porcine circovirus-associated disease (PCVAD). The approach was to react porcine sera with different CP polypeptide fragments that each contained one or more immunoreactive regions. Expression of polypeptides was performed using E.coli. Initial results showed that sera from vaccinated pigs preferentially recognized only the largest CP(43-233) polypeptide fragment and showed low levels of binding to other CP polypeptide fragments. The results of sera from pigs diagnosed with PMWS showed only minimal reactivity with CP polypeptide fragments, including the largest CP(43-233). PCV2 infected or PDNS diagnosed pigs reacted to all CP polypeptides: however, the strongest reactivity was primarily directed towards CP polypeptides containing residues in the 160-180 region. For this purpose, finer mapping studies were performed. These experiments involved reacting sera from experimentally infected PCV2 pigs and PDNS pigs with overlapping oligopeptides that covered amino acids 141-200. Overall, the results showed a subset of experimentally infected pigs and pigs with PDNS preferentially recognized the CP oligopeptide, 169-STIDYFQPNNKR-180. Alanine scanning identified Y-173, F-174, Q-175 and K-179 as important for antibody recognition. The results from this study support the notion of PCV2 modulation of immunity, including antibody responses that may represent a precursor for disease. The results from this study support the notion of PCV2 modulation of immunity. Furthermore, the methods incorporated in this study provide a means for characterizing the immune response upon vaccination, natural infection and disease.

Gene therapy has shown potential in alleviating a wide range of diseases, ranging from viral infections to autosomal diseases. One of the obstacles to gene therapy reaching its full potential is the inadequacy of methods to deliver therapeutic nucleic sequences. Current delivery of gene therapy entails use of viral and non-viral vectors. Viral vectors are however associated with drawbacks such as potential toxicity, high cost and labour-intensive production. Thus non-viral delivery alternatives are being developed in an attempt to overcome difficulties associated with nucleic acid delivery for gene therapy. Virus-like particles are potentially very useful delivery vehicles as their production is simple and cost effective, the particle surface is amenable to modification and the capsid interior can be altered to accommodate a variety of cargoes. One such particle is the recombinant HBV capsid, which comprises a single species of protein and is tolerant of amino acid substitutions on the surface exposed immunodominant loops. This study aimed to enhance the vector-like properties of the HBV virus-like particle by including amino acid substitutions on the particle surface. These substituted residues in turn provided a conjugation site for tropic and immuno evasive moieties. It was found that lysine substitutions resulted in poor conjugation to the capsid surface, whereas substituted cysteine residues resulted in almost all protein-moiety conjugates forming. In order to introduce lysine and cysteine substitutions, a novel method of cloning into the HBV was generated. In doing so, complicated procedures associated with cloning into the immunodominant loop of the HBV capsid have been alleviated. Ligands containing galactose were utilised on the surface of both the HBV capsid and liposomes to confer hepatotropism. The presence of the galactose moieties on the surface of the HBV capsid prevented indiscriminate cellular uptake in cultured cells, however did not improve hepatotropism. Galactose ligands on the surface of liposomes did improve transfection efficiency, however they required a short linker distance between liposome surface and galactose group. The inclusion of galactose in liposome formulations also provided a means to deliver siRNA to the liver of transgenic HBV mice. It is believed that with alterations to the ligand structure, it is possible to provide HBV capsids with hepatotropism in future experimentation. This study demonstrated that the exposed external surface of the HBV capsid is amenable to convenient conjugation, which potentially facilitates immune evasion and conferring of defined tropism.

A origem das doenças autoimunes é multifatorial, sendo que envolve condições ambientais e predisposição genética, dificultando sua identificação. Muitos pesquisadores têm estudado a associação entre agentes infecciosos e autoimunidade, a qual pode ser disparada pelo processo conhecido por mimetismo molecular. Neste caso, respostas imunes cruzadas envolvendo antígenos próprios têm sido documentadas. O presente projeto tem como objetivo a busca in silico por associações entre epítopos de microrganismos e autoantígenos humanos. Iniciaram-se as análises pela identificação de semelhanças de sequências de aminoácidos entre epítopos de microrganismos e autoantígenos humanos por meio do alinhamento local de sequências efetuado pelo programa BLASTP. As sequências de epítopos dos microrganismos e autoantígenos humanos foram previamente adquiridas nos bancos de dados Immune Epitope Database and Analysis Resource (IEDB) e no Genbank, respectivamente. Foram também realizadas modelagens de estruturas proteicas para o antígeno e o autoantígeno que obtiveram melhores valores de alinhamento, com base no valor do E-value, por meio dos programas Modeller e Rosetta. Por fim, a predição de epítopos foi executada, pelo uso dos softwares NetMHC e NetMHCII, para avaliar a possibilidade de epítopos de microrganismos e de autoantígenos humanos se associarem aos mesmos alelos de HLA. Como resultado, foram encontradas similaridades tanto de sequências proteicas quanto de afinidade a 4 tipos de alelos de HLA entre um epítopo do antígeno LSA-1 de Plasmodium falciparum e o autoantígeno de miosina, o que sugere uma associação entre eles, atingindo o objetivo deste trabalho. / The origin of autoimmune diseases is multifactorial. It involves environmental conditions and genetic predisposition that difficulties its identification. Several researchers have studied the association between infectious agents and autoimmunity, which can be initiated by a process named molecular mimicry. In this case, cross immune responses involving self antigens have been documented. This project aims to search in silico for associations between microorganisms epitopes and human autoantigens. The first step was the identification of similarities in amino acid sequences between microorganisms epitopes and human autoantigens by use of sequence local alignment performed by the program blastp. The sequences of the microorganisms epitope and the human autoantigens had been previously acquired in the Immune Epitope Database and Analysis Resource (IEDB) and Genbank, respectively. The modeling of protein structures for the antigen and autoantigen was also carried out to show the best alignment values, based on the E-value, using the programs Modeller and Rosetta. Finally, the prediction of epitopes was performed by use of NetMHC and NetMHCII softwares to evaluate the possibility of microorganisms epitopes and human autoantigens join the same HLA alleles. Similarities of protein sequences was found for both. It was possible to observe affinity of 4 HLA alleles between an epitope from LSA-1 Plasmodium falciparum antigen and the myosin, suggesting an association between them, reaching the goal of this work.

As taxas de resposta viral ao tratamento com Interferon- associado com Ribavirina ainda não estão bem definidas. Muitos estudos associam vários fatores virais e do hospedeiro, tais como a idade, sexo, peso, etnia, nível de enzimas hepáticas, estágio de fibrose, genótipo do HCV com os níveis de RNA viral. Outros estudos associam as células CD8+ específicas para epítopos do HCV com o controle da viremia. O objetivo desse trabalho foi verificar se há aumento na pressão seletiva contra o vírus nos pacientes em tratamento com Interferon- associado à Ribavirina respondedores em comparação com os pacientes não respondedores e associar esse aumento com a ação antiviral do tratamento e/ou com o aumento da resposta imune devido à ação imunomoduladora do Interferon-, utilizando-se modelos de máxima verossimilhança, de cálculo da razão dN/dS e realizando o mapeamento dos epítopos das proteínas NS5A. Nossos resultados demonstram que usando modelos par a par não foi detectado evidência de seleção positiva, entretanto utilizando modelos de máxima verossimilhança nós observamos evidência no grupo que não responde a terapia. O mapeamento dos epítopos revelou que o epítopo VLSDFKTWL estava associado com a resposta efetiva do tratamento com suporte estatístico. Estes resultados indicam que a resposta imunológica aumenta durante o período de tratamento, auxiliando na eliminação do vírus. Além das análises, foi desenvolvida uma ferramenta de mapeamento automático dos epítopos do HCV e análise de seleção natural aplicando modelos de máxima verossimilhança / The reason for low rates of sustained viral response (SVR) in HCV patients remains unknown. Several studies suggest that viral load is closely associated to viral and host factors, such age, sex, body weight, transaminase levels and HCV genotype. Moreover, an strong CD8+ T-cell immunity in acute resolving hepatitis C is matched by strong and sustained CD4+ T-cell proliferation to multiple recombinant structural and non-structural viral proteins is responsible for the control of viraemia in HCV infection. Here, we investigate the differences in CD8 epitopes frequencies from Los Alamos database between groups of patients that showed distinct response to pegylated alpha interpheron with ribavirin therapy, and test for evidence of natural selection on virus in treatment failure group, using five maximum likelihood evolutionary models. Our results indicated no evidence of positive selection by using pairwise models, however we identify evidence of positive selection in non responder group by applying maximum likelihood models. The epitope mapping showed that the epitope VLSDFKTWL was associated with efective therapy outcome, with statistical support. Those results suggest that the immune response increase during the treatment period, allowing the virus clearance. We also developed a tool for automatic mapping of epitopes of HCV that tests for evidence of natural selection by applying maximum likelihood models

S. pneumoniae pode causar infecções do trato respiratório. Uma alternativa às vacinas conjugadas, que conferem proteção sorotipo-específica, seria uma vacina baseada em epitopos de diferentes variantes de antígenos como PspA e PspC. O objetivo deste trabalho foi a identificação de epitopos de variantes de PspA e PspC, utilizando a técnica peptide array, visando a síntese de um antígeno composto por múltiplos epitopos. Os resultados obtidos indicaram que anticorpos contra epitopos lineares de PspA reconhecem as regiões inicial N-terminal e rica em prolinas, mas estes epitopos parecem ser apenas marcadores de exposição ao pneumococo e epitopos conformacionais seriam os de fato protetores, como observado nos experimentos realizados com os Frags de 100 aminoácidos construídos a partir do PspARx1, especialmente aqueles presentes nas regiões dos Frags 2 e 4. Epitopos lineares de PspC parecem ser importantes na região de ligação à sIgA e FH. Assim, uma vacina proteica de ampla cobertura, poderia conter as regiões do Frag 2 de PspA e de ligação de sIgA e FH de PspC. / S. pneumoniae can cause respiratory tract infections. An alternative to the conjugate vaccines, which confer serotype-specific protection, would be a vaccine based on epitopes of variants of antigens such as PspA and PspC. The objective of this study was to identify epitopes of variants of PspA and PspC, using the peptide array technique, aiming at the synthesis of a multi-epitope antigen. The results obtained with peptide arrays indicated that antibodies against linear epitopes of PspA recognize the initial N-terminal and proline-rich regions, but these epitopes seem to be only markers of exposure to pneumococcus and conformational epitopes would be in fact protective, as observed in the experiments with fragments of 100 amino acids constructed from PspARx1, especially those present in Frags 2 and 4. Linear epitopes of PspC seem to be important in the regions of sIgA and FH binding. Thus, a protein-based vaccine with broad coverage could contain the regions of Frag 2 of PspA and the regions of sIgA and FH binding of PspC.

Une nouvelle lignée homozygote de souris « humanisé » HLA transgéniques : HLA-A2.1+/+HLA-DP4+/+hCD4+/+mCD4-/-IAβ-/-β2m-/- (HLA-A2/DP4), a été obtenue en croisant entre les souris HLA transgéniques HLA-A2.1+/+β2m-/-(A2) et les souris HLA transgéniques HLA-DP4+/+hCD4+/+mCD4-/-IAβ-/-(DP4). Chez les souris HLA-A2/DP4, les réponses cellulaire T HLA-A2 restreint ou HLA-DP4 restreint contre l’antigène HBs du virus de l’Hépatite B suite à une immunisation avec le vaccin anti-AgHBs sont similaires à ceux observés chez les souris A2, chez les souris DP4, chez les humains infectés par le virus ou immunisés avec le même vaccin. Ces résultats montrent que les réponses cellulaires induites les souris HLA-A2/DP4 miment fidèlement les réponses homologues humaines. Ainsi, ces souris représentent un excellent modèle d’expérimentations précliniques animal pour évaluer ou comparer l’efficacité des réponses « humain » induites in vivo par des candidates vaccins. Le modèle facilitera également l'identification de nouvelles épitopes HLA-A2 et HLA-DP4 restreints, qui constituera de futurs réactives de suivi clinique des réponses contre l'infection chez les humains.En exploitant ces souris HLA-A2/DP4, nous avons identifié quatre nouveaux HLA-DP4-restricted épitopes issus de l'AgHBs et deux nouveaux HLA-A2 restreint épitopes dérivés de protéines M1. / A new homozygous humanized HLA transgenic mouse strain, HLA-A2.1+/+HLA-DP4+/+hCD4+/+mCD4-/-IAβ-/-β2m-/- (HLA-A2/DP4), was obtained by crossing the HLA transgenic HLA-A2.1+/+β2m-/-(A2) mice and HLA transgenic HLA-DP4+/+hCD4+/+mCD4-/-IAβ-/-(DP4) mice. In HLA-A2/DP4 mice, HLA-A2 restricted or HLA-DP4 restricted T cell responses against HBs antigen of hepatitis B virus after immunization with the HBsAg vaccine are similar to those induced in A2 mice, in DP4 mice, in HBV-infected or HBsAg-vaccinated humans. These results show that cellular responses induced in HLA-A2/DP4 mice faithfully mimic human responses counterparts. Thus, these mice represent an excellent animal model for preclinical experimentations to evaluate or compare the effectiveness of responses "human" induced in vivo by candidate vaccines. The model will also facilitate the identification of new epitopes HLA-A2 and HLA-DP4 restricted, which will be of future reactive for clinical monitoring response against infection in humans. By exploiting these HLA-A2/DP4 mice, we identified four new HLA-DP4-restricted epitopes from HBsAg and two new HLA-A2 restricted epitopes derived from protein M1.

Resumo: Os venenos dos insetos da ordem Hymenoptera contêm uma variedade de proteínas alergênicas. As ferroadas desses insetos podem induzir reações alérgicas e ocasionalmente, anafilaxias fatais. Há um crescente interesse nos componentes químicos dos venenos desses insetos, sobretudo no campo da alergia e imunologia clínica. As principais reações desses venenos são as reações inflamatórias e/ou imunológicas em suas vítimas, podendo ocorrer alguns efeitos sistêmicos. Dentre os Hymenoptera sociais, os venenos de abelhas e vespas têm sido extensivamente estudados e muitos de seus componentes moleculares já foram isolados e identificados. Fosfolipase, hialuronidase, antígeno-5 e serinoprotease são proteínas antigênicas de elevada massa molecular que, quando injetadas durante o ato de ferroar, iniciam uma resposta imune peculiar, sensibilizando alguns indivíduos. Porém, poucos estudos têm sido realizados para a identificação e o mapeamento dos epítopos desses alérgenos. O conhecimento sobre a interação molecular dos principais alérgenos destes venenos certamente deverá contribuir para o aperfeiçoamento dos diagnósticos de alergia, bem como para o desenvolvimento de tratamentos mais seletivos de reações alérgicas mediadas por IgE. No presente estudo identificamos e mapeamos os epítopos lineares de células-B do antígeno-5 do veneno da vespa social Polybia paulista. O antígeno-5 é conhecido como um dos principais alérgenos do veneno de Hymenoptera com massa molecular em torno de 23 kDa e função biológica desconhecida, porém muitos estudos demonstram a sua alergenicidade. Tendo conhecimento da sequência primária do antígeno-5, a identificação e o mapeamento dos epítopos foram realizados através da síntese múltipla de peptídeos, utilizando as técnicas do SPOT-Synthesis, imunodetecção e método indireto do ELISA com soro de pacientes sensíveis... (resumo completo, clicar acesso eletrônico abaixo) / Abstract: The venom insects of Hymenoptera order contain a variety of allergenic proteins. The stings of these insects can induce allergic reactions and occasionally fatal anaphylaxis. There is a growing interest in the knowledge about the chemical components of the venom of these insects, especially in the field of allergy and clinical immunology. The main reactions of these venoms are inflammation and / or the induction of immune process in the victims; sometimes systemic effects also may be observed. Among the social Hymenoptera, the venoms of bees and wasps have been extensively studied and many of their molecular components have been isolated and identified. Phospholipase, hyaluronidase, antigen-5 and serine protease are antigenic proteins of high molecular weight, which may initiate a peculiar immune response to sensitize some individuals. However, few studies have been performed for the identification and mapping of the epitopes these allergens. The knowledge about the molecular interaction of the major allergens of these venoms with IgG and/or IgE will certainly contribute for improving the diagnosis of allergy, as well as to develop more selective treatments of reactions IgE-mediated allergy. In this study we identified and mapped the linear epitopes of B-cells of the antigen-5 from the venom of the social wasp Polybia paulista. The antigen-5 is known as one of the major allergens from Hymenoptera venoms with molecular weight around 23 kDa and unknown biological function, but many studies show its allergenicity. The aim of this study was to identify and to map the linear epitopes of B-cells of this allergen. Taking into account the knowledge the primary sequence of antigen-5, the identification and mapping of epitopes was performed by using multiple synthesis of peptides with the combination of different protocols: SPOT-Synthesis, immunoblotting and indirect method of ELISA with the sera... (Complete abstract click electronic access below) / Orientador: Mario Sergio Palma / Coorientador: Lucilene Delazari dos Santos / Banca: Salvatore Giovanni de Simone / Banca: Luisa Karla de Paula Arruda / Mestre