Made available in DSpace on 2014-12-17T14:16:32Z (GMT). No. of bitstreams: 1 DalianaMBOS_DISSERT.pdf: 1178965 bytes, checksum: a8c57235d95835138c537bc774c7af70 (MD5) Previous issue date: 2012-02-27 / The expression of human leukocyte antigen G (HLA-G) and human leukocyte antigen E (HLA-E) in physiological and pathological processes remains unknown, it is believed that these molecules play a fundamental role in the establishment and maintenance of immune tolerance by inhibiting the functions of immunocompetent cells. In literature we found no published study involving the bacterium Helicobacter pylori (H. pylori) with expression of HLA-G and HLA-E. The objective this study is investigated the expression of this protein in gastric biopsies of patients with the bacterium H. pylori. Sixty-four biopsies of the patients with diagnosis of infection by H. pylori were evaluated to expression of HLA-G and HLA-E. The samples were stratified according to the presence of carcinoma or peptic ulcers. Patients without H. pylori were used to control. To investigate the expression of this protein were used immunohistochemistry technique with monoclonal antibody anti-HLA-G and anti-HLA-E. Other criteria such as analysis of the inflammatory infiltrate (hematoxylin-eosin) and identification of H. pylori (Giemsa) were analyzed. We detected HLA-G and HLA-E molecules in the most samples containing ulcer and gastric carcinoma. In negative control group was not detected the presence of HLA-G and HLA-E. The presence of H. pylori seems modulate the expression of HLA-G and HLA-E, favoring the evolution of infection, giving different degrees of gastric lesion in epithelium of these patients / A express?o do ant?geno leucocit?rio humano G (HLA-G) e do ant?geno leucocit?rio humano E (HLA-E) em processos fisiol?gicos e patol?gicos permanece pouco conhecida. Acredita-se que essas mol?culas desempenham papel fundamental no estabelecimento e manuten??o da toler?ncia imunol?gica, inibindo as fun??es das c?lulas imunocompetentes. Na literatura internacional, at? o momento, n?o foi encontrado nenhum estudo publicado correlacionando Helicobacter pylori (H. pylori) com express?o de HLA-G e HLA-E. O presente trabalho tem como objetivo correlacionar a express?o dessas prote?nas em bi?psias g?stricas de pacientes acometidos com H. pylori. Sessenta e quatro esp?cimes g?stricas de pacientes acometidos com H. pylori foram avaliados para express?o de HLA-G e HLA-E. As amostras foram estratificadas de acordo com a presen?a de carcinoma ou de ?lcera p?ptica. Como controle foram analisados esp?cimes g?stricas de pacientes vivos sem H. pylori. Para detectar a express?o dessas mol?culas utilizou-se a t?cnica de imunohistoqu?mica com os anticorpos monoclonais anti-HLA-G e anti-HLA-E. Outros crit?rios como an?lise do infiltrado inflamat?rio (hematoxilina-eosina) e identifica??o do H. pylori (Giemsa) foram analisados. As mol?culas de HLA-G e HLA-E foram detectadas em grande parte das amostras contendo ?lcera e carcinoma g?strico. No grupo controle n?o foi detectada a presen?a de HLA-G e HLA-E, indicando que a bact?ria H. pylori modula a express?o dessas mol?culas no grupo dos pacientes que apresentaram ?lcera ou carcinoma g?strico. A presen?a da bact?ria H. pylori parece modular a express?o do HLA-G e do HLA-E, favorecendo assim a evolu??o da infec??o, o que confere diferentes graus de les?o do epit?lio g?strico desses pacientes

<p>Southern Africa is facing one of the most serious HIV epidemics. This project contributes to the HIVNET, Network for Prevention Trials cohort for vaccine development. HIV’s biology and rapid mutation rate have made vaccine design difficult. We examined HIV-1 subtype C diversity and how it relates to CTL epitope location along viral gag sequences. We found a negative correlation between codon sites under positive selection and epitope regions / suggesting epitope regions are evolutionarily conserved. It is possible that epitopes exist in non-conserved regions, yet fail to be detected due to the reference strain diverging from the circulating viral population. To test if CTL clustering is an artifact of the reference strain, we calculated differences between the gag codons and the reference strain. We found a weak negative correlation, suggesting epitopes in less conserved regions maybe evading detection. Locating conserved and optimal epitopes that can be recognized by CTLs is essential for the design of vaccine reagents.</p>

<p>Southern Africa is facing one of the most serious HIV epidemics. This project contributes to the HIVNET, Network for Prevention Trials cohort for vaccine development. HIV’s biology and rapid mutation rate have made vaccine design difficult. We examined HIV-1 subtype C diversity and how it relates to CTL epitope location along viral gag sequences. We found a negative correlation between codon sites under positive selection and epitope regions / suggesting epitope regions are evolutionarily conserved. It is possible that epitopes exist in non-conserved regions, yet fail to be detected due to the reference strain diverging from the circulating viral population. To test if CTL clustering is an artifact of the reference strain, we calculated differences between the gag codons and the reference strain. We found a weak negative correlation, suggesting epitopes in less conserved regions maybe evading detection. Locating conserved and optimal epitopes that can be recognized by CTLs is essential for the design of vaccine reagents.</p>

Orientador: Manoel Barros Bértolo / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-16T11:59:40Z (GMT). No. of bitstreams: 1 Nishimura_WesterEidi_M.pdf: 1381412 bytes, checksum: a01c05ab2c7b9409c11bde6b5d507e4f (MD5) Previous issue date: 2010 / Resumo: O objetivo do presente estudo foi avaliar a freqüência e a associação clínica do HLA classe I e II em pacientes brasileiros com vasculite reumatóide (VR). Nós avaliamos 57 pacientes com artrite reumatóide (AR) estabelecida pelos critérios do Colégio Americano de Reumatologia (ACR) - 1987. Dezessete apresentavam VR de acordo com os critérios de Scott e Bacon - 1984. Foram avaliados nestes pacientes dados demográficos, fator reumatóide (FR), anticorpo anti-peptídio citrulinado cíclico (anti-CCP), tempo de diagnóstico da AR e a atividade da doença pelo escore de atividade da doença (DAS 28). Os alelos HLA foram tipados usando a reação em cadeia da polimerase hibridizado com seqüências específicas de "primers" de baixa resolução. Quanto à atividade da doença nos pacientes sem VR observou-se freqüência aumentada do HLA-B*15 (p=0.033) e HLA-DRB1*01 (p=0.014) com média de DAS 28 >3.2 _ 5.1 e o HLA-Cw*16 (p=0.027) e HLA-B*07 (p=0.027) com média de DAS 28>5.1. Não houve significância estatística de qualquer classe do HLA com o DAS 28 nos pacientes com VR. A comparação entre os 2 grupos mostrou diferença estatística (p=0.001) para o DAS 28 com rank médio = 39.94 para os pacientes com VR. O HLADQB1* 05 (p=0.035) esteve presente em 5 pacientes com VR com média de tempo de diagnóstico de AR de 17 anos e ausente em 12 pacientes com VR com média de tempo de diagnóstico AR de 11.45 anos. Os pacientes com VR tiveram freqüência aumentada do HLA-B*14 (p=0.006) e HLA-Cw*08 (p=0.006). Uma freqüência aumentada do HLA-DRB5*01 (p=0.048) foi encontrada em pacientes sem VR. Nossos resultados mostram na amostra estudada que a VR está associada ao sexo feminino, raça branca, FR e anti-CCP positivos. O HLA-B*15 e HLA-DRB1*01 podem estar envolvidos na atividade moderada da AR sem VR e o HLA-Cw*16 e HLA-B*07 podem estar envolvidos na atividade intensa da AR sem VR. Não houve diferença estatística das classes do HLA com o DAS 28 para VR, porém a doença foi mais ativa em pacientes com VR quando comparados com pacientes sem VR. O HLA-DQB1*05 pode estar envolvido nos casos tardios de AR para a manifestação da VR. O HLA-B*14 e HLACw* 08 podem estar envolvidos na suscetibilidade para VR. O HLA-DRB5*01 pode conferir proteção contra esta manifestação extra-articular da AR / Abstract: Our purpose was to evaluate the frequency and clinical association of HLA class I and class II in Brazilian patients with rheumatoid vasculitis (RV). We evaluated 57 patients with rheumatoid arthritis (RA) (American College of Rheumatology -ACR, 1987 criteria). Seventeen had RV according to Scott and Bacon's criteria - 1984. Demographic data, time of RA diagnosis, disease activity by the Disease Activity Score (DAS 28), rheumatoid factor (RF) and cyclic citrullinated peptide (anti-CCP) were analyzed. HLA alleles were typed using polymerase chain reaction-amplified DNA hybridized with low-resolution sequence-specific primers. HLA-B*15 (p=0.033) and HLA-DRB1*01 (p=0.014) were associated with moderate activity of RA without RV, and HLA-B*07 (p=0.027) and HLA-Cw*16 (p=0.027) with intense activity of RA without RV; no statistical significance of HLA class and DAS 28 was observed in RV. HLA-DQB1*05 (p=0.035) was related to RV in patients with late RA. The comparison between the groups showed an increased frequency of HLA-B*14 (p = 0.006) and HLA-Cw*08 (p = 0.006) in patients with RV, and an increased frequency of HLADRB5* 01 (p = 0.048) in patients without RV. In conclusion, the HLA-B*14 and HLACw* 08 may be involved in susceptibility to RV and HLA-DRB5*01 may confer protection against this extra articular manifestation of RA / Mestrado / Clinica Medica / Mestre em Clinica Medica

Magister Scientiae - MSc / Southern Africa is facing one of the most serious HIV epidemics. This project contributes to the HIVNET, Network for Prevention Trials cohort for vaccine development. HIVÂ’s biology and rapid mutation rate have made vaccine design difficult. We examined HIV-1 subtype C diversity and how it relates to CTL epitope location along viral gag sequences. We found a negative correlation between codon sites under positive selection and epitope regions; suggesting epitope regions are evolutionarily conserved. It is possible that epitopes exist in non-conserved regions, yet fail to be detected due to the reference strain diverging from the circulating viral population. To test if CTL clustering is an artifact of the reference strain, we calculated differences between the gag codons and the reference strain. We found a weak negative correlation, suggesting epitopes in less conserved regions maybe evading detection. Locating conserved and optimal epitopes that can be recognized by CTLs is essential for the design of vaccine reagents. / South Africa

Carcinomatose péritonéale est un terme utilisé pour désigner la dissémination métastatique généralisée du cancer dans la cavité péritonéale. Il se caractérise par l’accumulation de liquide appelé « ascite » et est considéré comme étant au stade terminal du cancer, car il est difficile à traiter. L'ascite accumulée dans la PC comprend des cellules tumorales, cytokines et cellules immunitaires. Les cellules cancéreuses expriment des protéines spécifiques qui les aident à supprimer les cellules immunitaires et à survivre, appelées points de contrôle immunitaires. Des points de contrôle immunitaires sont présents pour réguler le système immunitaire et sont cruciaux contre la tolérance de soi. PD-1 / PD-L1 et CTLA-4 sont des voies de contrôle immunitaire bien établies adaptées au cancer pour échapper à l'immunité. Récemment, HLA-G a été reconnu comme un point de contrôle et il a été constaté que la survie globale était diminuée dans plusieurs types de cancers solides.Au cours de ma thèse, nous avons évalué l'expression de HLA-G dans la carcinomatose ovarienne. Nous avons constaté que les cellules cancéreuses dans l'ascite de presque tous les patients atteints de carcinomatose ovarienne exprimaient HLA-G. De plus, des taux croissants de sHLA-G1 et de HLA-G5 ont été trouvés dans les ascites. Cette présence de sHLA-G s'est révélée être corrélée positivement avec les Tregs et en corrélation négative avec les cellules T cytotoxiques (CD8) et les cellules NK. De plus, nous avons constaté que les ascites peuvent induire l’expression de HLA-G dans des «Hospicells» via des cytokines inflammatoires. Parmi les cytokines inflammatoires, le TGF-β et IL-1β ont une importance capitale dans l’induction de HLA-G. En outre, nous avons constaté que IL-1β implique la voie NF-κB. Dans une cohorte distincte de carcinomatose péritonéale, composée de patients atteints de PC d'origine différente, nous avons constaté que le groupe de cellules cancéreuses dans l'ascite avait une expression génique hétérogène de PD-L1, CTLA-4 et HLA- G. En outre, nous avons constaté que tous les patients présentaient des taux solubles de HLA-G et PD-L1 dans leur ascite. Cependant, seulement 5 patients présentaient des taux de CTLA-4 solubles dans leur ascite. De plus, nous avons trouvé une très forte corrélation positive entre le niveau de gène de PD-L1 et de CTLA-4, alors qu'aucune corrélation n'a été trouvée pour HLA-G avec PD-11 et CTLA-4 suggérant que HLA-G agit indépendamment des deux points de contrôle immunitaires. En outre, nous avons évalué l'expression de ces points de contrôle immunitaires par des nodules de cancer présents sur la membrane péritonéale. Nous avons trouvé une faible expression de HLA-G et PD-L1, mais la moitié des échantillons étaient fortement positifs pour sHLA-G. Nous avons également constaté que le sHLA-G pouvait être absorbé par l'ascite par la couche mésothéliale. Cette sHLA-G absorbée peut fournir un environnement immunosuppresseur pour la fixation des grappes de cellules cancéreuses à la membrane péritonéale. In vitro, nous avons constaté que l'ascite peut exercer une action immunosuppressive et retarder la lyse des cellules cancéreuses par les cellules immunitaires.De plus, nous avons constaté que la différenciation des cellules cancéreuses se traduit par une augmentation des propriétés immunosuppressives par une expression accrue de HLA-G ou PD-L1. En outre, l'expression de HLA-G et PD-L1 dépend de la phase du cycle cellulaire. Les cellules cancéreuses, si elles sont bloquées dans les cellules mitotiques, expriment des niveaux élevés de HLA-G et de PD-L1, tandis qu'une expression plus faible a été observée en phase G1. Par conséquent, nous suggérons d’éviter l’utilisation d’inhibiteurs de la mitose car ils pourraient augmenter la suppression immunitaire du cancer. De plus, le Ki-67 étant directement lié à l'index mitotique, nous suggérons de développer une échelle de Ki-67 pour évaluer le profil d'immunosuppresseur des patients cancéreux. / Peritoneal carcinomatosis (PC) is a term used for widespread metastatic dissemination of cancer to the peritoneal cavity. It is characterized by the accumulation of fluid called “ascites” and is considered a terminal stage of cancer, as it is hard to treat. The overall survival rate for untreated patients is six-months. However, owing to modern techniques like HIPEC, the survival rate can be increased up to five years. The ascites accumulated in PC, consists of tumor cells, cytokines and immune cells. Cancer cells express specific proteins to suppress immune cells activity and their attack, known as immune checkpoints. PD-1/PD-L1 and CTLA-4 are well established immune checkpoint pathways adapted by cancer in evading immunity. Recently, HLA-G has been recognized as an immune checkpoint and has been found to decrease overall survival in several types of solid cancers. We evaluated the expression of HLA-G in ascites from ovarian carcinomatosis. We found that HLA-G is expressed by cancer cells in ascites from all of the patients(n=16) with ovarian carcinomatosis. Moreover, increased levels of sHLA-G1 and HLA-G5 were found in ascites. This presence of sHLA-G isoforms was found to be positively correlated with Tregs and negatively correlated with cytotoxic T-cells (CD8) and NK-cells suggesting the role of HLA-G in immune suppression. Further, we found that ascites can induce the expression of HLA-G in “Hospicells” via inflammatory cytokines. Among the inflammatory cytokines, TGF-β and IL-1β are of crucial importance in HLA-G induction with IL-1β being more potent compared to TGF-β. Further, we found that IL-1β induces HLA-G expression through NF-κB pathway.In a separate cohort of peritoneal carcinomatosis(n=27), consisting of patients with cancer from a different origin, we found that cancer cell cluster in ascites (n=23) had a heterogeneous gene expression of PD-L1, CTLA-4 and HLA-G. Further, we found that all of the patients presented soluble levels of HLA-G in their ascites. However, one patient was negative for soluble PD-L1 and only 5 patients presented soluble CTLA-4 levels in their ascites. This heterogeneity explains why some of the patients respond to immune therapy while others don’t. This also suggests the need for prescreening patients before immune therapy. Moreover, we found a very strong positive correlation (rs=0.793) between gene level of PD-L1 and CTLA-4, while no correlation was found for HLA-G with PD-L1 and CTLA-4 suggesting that HLA-G acts independently of both the immune checkpoints. Also, we evaluated the expression of these immune checkpoints by cells in peritoneal tissue (n=20). We found low expression of HLA-G and PD-L1, but the majority of the samples were found strongly positive for sHLA-G presence. This sHLA-G can provide an immune-suppressive environment for the attachment of the cancer cell clusters to the peritoneal membrane to form cancer nodule. Additionally, we developed an in-vitro cytotoxicity assay to show that the ascites can provide the immune-suppressive action by interfering with immune cell interaction and delaying the lysis of cancer cells by the immune cells.In parallel, we found that the differentiation of the cancer cells results in increased expression of immune checkpoints like HLA-G or PD-L1. This may render these cells more immune resistant and can protect against immune attack. However, in-vivo mice model is needed to study the oncogenic potential of these differentiated cells. Further, we report that the expression of HLA-G and PD-L1 is dependent on the cell cycle phase. The cancer cells, if blocked in mitotic phase express high levels of HLA-G and PD-L1, while lowest expression was observed in G1-phase. Therefore, we suggest avoiding the use of mitotic inhibitors as it may increase the immune suppression of cancer. Moreover, as Ki-67 is directly related to the mitotic index, we suggest developing a Ki-67 scale to evaluate the immune-suppressive profile of cancer patients.

Cytotoxic T-lymphocytes (CTLs) are important components of the adaptive immune system and function by scanning the intracellular environment so as to detect and de-stroy infected cells. CTL responses play a major role in controlling virus-infected cells such as in HIV or influenza and cells infected with intracellular bacteria such as in tuberculosis. To do so they require the antigens to be presented to them, which is fulfilled by the major histocompatibility complex (MHC), commonly known as human leukocyte antigen or HLA molecules in humans. Recognition of antigenic peptides to Class-1 HLA molecules is a prerequisite for triggering CTL immune responses. Individuals differ significantly in their ability to respond to an infection. Among the factors that govern the outcome of an infection, HLA polymorphism in the host is one of the most important. Despite a large body of work on HLA molecules, much remains to be understood about the relationship between HLA diversity and disease susceptibility. High complexity arises due to HLA allele polymorphism, extensive antigen cross-presentability, and host-pathogen heterogeneity. A given allele can recognize a number of different peptides from various pathogens and a given peptide can also bind to a number of different individuals. Thus, given the plurality in peptide-allele pairs and the large number of alleles, understanding the differences in recognition profiles and the implications that follow for disease susceptibilities require mathematical modelling and computational analysis. The main objectives of the thesis were to understand heterogeneity in antigen presentation by HLA molecules at different scales and how that heterogeneity translates to variations in disease susceptibilities and finally the disease dynamics in different populations. Towards this goal, first the variations in HLA alleles need to be characterized systematically and their recognition properties understood. A structure-based classification of all known HLA class-1 alleles was therefore attempted. In the process, it was also of interest to see if understanding of sub-structures at the binding grooves of HLA molecules could help in high confidence prediction of epitopes for different alleles. Next, the goal was to understand how HLA heterogeneity affect disease susceptibilities and disease spread in populations. This was studied at two different levels. Firstly, modelling the HLA genotypes and CTL responses in different populations and assessing how they recognized epitopes from a given virus. The second approach involved modelling the disease dynamics given the predicted susceptibilities in different populations. Influenza H1N1 infection was used as a case study. The specific objectives addressed are: (a) To develop a classification scheme for all known HLA class-1 alleles that can explain epitope recognition profiles and further to dissect the physic-chemical features responsible for differences in peptide specificities, (b) A statistical model has been derived from a large dataset of HLA-peptide complexes. The derived model was used to identify the interdependencies of residues at different peptide and thereby, rationalize the HLA class-I allele binding specificity at a greater detail, (c) To understand the effect of HLA heterogeneity on CTL mediated disease response. A model of HLA genotypes for different populations was required for this, which was constructed and used for estimating disease response to H1N1 via the prediction of epi-topes and (d) To model disease dynamics in different populations with the knowledge of the CTL response-grouping and to evaluate the effect of heterogeneity on different vaccination strategies. Each of the four objectives listed above are described subsequently in chapters 2 to 5, followed by Chapter 6 which summarises the findings from the thesis and presents future directions. Chapter 1 presents an introduction to the importance of the function of HLA molecules, describes structural bioinformatics as a discipline and the methods that are available for it. The chapter also describes different mathematical modelling strategies available to study host immune responses. Chapter 2 describes a novel method for structure-based hierarchical classification of HLA alleles. Presently, more than 2000 HLA class-I alleles are reported, and they vary only across peptide-binding grooves. The polymorphism they exhibit, enables them to bind to a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern due to multiplicity in their associations. Thus, a powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. The study reports a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification with 7 supergroups was derived, each further categorized to yield a total of 72 groups. An independent clustering scheme based only on the similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explains the basis for the observed clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues that contribute to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants. The results are presented in an interactive web- server http://proline.iisc.ernet.in/hlaclassify. In Chapter 3, the knowledge of structural features responsible for generating peptide recognition specificities are first analysed and then utilized for predicting T-cell epi-topes for any class-1 HLA allele. Since identification of epitopes is critical and central to many of the questions in immunology, a study of several HLA-peptide complexes is carried out at the structural level and factors are identified that discriminate good binder peptides from those that do not. T-cell epitopes serve as molecular keys to initiate adaptive immune responses. Identification of T-cell epitopes is also a key step in rational vaccine design. Most available methods are driven by informatics, critically dependent on experimentally obtained training data. Analysis of the training set from IEDB for several alleles indicate that sampling of the peptide space is extremely sparse covering only a tiny fraction of all possible nonamer space, and also heavily skewed, thus restricting the range of epitope prediction. A new epitope prediction method is therefore developed. The method has four distinct modules, (a) structural modelling, estimating statistical pair-potentials and constraint derivation, (b) implicit modelling and interaction profiling, (c) binding affinity prediction through feature representation and (d) use of graphical models to extract peptide sequence signatures to predict epitopes for HLA class I alleles . HLaffy is a novel and efficient epitope prediction method that predicts epitopes for any HLA Class-1 allele, by estimating binding strengths of peptide-HLA complexes which is achieved through learning pair-potentials important for peptide binding. It stands on the strength of mechanistic understanding of HLA-peptide recognition and provides an estimate of the total ligand space for each allele. The method is made accessible through a webserver http://proline.biochem.iisc.ernet.in/HLaffy. In chapter 4, the effect of genetic heterogeneity on disease susceptibilities are investigated. Individuals differ significantly in their ability to respond to an infection. Among the factors that govern the outcome of an infection, HLA polymorphism in the host is one of the most important. Despite a large body of work on HLA molecules, much remains to be understood about how host HLA diversity affects disease susceptibilities. High complexity due to polymorphism, extensive cross-presentability among HLA alleles, host and pathogen heterogeneity, demands for an investigation through computational approaches. Host heterogeneity in a population is modelled through a molecular systems approach starting with mining ‘big data’ from literature. The in-sights derived through this is used to investigate the effect of heterogeneity in a population in terms of the impact it makes on recognizing a pathogen. A case study of influenza virus H1N1 infection is presented. For this, a comprehensive CTL immunome is defined by taking a consensus prediction by three distinct methods. Next, HLA genotypes are constructed for different populations using a probabilistic method. Epidemic incidences in general are observed to correlate with poor CTL response in populations. From this study, it is seen that large populations can be classified into a small number of groups called response-types, specific to a given viral strain. Individuals of a response type are expected to exhibit similar CTL responses. Extent of CTL responses varies significantly across different populations and increases with increase in genetic heterogeneity. Overall, the study presents a conceptual advance towards understanding how genetic heterogeneity influences disease susceptibility in individuals and in populations. Lists of top-ranking epitopes and proteins are also derived, ranked on the basis of conservation, antigenic cross-reactivity and population coverage, which pro- vide ready short-lists for rational vaccine design (flutope). Next, in Chapter 5, the effect of genetic heterogeneity on disease dynamics has been investigated. A mathematical framework has been developed to incorporate the heterogeneity information in the form of response-types described in the previous chap-ter. The spread of a disease in a population is a complex process, controlled by various factors, ranging from molecular level recognition events to socio-economic causes. The ‘response-typing’ described in the previous chapter allows identification of distinct groups of individuals, each with a different extent of susceptibility to a given strain of the virus. 3 different approaches are used for modelling: (i) an SIR model where different response types are considered as partitions of each S, I and R compartment. Initially SIR models are developed, such that the S compartment is sub-divided into further groups based on the ‘response-types’ obtained in the previous chapter. This analysis shows an effect in infection sweep time, i.e., how long the infection stays in the population. A stochastic model incorporates the environmental noise due to random variation in population influx, due to birth, death or migration. The system is observed to show higher stability in the presence of genetic heterogeneity. As the contagion spreads only through direct host to host contact. The topology of the contact network, plays major role in deciding the extent of disease dynamics. An agent based computational framework has been developed for modelling disease spread by considering spatial distribution of the agents, their movement patterns and resulting contact probabilities. The agent-based model (ABM) incorporates the temporal patterns of contacts. The ABM is based on a city block model and captures movement of individuals parametrically. A new concept of system ‘characteristic time’ has been introduced in context of a time-evolving network. ‘Characteristic time’ is the minimum time required to ensure, every individual is connected to all other individuals, in the time aggregated contact network. For any given temporal system, disease time must exceed ‘characteristic time’ in order to spread throughout the population. Shorter ‘characteristic time’ of the system is suggestive of faster spread of the disease. A disease spread network is constructed which shows how the disease spreads from one infected individual to others in the city, given the contact rules and their relative susceptibilities to that viral strain. A high degree of population heterogeneity is seen to results in longer disease residence time. Susceptible individuals preferentially get infected first thereby exposing more susceptible individuals to the disease. Vaccination strategies are derived from the model, which indicates that vaccinating only 20% of the agents, who are hub nodes or highly central nodes and who also have a high degree to susceptible agents, lead to high levels of herd immunity and can confer protection to the rest of the population. Overall, the thesis has provided biologically meaningful classification of all known HLA class-1 alleles and has unravelled the physico-chemical basis for their peptide recognition specificities. The thesis also presents a new algorithm for estimating pep-tide binding affinities and consequently predicting epitopes for all alleles. Finally the thesis presents a conceptual advance in relating HLA diversity to disease susceptibilities and explains how different populations can respond differently to a given infection. A case study with the influenza H1N1 virus identified populations who are most susceptible and those who are least susceptible, in the process identifying important epitopes and responder alleles, providing important pointers for vaccine design. The influence of heterogeneity and response-typing on disease dynamics is also presented for influenza H1N1 infection, which has led to the rational identification of effective vaccination strategies. The methods and concepts developed here are fairly generic and can be adapted easily for studying other infectious diseases as well. Three new web-resources, a) HLAclassify, b) HLaffy and c) Flutope have been developed, which host pre-computed results as well as allow interactive querying to an user to perform analysis with a specific allele, peptide or a pathogenic genome sequence.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2010.

Made available in DSpace on 2014-12-17T14:16:34Z (GMT). No. of bitstreams: 1 HeglaynePVS_DISSERT.pdf: 2645894 bytes, checksum: da2c7ec39b2e87b75a199511857a4e83 (MD5) Previous issue date: 2013-03-27 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico / Of all of the genes associated with the development of Diabetes mellitus type 1 (T1D), the largest contribution comes from the genes in the Human Leukocyte Antigen (HLA) region, mostly the class II DR e DQ genes. Specific combinations of alleles DRB1, DQA1 and DQB1 constituting haplotypes, and further, a combination of more than one haplotype, providing multilocus genotypes are associated with susceptibility, protection and neutrality to DM1. Thus, the aim of present study was to verified the association of polymorphisms of HLA genes class II with susceptibility to type 1 diabetes mellitus (T1D). Ninety-two patients with T1D and 100 individuals normoglycemics (NG) aged between 6 and 20 years were studied. Genomic DNA was obtained from peripheral whole blood, collected in EDTA tube, using the extraction kit Illustra Triple Prep?, GE Healthcare. For HLA typing was used DNA LABType system by One Lambda kit applying Luminex? technology to the method of PCRSSO typing reverse. The alleles DRB1*03:01, *04:05, *04:01, *04:02, DQA1*03:01g, *05:01g, DQB1*02:01g, *03:02, the haplotypes DRB1*03:01-DQA1*05:01-DQB1*02:01, DRB1*04:05-DQA1*03:01g-DQB1*03:02, DRB1*04:02-DQA1*03:01g-DQB1*03:02, DRB1*04:01-DQA1*03:01g-DQB1*03:02 and DR3-DQ2/DR4-DQ8 genotype were significantly associated with the chance of developing T1D. The alleles DRB1*11:01, *15:03, *15:01, *13:01, DQA1*01:02, *04:01g, *01:03, DQB1*06:02, *03:01g, *06:03, *04:02, the haplotypes DRB1*11:01-DQA1*05:01-DQB1*03:01, DRB1*13:01-DQA1*01:03-DQB1*06:03 and DRX-DQX/DRX-DQX genotype, formed by other than the DR3-DQ2 or DR4-DQ8 haplotypes, were significantly associated with T1D protection Despite the major racial Brazilian, even at the regional level, these results are similar to the majority of alleles, genotypes and haplotypes of HLA class II-related susceptibility or resistance to T1D, extensively described in the literature for Caucasian population. Children with age at diagnosis less than 5 years of age had significantly higher frequency of the heterozygous genotype DR3-DQ2/DR4-DQ8 compared to children with age at diagnosis than 5 years old. These results also demonstrate strong association of the genetic profile of the class II HLA for this age group, possibly associated with the severity and rapid progression to the onset of T1D. The knowledge of HLA class II genes may be useful in genetic screens that allow the prediction of T1D / De todos os genes j? relacionados com o desenvolvimento do Diabetes mellitus tipo 1 (DM1), a maior contribui??o vem da regi?o do genoma onde est?o localizados os genes do Ant?geno Leucocit?rio Humano (HLA), sobretudo os genes da classe II do HLA: DR e DQ. Espec?ficas combina??es de alelos DRB1, DQA1 e DQB1 formando hapl?tipos, e ainda, a combina??o de mais de um hapl?tipo, formando gen?tipos multilocus s?o associados com a susceptibilidade, neutralidade e prote??o ao DM1. Dessa forma, o objetivo do estudo foi verificar a associa??o dos polimorfismos dos genes do complexo HLA classe II com a susceptibilidade ao DM1, em pacientes do Rio Grande do Norte. Foram estudados 92 indiv?duos com DM1 e 100 indiv?duos normoglic?micos (NG), com idade entre 6 e 20 anos. O DNA gen?mico foi obtido a partir do sangue total perif?rico, coletado em tubo com EDTA, utilizando o kit de extra??o Illustra Triple Prep?, GE Healthcare. Para a tipagem do HLA foi utilizado o sistema DNA LABType atrav?s de kits One Lambda, que aplica a tecnologia Luminex? ao m?todo de tipagem por PCR-SSO reverso. Os alelos DRB1*03:01, *04:05, *04:01, *04:02; DQA1*03:01g, 05:01g; DQB1*02:01g, *03:02; os hapl?tipos DRB1*03:01-DQA1*05:01-DQB1*02:01, DRB1*04:05-DQA1*03:01g- DQB1*03:02, DRB1*04:02-DQA1*03:01g-DQB1*03:02, DRB1*04:01-DQA1*03:01g- DQB1*03:02 e o gen?tipo heterozigoto, DR3-DQ2/DR4-DQ8 foram significativamente associados com a chance de desenvolvimento do DM1. J? os alelos DRB1*11:01, *15:03, *15:01, *13:01; DQA1*01:02, *04:01g, *01:03; DQB1*06:02, *03:01g, *06:03, *04:02; os hapl?tipos DRB1*11:01-DQA1*05:01-DQB1*03:01, DRB1*13:01-DQA1*01:03-DQB1*06:03 e o gen?tipo DRX-DQX/DRX-DQX, formado por outros hapl?tipos que n?o DR3-DQ2 ou DR4-DQ8, foram significativamente associados a prote??o ao DM1. Apesar da grande miscigena??o racial brasileira, at? em n?vel regional, estes resultados s?o semelhantes a maioria dos alelos, hapl?tipos e gen?tipos de HLA classe II relacionados ? susceptibilidade ou prote??o ao DM1, extensivamente descritos na literatura para a popula??o caucasiana. Crian?as com idade ao diagn?stico inferior a 5 anos de idade apresentaram significativamente maior frequ?ncia do gen?tipo heterozigoto DR3-DQ2/DR4-DQ8, quando comparada ?s crian?as com idade ao diagn?stico superior a 5 anos de idade. Esses resultados demonstram tamb?m forte envolvimento do perfil gen?tico da classe II do HLA para esta faixa et?ria, que estaria relacionada possivelmente com a gravidade e a r?pida progress?o para o in?cio do DM1. O conhecimento dos genes HLA de classe II pode ser ?til em triagens gen?ticas que possibilitem a predi??o do DM1

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