L’immunologie anti-tumorale et l’immunothérapie ont connu dernièrement de grandes avancées avec la mise en évidence du processus d’immuno-surveillance et le développement de plusieurs approches vaccinales. Il n’en demeure pas moins que l’induction d’une réponse immunitaire anti-tumorale se traduit peu par l’éradication de la tumeur. Comme phénomène dynamique et interactif, la réponse cytotoxique anti-tumorale implique les effecteurs cytotoxiques et les cibles tumorales; pourtant, le microenvironnement tumoral et sa plasticité influent largement sur l’efficacité de celle-là. Avec l’appui de récentes données expérimentales, il apparaît crucial de prendre en compte la susceptibilité tumorale à la lyse par les effecteurs cytotoxiques anti-tumoraux, notamment les lymphocytes T cytotoxiques (CTLs), et plus particulièrement dans un contexte de plasticité cellulaire. Ainsi, le principal objectif de mes travaux de thèse est de saisir le rôle de la Transition Épithélio-Mésenchymateuse (EMT) dans la susceptibilité des cellules tumorales à la lyse par les CTLs dans des modèles cellulaires de cancer du sein. Nos résultats montrent que l’EMT est capable d’induire une diminution de la susceptibilité des cellules mésenchymateuses à la lyse spécifique. Elle engage de ce fait de multiples acteurs. Tout d’abord, dans les deux modèles d’étude, il s’avère que l’EMT est capable de réguler négativement l’expression de la molécule HLA-A2. Ensuite, dans le premier modèle expérimental, nous avons établi que l’EMT induit une altération de la signalisation au niveau de la synapse immunologique. De plus, le régulateur de l’autophagie, Becline 1, joue un rôle crucial dans l’induction de la diminution de la sensibilité à la lyse par les lymphocytes T-CD8+ suite à l’induction de l’EMT. Dans le deuxième modèle d’étude, le mécanisme mis en jeu par l’EMT pour réguler la susceptibilité des cellules mésenchymateuses à la lyse par les CTLs se manifeste dans l’induction du facteur de transcription inducteur des propriétés de cellules souches cancéreuses, le KLF4 ainsi que via la régulation négative de l’expression du miR-7. Ensemble, ces résultats élucident de nouveaux mécanismes d’échappement des cellules tumorales malignes à la lyse par les lymphocytes T-CD8+ suite à l’induction de l’EMT. Cette étude soutient ainsi l’importance du ciblage des facteurs de transcription inducteurs de l’EMT et responsables de la plasticité cellulaire afin de neutraliser leur fonction. Cela pourrait aider à construire une nouvelle stratégie pour mieux contrôler l’échappement des cellules tumorales invasives à la lyse spécifique et in fine pour garantir une immunothérapie plus efficace contre le cancer. / The anti-tumor immunology and immunotherapy have recently undergone major breakthroughs, with the identification of immune surveillance process and the development of several vaccine approaches. However, the fact remains that the induction of an antitumor immune response is still not effective enough. Certainly, the antitumor cytotoxic response is a dynamic and interactive phenomenon, involving cytotoxic effectors and tumor targets, but its effectiveness is considerably influenced by the tumor microenvironment and its plasticity. Recent studies support the importance of taking into account the tumor susceptibility to lysis by anti-tumor cytotoxic effectors, notably Cytotoxic T Lymphocytes (CTLs), especially in a context of cellular plasticity. On the grounds of these studies, this research aims at understanding the role of Epithelial to Mesenchymal Transition (EMT) in the susceptibility of tumor cells to CTLs mediated lysis in different models of breast cell carcinoma. Our results reveal that EMT is able to induce a decrease in the susceptibility of mesenchymal cells to specific lysis. It calls therefore multiple actors. First, in both study models, it turns out that the EMT is able to downregulate the expression of HLA-A2 molecule. Then, in the first experimental model, we show that EMT induces an alteration of signalling at the immunological synapse. Moreover, the regulator of autophagy, Beclin 1, plays a crucial role in the induction of reduced susceptibility to lysis by T-CD8+ lymphocytes following induction of EMT. In the second experimental model, we show that the mechanisms used by EMT to regulate the susceptibility of mesenchymal cells to lysis by CTLs involve the induction of the transcription factor inducing cancer stem cells properties, KLF4, as well as the downregulation of miR-7 expression. Together, these results shed light on new mechanisms used by malignant tumor cells to escape to lysis by T-CD8+ lymphocytes following the induction of EMT. Thus, this study advocates the importance of targeting transcription factors, which are inducers of EMT and responsible for cellular plasticity, in order to neutralize their function. These insights may prove useful for the development of new strategies aimed at better controlling the escape of invasive tumor cells to specific lysis, and ultimately ensuring a more effective immunotherapy against cancer.

Les lymphocytes T cytotoxiques (CTLs) présents au niveau des tumeurs reconnaissent des antigènes présentés par les cellules cancéreuses, mais ne parviennent pas à induire le rejet de ces tumeurs chez les patients cancéreux. Cette observation a amené les immunologistes à étudier les différents mécanismes d'immunosuppression induits par les tumeurs qui permettent aux cellules cancéreuses d'échapper à la reconnaissance et à la destruction immunitaires. L'un des mécanismes contribuant à la résistance des tumeurs aux réponses immunitaires est le recrutement de lymphocytes T CD4+ régulateurs (Tregs). Les Tregs s'accumulent au niveau des sites tumoraux et jouent un rôle important dans la suppression des réponses immunitaires dirigées contre les cellules tumorales. Dans ce travail de thèse, nous rapportons que des épitopes tumoraux dérivés des protéines NY-ESO-1 et TRAG-3 stimulent à la fois des lymphocytes T CD4+ auxiliaires (Th) et des Tregs chez des patients porteurs de mélanome. Grâce à une analyse clonotypique, nous démontrons que, contrairement aux cellules CD4+ Th, les TCR des Tregs dirigés contre NY-ESO-1 et TRAG-3 sont retrouvés à la fois dans le répertoire des Tregs naturels (CD4+CD25high) et dans celui des cellules T CD4+ classiques/Th (CD4+CD25-), au niveau des PBMCs des patients. Cette observation suggère que le recrutement des Tregs spécifiques d'antigènes tumoraux se fait en partie par la conversion des cellules T CD4+ classiques suite à leur stimulation chronique par des antigènes de tumeurs. / Cytotoxic T lymphocytes (CTLs) present in tumors recognize tumor antigens presented by cancer cells but fail to induce tumor rejection in patients. This observation has led immunologists to study the different mechanisms of tumor-induced immunosuppression that allow cancer cells to escape from recognition and destruction by the immune system. One of the mechanisms contributing to tumor resistance to immune responses is the recruitment of CD4+ regulatory T cells (Tregs). Tregs accumulate at tumor sites and play an important role in suppressing immune responses against tumor cells. In this thesis, we report that tumor epitopes derived from the proteins NY-ESO-1 and TRAG-3 stimulate both CD4+ T helper cells (Th) and Tregs in patients with metastatic melanoma. Through clonotypic analysis, we show that, within PBMCs of melanoma patients, tumor antigen-specific Tregs, but not Th cells, share a common TCR usage with naturally-occuring Tregs (CD4+CD25high) and Th cells (CD4+CD25-), suggesting that their recruitment occurs through the peripheral conversion of CD4+CD25- T cells upon chronic antigen exposure. The second part of this thesis consists of the study of inhibitory receptors expressed by CTLs directed against tumor antigens which, upon engagement by their ligands presented on the surface of tumor cells, activate negative regulatory pathways. Here, we report that tumor-induced CTLs directed against a peptide derived from NY-ESO-1 in melanoma patients upregulate the expression of the inhibitory receptors PD-1, Tim-3 and BTLA. Additionaly, the co-expression of PD-1 with Tim-3 and/or BTLA defines populations of dysfunctional tumor antigen-specific CTLs.

Das Neuroblastom ist der am weitesten verbreitete solide, extrakranielle Tumor im Kindesalter. Trotz intensiver Forschung sind die Überlebensraten von Patienten mit fortgeschrittenem Tumorwachstum nach wie vor schlecht. Die Idee, eine zelluläre, langanhaltende Immunantwort im Körper zu induzieren, vermittelt durch zytotoxische CD8+T-Zellen, die sich gegen den Tumor richten, scheint dabei besonders attraktiv. Als tumorassoziiertes Antigen (TAA) wurde zu diesem Zweck für diese Arbeit die murine Tyrosinhydroxylase (mTH), das Schrittmacherenzym der Katecholaminbiosynthese, gewählt, da sie in der Mehrzahl der Neuroblastome stark überexprimiert ist. Für die Impfexperimente wurden sog. DNA-Minigen-Vakzine, die für Peptide aus der mTH-Sequenz kodieren, konstruiert. Die Auswahl Minigen-Peptide erfolgte mit dem MHC-Klasse-I-Liganden-Vorhersageprogramm syfpeithi, welches drei vorhergesagte starke H2-Kk-Liganden lieferte (mTH3k). Außerdem wurden zwei weitere Vakzine hergestellt: als Negativkontrolle das Vakzin mTHlowest, dessen mTH-Peptide laut syfpeithi schlechte MHC-Klasse-I-Liganden darstellen und das Vakzin Ersatzepis, dessen Peptide auf der Oberfläche von murinen NXS2-Neuroblastomzellen aus MHC-Klasse-I-Komplexen isoliert werden konnten. Sowohl in prophylaktischen als auch therapeutischen Impfversuchen in Mäusen konnte das Tumorwachstum und die spontane Metastasierung in sekundäre Organe wie die Leber signifikant verhindert werden. Außerdem konnte gezeigt werden, daß der Antitumoreffekt auf der Induktion mTH-spezifischer, zytotoxischer CD8+T Zellen (CTLs) beruht. Zusätzlich und insbesondere interessant für eine eventuelle klinische Anwendung eines auf der TH basierenden DNA-Vakzins verursachte das mTH-Minigen-Vakzin zumindest in Mäusen keine Aktivierung selbst-reaktiver CD8+T-Zellen. Alles in allem lassen die in dieser Arbeit erhaltenen Ergebnisse den Schluß zu, daß sich die Tyrosinhydroxylase als TAA in Form eines DNA-Vakzins zur adjuvanten Therapie des Neuroblastoms eignet. / Therapeutic vaccination against tumor antigens without induction of autoimmunity remains a major challenge in cancer immunotherapy. Here, we demonstrate for the first time effective therapeutic vaccination followed by eradication of established spontaneous neuroblastoma metastases using a tyrosine hydroxylase (TH) DNA minigene vaccine. We identified three novel mouse TH (mTH3) derived peptides with high predicted binding affinity to MHC class I H2-Kk according to prediction program syfpeithi and computer modeling of epitopes into MHC class I binding groove. Subsequently, a DNA minigene vaccine based on pCMV-F3Ub encoding for mutated ubiquitin (G76 to A76) and mTH3 was generated. Prophylactic and therapeutic efficacy of this vaccine was established following oral delivery using attenuated Salmonella typhimurium SL7207. Only mice immunized with mTH3 were free of spontaneous liver metastases. This effect was clearly dependant on ubiquitin and high affinity of the mTH epitopes to MHC class I. Specifically, we demonstrated a crucial role for minigene expression as a stable ubiquitin-Ala76 fusion peptide for vaccine efficacy. Interestingly, the unstable wild type ubiquitin-Gly76 vaccine was completely ineffective. The immune response following mTH3 DNA minigene vaccination was mediated by CD8+ T-cells as indicated by infiltration of primary tumors and TH specific cytolytic activity in vitro. Importantly, no infiltration was detectable in TH expressing adrenal medulla, indicating the absence of auto immunity. In summary, we demonstrate effective therapeutic vaccination against neuroblastoma with a novel rationally designed tyrosine hydroxylase minigene vaccine without induction of autoimmunity providing an important base line for clinical application of this strategy.

Human immunodeficiency virus type 1 (HIV-1) is the cause of acquired immune deficiency syndrome (AIDS). HIV-1 is a worldwide epidemic that currently affects over 35 million people worldwide, and continues to spread at an appalling rate. A universal HIV-1 preventive vaccine is considered to be the optimal solution in achieving the ultimate goal of AIDS eradication. Regretfully, most endeavors thus far of developing a prophylactic vaccine have been largely disappointing. Highly Active Anti-Retroviral Therapy (HAART) has been shown to reduce the plasma HIV-1 RNA level to below the detection limit of clinical assays (50 copies/ml); it combines three or more antiretroviral drugs which belong to at least two different classes – targeting distinct steps in the viral life cycle, and inhibiting viral replication. However, unless the infection is eradicated, strict adherence to a lifelong treatment regimen is required. HAART is limited by its high cost, drug availability, complicated administration schedules, serious side effects, and the potential that the virus will ultimately develop drug resistance. A more plausible approach lies in therapeutic vaccines that provide immunity to partially control viral replication postinfection – delaying or minimizing ART, and offering “drug holidays”. The primary goal of a therapeutic vaccine is to effectively induce HIV-1 specific cytotoxic T lymphocyte (CTL) responses, which plays a critical role in control of viral proliferation. Dendritic cells (DCs)-based therapeutic vaccines have been showing the most promising results. However, the therapeutic efficacy of DCs based vaccines is limited. This is partially due to the fact that DCs induced CD8+ T cell responses are largely CD4+ T cell dependent, while HIV-1 infection usually renders the immune system very “helpless” from CD4+ T cells. In addition, infection, impaired function, and physical depletion of DCs are often reported during the early stage. Furthermore, DCs are often found to be inflammatory and immunosuppressive, which is mainly mediated by the interaction between HIV-1 Env gp120 and DC receptors. Thus, the search for a novel therapeutic vaccine strategy is warranted. Using T-APC (T cells-antigen-presenting cells) as a novel T cell-based vaccine has emerged as a potential candidate for a HIV-1 therapeutic vaccine, which aims at boosting HIV-specific CTL responses. Our previous work demonstrated that CD4+ and CD8+ T cells derived from ovalbumin (OVA)-specific T cell receptor (TCR) transgenic OT II and OT I mice via co-culture with OVA-pulsed DCs (DCOVA) can be activated, acquiring pMHC I, pMHC II, and costimulatory molecules, thus act as CD4+ T helper-antigen-presenting cells (Th-APCs) and CD8+ cytotoxic T-antigen-presenting cells (Tc-APCs). We also elucidated that DC-derived exosomes (EXO), which are 50- to 90-nm diameter vesicles containing antigen-presenting, tetraspan, adhesion, and costimulatory molecules, can transfer the antigen-presenting activity of DCs to activated CD4+T cells through EXO uptake. EXOOVA-targeted activated CD4+T (aTexo) cells can (1) stimulate more efficient central memory CD8+ CTL responses and T cell memory than EXOOVA or DCOVA, (2) activate CD8+ CTL responses independent of CD4+Th cells, and (3) counteract CD4+25+regulatory T (Tr) cell-mediated immune suppression. These results formed the new concept of novel EXO-targeted CD4+ T cell vaccines. In this study, we tailored EXO-targeted T cells vaccine by using polyclonal activated CD8+ T cells instead of CD4+ T cells, as CD4+ T cells served as the primary target for HIV-1 infection. We showed that (1) OVA-specific exosome-targeted CD8+ T cell-based vaccine (OVA-Texo) can stimulate efficient OVA-specific CD8+ CTL and memory responses, inducing sufficient antitumor immunity against OVA-expressing tumor cells in mouse models. (2) This exosome-targeted CD8+ T cell-based vaccine strategy could be applied to HIV-1-Gag protein, provoking effective Gag-specific CD8+ CTL, T cell memory, and antitumor immunity against Gag-expressing tumor cells. (3) Engineering Gag-Texo with up-regulated 4-1BBL (APC derived costimulatory molecule) expression could improve the performance of Gag-Texo vaccine. (4) OVA-Texo is able to evoke a successful immune response in bystander chronic infection, converting CD8+ T cell exhaustion, restoring effector functions of exhausted CD8+ T cells. Moreover, combination of OVA-Texo vaccine with PD-L1 blockage in a dual treatment could result in a synergistic effect in rescuing CTLs exhaustion in chronic infection. Those desired features make EXO-targeted CD8+ T cells vaccine an appealing novel strategy in HIV-1 infection. The EXO-targeted CD8+ T cells vaccine may be applicable to therapeutic HIV treatment through the use of autologous T cells with uptake of EXOs derived from engineered DCs.

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.

Tumor-induced immunosuppression can occur by multiple mechanisms, each posing a significant obstacle to immunotherapy. Evidence presented in this dissertation suggests that aberrant cytokine signaling, as a result of altered metabolism of Chronic Lymphocytic Leukemia (CLL) cells, confers a selective advantage for tumor survival and growth. Cells from CLL patients with aggressive disease (as indicated by high-risk cytogenetics) were found to exhibit prolongation in Interferon (IFN)-induced STAT3 phosphorylation, and increased levels of reactive oxygen species (ROS) in these cells reflected these signaling processes. Changes in the relative balance of phospho-STAT3 and phospho-STAT1 levels, in response to combinations of IL-2 + Toll-like receptor (TLR)-7 agonist + phorbol esters, as well as IFN, were associated with the immunosuppressive and immunogenic states of CLL cells. In addition, immunosuppressive leukemic cells were found to express high levels of proteins with O-linked N-acetylglucosamine (O-GlcNAc) modifications, due to increased metabolic activity through the Hexosamine Biosynthetic Pathway (HBP), which caused impaired intracellular signaling responses and affected disease progression. A conclusion of the studies presented here is that the intrinsic immunosuppressive properties of leukemic cells may be overcome by agents such as Resveratrol that target metabolic pathways of these cells.

Tumor-induced immunosuppression can occur by multiple mechanisms, each posing a significant obstacle to immunotherapy. Evidence presented in this dissertation suggests that aberrant cytokine signaling, as a result of altered metabolism of Chronic Lymphocytic Leukemia (CLL) cells, confers a selective advantage for tumor survival and growth. Cells from CLL patients with aggressive disease (as indicated by high-risk cytogenetics) were found to exhibit prolongation in Interferon (IFN)-induced STAT3 phosphorylation, and increased levels of reactive oxygen species (ROS) in these cells reflected these signaling processes. Changes in the relative balance of phospho-STAT3 and phospho-STAT1 levels, in response to combinations of IL-2 + Toll-like receptor (TLR)-7 agonist + phorbol esters, as well as IFN, were associated with the immunosuppressive and immunogenic states of CLL cells. In addition, immunosuppressive leukemic cells were found to express high levels of proteins with O-linked N-acetylglucosamine (O-GlcNAc) modifications, due to increased metabolic activity through the Hexosamine Biosynthetic Pathway (HBP), which caused impaired intracellular signaling responses and affected disease progression. A conclusion of the studies presented here is that the intrinsic immunosuppressive properties of leukemic cells may be overcome by agents such as Resveratrol that target metabolic pathways of these cells.