Integrating Innate and Adaptive Immunity for Intrusion Detection

Network Intrusion Detection Systems (NIDS) monitor a net- work with the aim of discerning malicious from benign activity on that network. While a wide range of approaches have met varying levels of success, most IDS’s rely on having access to a database of known attack signatures which are written by security experts. Nowadays, in order to solve problems with false positive alerts, correlation algorithms are used to add additional structure to sequences of IDS alerts. However, such techniques are of no help in discovering novel attacks or variations of known attacks, something the human immune system (HIS) is capable of doing in its own specialised domain. This paper presents a novel immune algorithm for application to an intrusion detection problem. The goal is to discover packets containing novel variations of attacks covered by an existing signature base.

Sialyl Tn-Expressing Bladder Cancer Cells Induce a Tolerogenic Phenotype in Innate and Adaptive Immune Cells

Despite the wide acceptance that glycans are centrally implicated in immunity, exactly how they contribute to the tilt immune response remains poorly defined. In this study, we sought to evaluate the impact of the malignant phenotype-associated glycan, sialyl-Tn (STn) in the function of the key orchestrators of the immune response, the dendritic cells (DCs). In high grade bladder cancer tissue, the STn antigen is significantly overexpressed and correlated with the increased expression of ST6GALNAC1 sialyltransferase. Bladder cancer tissue presenting elevated expression of ST6GALNAC1 showed a correlation with increased expression of CD1a, a marker for bladder immature DCs and showed concomitant low levels of Th1-inducing cytokines IL-12 and TNF-α. In vitro, human DCs co-incubated with STn+ bladder cancer cells, had an immature phenotype (MHC-IIlow, CD80low and CD86low) and were unresponsive to further maturation stimuli. When contacting with STn+ cancer cells, DCs expressed significantly less IL-12 and TNF-α. Consistent with a tolerogenic DC profile, T cells that were primed by DCs pulsed with antigens derived from STn+ cancer cells were not activated and showed a FoxP3high IFN-γlow phenotype. Blockade of STn antigens and of STn+ glycoprotein, CD44 and MUC1, in STn+ cancer cells was able to lower the induction of tolerance and DCs become more mature. Overall, our data suggest that STn-expressing cancer cells impair DC maturation and endow DCs with a tolerogenic function, limiting their capacity to trigger protective anti-tumour T cell responses. STn antigens and, in particular, STn+ glycoproteins are potential targets for circumventing tumour-induced tolerogenic mechanisms.

MyD88 Signaling Is Required for Efficient Innate and Adaptive Immune Responses to Paracoccidioides brasiliensis Infection

The mechanisms that govern the initial interaction between Paracoccidioides brasiliensis, a primary dimorphic fungal pathogen, and cells of the innate immunity need to be clarified. Our previous studies showed that Toll-like receptor 2 (TLR2) and TLR4 regulate the initial interaction of fungal cells with macrophages and the pattern of adaptive immunity that further develops. The aim of the present investigation was to assess the role of MyD88, an adaptor molecule used by TLRs to activate genes of the inflammatory response in pulmonary paracoccidioidomycosis. Studies were performed with normal and MyD88(-/-) C57BL/6 mice intratracheally infected with P. brasiliensis yeast cells. MyD88(-/-) macrophages displayed impaired interaction with fungal yeast cells and produced low levels of IL-12, MCP-1, and nitric oxide, thus allowing increased fungal growth. Compared with wild-type (WT) mice, MyD88(-/-) mice developed a more severe infection of the lungs and had marked dissemination of fungal cells to the liver and spleen. MyD88(-/-) mice presented low levels of Th1, Th2, and Th17 cytokines, suppressed lymphoproliferation, and impaired influx of inflammatory cells to the lungs, and this group of cells comprised lower numbers of neutrophils, activated macrophages, and T cells. Nonorganized, coalescent granulomas, which contained high numbers of fungal cells, characterized the severe lesions of MyD88(-/-) mice; the lesions replaced extensive areas of several organs. Therefore, MyD88(-/-) mice were unable to control fungal growth and showed a significantly decreased survival time. In conclusion, our findings demonstrate that MyD88 signaling is important in the activation of fungicidal mechanisms and the induction of protective innate and adaptive immune responses against P. brasiliensis.

Modulation of cell proliferation, survival and gene expression by RAGE and TLR signaling in cells of the innate and adaptive immune response: role of p38 MAPK and NF-KB

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Improved Innate and Adaptive Immunostimulation by Genetically Modified HIV-1 Protein Expressing NYVAC Vectors.

Attenuated poxviruses are safe and capable of expressing foreign antigens. Poxviruses are applied in veterinary vaccination and explored as candidate vaccines for humans. However, poxviruses express multiple genes encoding proteins that interfere with components of the innate and adaptive immune response. This manuscript describes two strategies aimed to improve the immunogenicity of the highly attenuated, host-range restricted poxvirus NYVAC: deletion of the viral gene encoding type-I interferon-binding protein and development of attenuated replication-competent NYVAC. We evaluated these newly generated NYVAC mutants, encoding HIV-1 env, gag, pol and nef, for their ability to stimulate HIV-specific CD8 T-cell responses in vitro from blood mononuclear cells of HIV-infected subjects. The new vectors were evaluated and compared to the parental NYVAC vector in dendritic cells (DCs), RNA expression arrays, HIV gag expression and cross-presentation assays in vitro. Deletion of type-I interferon-binding protein enhanced expression of interferon and interferon-induced genes in DCs, and increased maturation of infected DCs. Restoration of replication competence induced activation of pathways involving antigen processing and presentation. Also, replication-competent NYVAC showed increased Gag expression in infected cells, permitting enhanced cross-presentation to HIV-specific CD8 T cells and proliferation of HIV-specific memory CD8 T-cells in vitro. The recombinant NYVAC combining both modifications induced interferon-induced genes and genes involved in antigen processing and presentation, as well as increased Gag expression. This combined replication-competent NYVAC is a promising candidate for the next generation of HIV vaccines.

Monitoring of innate and adaptive immune responses in the context of human immunotherapy

Summary1 SummaryCancer patients have a better clinical outcome when their tumours display marked infiltration by memory Τ cells. Moreover, the overrepresentation of Th1 gene signatures in primary tumours correlates with favourable prognosis. Thus, vaccination to induce Τ cells capable of infiltrating and eradicating the tumour seems a promising strategy for the treatment of cancer. Here, I monitored CD4 Τ cell responses in melanoma patients vaccinated with the long synthetic peptides Melan- A16-35(A27L) and NY-ESO-179.108. Most of the patients developed strong and diverse peptide antigen specific CD4 Τ cell responses. Analysis of the fine specificity of CD4 Τ cell antigen recognition led to the identification of two new epitopes. The peptide Melan-A16_35(A27L) was delivered by virus-like particles (VLPs) derived from bacteriophage Οβ, which themselves displayed strong immunogenicity. I show evidence for induction of Οβ- and Melan-A specific CD4 Τ cell responses that developed a Th1 functional profile after repeated vaccination cycles. They also specifically released the chemokines CCL-3 and CCL-4, which play important roles in attracting CD8 Τ cells to the APC surface for priming and formation of Τ cell memory. We further found induction of robust humoral IgG responses upon VLP vaccination, and the lgG1-lgG4 isotype composition depended on the adjuvant used. Since heavy chain class switching largely dépends on the presence of CD4 Τ cell help, this result suggests that the adjuvant can influence the differentiation of elicited CD4 Τ cells, thereby contributing to the quality and function of both Β cells and CD8 Τ cells. The nature of the inflammatory processes in the tumour microenvironment can modulate CD8 Τ cell function. A collaboration was established for the investigation regulation of inflammasome activation in human primary monocytes. We identified IL- 4 and TGF-β as strong inhibitors of IL-1 β secretion, Indicating some level of regulation from effector Th2 and Treg responses. We further found a potent inhibition of inflammasome activation by type I interferon, and demonstrated in vivo inhibition of IL-1 β responses in monocytes from active multiple sclerosis patients under IFN-β therapy. This finding further offers a possible explanation for its success, which mechanism of action is still largely unclear. Interestingly, type I interferon is also being used as adjuvant treatment for tumour free metastatic cutaneous melanoma patients. While its clinical benefit has remained controversial, recent data suggest that the subset of patients with ulcerated primary melanoma lesions can benefit from this therapy. Future investigations will shed light on the implication of the inflammasome in this context, and may offer new strategies for improved adjuvant treatments of melanoma.2 RésuméLes patients atteints de cancer ont une meilleure chance de survie si leurs tumeurs s'avèrent être largement infiltrées par des cellules Τ mémoires. De plus, la surreprésentation d'une signature génique Th1 est en corrélation avec un pronostic favorable. Ainsi, la vaccination visant à induire des cellules Τ capables d'infiltrer et de détruire la tumeur parait être une stratégie prometteuse pour le traitement du cancer. Dans ce travail, j'ai procédé au monitoring de la réponse des cellules Τ CD4 dans des patients atteints de mélanome vaccinés avec les longs peptides synthétiques Melan-A16_35(A27L) et NY-ESO-179_108. Ces peptides représentent des antigènes tumoraux reconnus par des lymphocytes T. La majorité des patients a développé une réponse forte et diversifiée des cellules Τ CD4 spécifiques contre les peptides. L'analyse de la spécificité fine de la reconnaissance antigénique des cellules Τ CD4 nous a conduits à l'identification de deux nouveaux épitopes. Le peptide Melan-Aie. 35(A27L) a été délivré par des particules de type viral (VLPs) dérivés de bactériophages Qβ, qui ont eux-mêmes démontré une forte immunogénicité. Mon travail montre les preuves d'une induction de réponses spécifiques des cellules Τ CD4 contre les Qβ et Melan-A développant un profil fonctionnel Th1 après plusieurs cycles de vaccination. Elles secrètent aussi spécifiquement les chimiokines CCL-3 et CCL-4, qui jouent un rôle important dans l'attraction des cellules Τ CD8 à la surface des cellules présentatrices d'antigènes et contribuent ainsi à induire et former la mémoire cellulaire Τ CD8. Nous avons également remarqué une induction de fortes réponses humorales IgG après vaccination avec les VLPs, et que la composition des isotypes lgG1-lgG4 dépendait de l'adjuvant utilisé. Etant donné qu'une commutation de classe de la chaîne lourde dépend largement ùie l'aide des cellules Τ CD4, ce résultat suggère que l'adjuvant puisse influencer la différeritiation de cellules Τ CD4 en différent types, contribuant ainsi à la qualité et à la fonction des cellules Β et des cellules Τ CD8.La nature des processus d'inflammation dans le microenvironnement tumoral peut moduler la fonction des cellules Τ CD8. Une collaboration a été établie pour investiguer la régulation de l'activation de l'inflammasome dans des monocytes primaires humains. Nous avons identifié l'IL-4 et le TGF-β comme étant de puissants inhibiteurs de la sécrétion de IL-Ιβ, indiquant une certaine régulation de la réponse inflammatoire induite par les cellules Th2 et Τ régulatrices. Nous avons également trouvé une forte inhibition de l'activation de l'inflammasome par l'interféron type I, et nous avons démontré une inhibition in vivo de la réponse IL-1 β dans des monocytes de patients atteints d'une sclérose en plaque active sous traitement IFN-β. Ce résultat nous offre une possible explication du succès de cette thérapie, dont le mécanisme reste à ce jour encore largement obscur. Il est intéressant de noter que l'interféron de type I est également utilisé pour le traitement de patients atteints de mélanome cutané métastasique sans tumeurs. Bien que le bénéfice clinique de ce traitement reste controversé, des études récentes montrent qu'une partie des patients atteints de mélanome primaire ulcéré peut tirer bénéfice de cette thérapie. De futures investigations pourront mieux nous renseigner sur l'implication de l'inflammasome dans ce contexte et offrir de nouvelles stratégies pour améliorer les traitements adjuvants du mélanome.

Innate and adaptive effects of inflammasomes on T cell responses.

Inflammasomes are protein complexes that form in response to pathogen-derived or host-derived stress signals. Their activation leads to the production of inflammatory cytokines and promotes a pyrogenic cell death process. The massive release of inflammatory mediators that follows inflammasome activation is a key event in alarming innate immune cells. Growing evidence also highlights the role of inflammasome-dependent cytokines in shaping the adaptive immune response, as exemplified by the capacity of IL-1β to support Th17 responses, or by the finding that IL-18 evokes antigen-independent IFN-γ secretion by memory CD8(+) T cells. A deeper understanding of these mechanisms and on how to manipulate this powerful inflammatory system therefore represents an important step forward in the development of improved vaccine strategies.

5-Lipoxygenase Deficiency Impairs Innate and Adaptive Immune Responses during Fungal Infection

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

5-Lipoxygenase Deficiency Impairs Innate and Adaptive Immune Responses during Fungal Infection

5-lipoxygenase-derived products have been implicated in both the inhibition and promotion of chronic infection. Here, we sought to investigate the roles of endogenous 5-lipoxygenase products and exogenous leukotrienes during Histoplasma capsulatum infection in vivo and in vitro. 5-LO deficiency led to increased lung CFU, decreased nitric oxide production and a deficient primary immune response during active fungal infection. Moreover, H. capsulatum-infected 5-LO-/- mice showed an intense influx of neutrophils and an impaired ability to generate and recruit effector T cells to the lung. The fungal susceptibility of 5-LO-/- mice correlated with a lower rate of macrophage ingestion of IgG-H. capsulatum relative to WT macrophages. Conversely, exogenous LTB4 and LTC4 restored macrophage phagocytosis in 5-LO deficient mice. Our results demonstrate that leukotrienes are required to control chronic fungal infection by amplifying both the innate and adaptive immune response during histoplasmosis.

SAG2A protein from Toxoplasma gondii interacts with both innate and adaptive immune compartments of infected hosts

Abstract Background Toxoplasma gondii is an intracellular parasite that causes relevant clinical disease in humans and animals. Several studies have been performed in order to understand the interactions between proteins of the parasite and host cells. SAG2A is a 22 kDa protein that is mainly found in the surface of tachyzoites. In the present work, our aim was to correlate the predicted three-dimensional structure of this protein with the immune system of infected hosts. Methods To accomplish our goals, we performed in silico analysis of the amino acid sequence of SAG2A, correlating the predictions with in vitro stimulation of antigen presenting cells and serological assays. Results Structure modeling predicts that SAG2A protein possesses an unfolded C-terminal end, which varies its conformation within distinct strain types of T. gondii. This structure within the protein shelters a known B-cell immunodominant epitope, which presents low identity with its closest phyllogenetically related protein, an orthologue predicted in Neospora caninum. In agreement with the in silico observations, sera of known T. gondii infected mice and goats recognized recombinant SAG2A, whereas no serological cross-reactivity was observed with samples from N. caninum animals. Additionally, the C-terminal end of the protein was able to down-modulate pro-inflammatory responses of activated macrophages and dendritic cells. Conclusions Altogether, we demonstrate herein that recombinant SAG2A protein from T. gondii is immunologically relevant in the host-parasite interface and may be targeted in therapeutic and diagnostic procedures designed against the infection.

Tumour susceptibility to innate and adaptive immunotherapy changes during tumour maturation

Immunotherapy of tumours using T cells expanded in vitro has met with mixed clinical success suggesting that a greater understanding of tumour/T-cell interaction is required. We used a HPV16E7 oncoprotein-based mouse tumour model to study this further. In this study, we demonstrate that a HPV16E7 tumour passes through at least three stages of immune susceptibility over time. At the earliest time point, infusion of intravenous immune cells fails to control tumour growth although the same cells given subcutaneously at the tumour site are effective. In a second stage, the tumour becomes resistant to subcutaneous infusion of cells but is now susceptible to both adjuvant activated and HPV16E7-specific immune cells transferred intravenously. In the last phase, the tumour is susceptible to intravenous transfer of HPV16E7-specific cells, but not adjuvant-activated immune cells. The requirement for IFN-gamma and perforin also changes with each stage of tumour development. Our data suggest that effective adoptive T-cell therapy of tumour will need to be matched with the stage of tumour development.