The innate immune system is a multicomponent response governed by intricate mechanisms of induction, regulation and resolution to elicit antimicrobial defenses. In recent years, the complexity of eukaryotic transcriptomes has become the subject of intense scrutiny and curiosity. It has been established, that RNA polymerase II (RNAPII) transcribes hundreds to thousands of long noncoding RNAs (lncRNAs), often in a stimulus and cell-type specific manner. However, the functional significance of these transcripts has been particularly controversial. While the number of identified lncRNAs is growing, our understanding of how lncRNAs themselves regulate other genes is quite limited. In chapter 2, a novel lncRNA is identified, more specifically, a natural antisense transcript, that mediates the transcription of the pro-inflammatory cytokine IL-1α. Through loss-of-function studies, I report the necessity of this transcript in mediating IL-1α mRNA expression by affecting RNAPII binding to the IL-1α promoter after toll-like receptor signaling. For the first time, I show that IL-1α is regulated at the transcriptional level. As a second independent component of this thesis, we explore the role of the innate immune response after infection by the malaria-causing parasite, Plasmodium berghei ANKA (PbA), and how innate immune components are both beneficial and detrimental to the host depending on when and where inflammation is triggered during infection. We attempt to identify the “malarial toxin” responsible for aberrations in the immune response that is detrimental for disease outcomes and the innate signaling pathways that are involved. Many pathogens induce pathological inflammatory conditions that lead to irreparable homeostatic imbalances and become fatal to the host. Here, type I Interferon signaling is required to dampen parasite load during liver-stage infections, but leads to host mobidity if these pathways are activated in the erythrocytic phase of infection. Together, this thesis provides new insights on how components of the innate immune system are regulated, and how dysregulation of immunity can potentially lead to adverse effects during active infections.

In recent years, heterologous prime-boost vaccination constructs have emerged as a promising strategy to generate broad and protective immunity against a variety of pathogens. The utility of DNA vaccination in priming the immune system, in particular, has improved the immunogenicity of vaccines against difficult pathogens such as HIV-1. In addition, many vaccine formulations include an adjuvant to augment immune responses. However, the mechanisms and profiles of many adjuvants remain largely unknown, particularly in the context of such combination immunization approaches. My thesis research studied the effects of several adjuvants, QS-21, aluminum hydroxide, MPL, and ISCOMATRIX™ adjuvant in the context of a previously described pentavalent HIV-1 Env DNA prime-protein boost vaccine, DP6-001. In a murine model, we quantified HIV antigen-specific humoral and T cell responses, as well as pro-inflammatory serum cytokine and chemokines, both shortly after immunization and at the termination of studies. Our data indicates that each candidate adjuvant generates a unique pattern of biomarkers as well as improved immunogenicity in the context of the DP6-001 DNA prime-protein boost vaccine. Additionally, we examined the impact of several innate signaling pathways on the adaptive immunity raised by DP6-001 and adjuvants, as well as on the unique serum cytokine profiles. These studies provide valuable information in selection of an adjuvant for inclusion in future prime-boost strategies, with the goal of enhancing immunogenicity while minimizing reactogenicity. Furthermore, these studies provided insight about the utility of different current adjuvants in a prime-boost formulation, and the unique immune environment induced by DNA priming.

Os peptídeos antimicrobianos desempenham papéis protetores críticos em uma gama de doenças humanas, incluindo o câncer. Vários estudos demonstraram funções - tais como proliferação, angiogênese, apoptose e imunomodulação - desses peptídeos em vias cancerígenas cruciais. Investigamos o papel do Peptídeo antimicrobiano LL-37 sobre stemness em câncer de mama (SKBR3) e células de melanoma (A375). Análise por PCR array da expressão diferencial de genes em SKBR3 e A375 com knockdown por siRNA para o mRNA de LL-37 revelou uma regulação negativa de genes relacionados com stemness, incluindo transcriptase reversa da telomerase, forkhead box D3 e para o fator indiferenciado de transcrição de células embrionárias 1, notavelmente em células de câncer de mama.Além disso, as células SKBR3 com knockdown para a expressão de LL-37 mostraram uma diminuição da produção de oncosferas em comparação com controles negativos, enquanto as células A375 exibiram uma produção aumentada. Tomados em conjunto, nossos achados indicam um papel para LL- 37 em stemness, dependendo do tipo de celular analisado / Antimicrobial peptides play critical protective roles in a range of human diseases, including cancer. Multiple studies have demonstrated functions -- such as proliferation, angiogenesis, apoptosis and immunomodulation -- of these peptides in crucial cancer pathways. We investigated the role of the antimicrobial peptide LL-37 on stemness in breast cancer (SKBR3) and melanoma cells (A375). PCR array analysis of differential gene expression in SKBR3 and A375 cancer cell lines downregulated for LL-37 expression by siRNA revealed downregulation of genes related to stemness, including telomerase reverse transcriptase, forkhead box D3 and undifferentiated embryonic cell transcription factor 1, remarkably in breast cancer cells. Furthermore, SKBR3 cells knocked down for LL-37 expression showed a decreased production of oncospheres in comparison with negative controls, while A375 cells exhibited increased production. Taken collectively, our findings indicate a role for LL-37 in cancer cell stemness depending on the cell type

INTRODUÇÃO: Apesar do contínuo progresso no tratamento e suporte clínico a sepse continua sendo uma das principais causas de morbidade e mortalidade nas unidades de terapia intensiva, com desfechos semelhantes ao longo dos últimos 50 anos. A suscetibilidade à infecção grave no recém-nascido é parcialmente devida à imaturidade do sistema imune inato associado à mínima em exposição antigênica in utero e à ação ineficaz das células T efetoras e das célula B. Embora a ativação do sistema imune inato por padrões de reconhecimento (PRR) como os dos receptores Toll-like (TLR) tenham sua importância amplamente reconhecida nos últimos anos, seu comportamento frente a uma infecção in vivo ainda não foi completamente compreendido. Neste trabalho nós analisamos a expressão dos TLR-2 e TLR-4 em células apresentadoras de antígeno em recém-nascidos com e sem sepse. CAUSUÍSTICA E MÉTODO: Trata-se de um estudo prospectivo realizado no período entre fevereiro de 2011 e janeiro de 2013 onde foram incluídos quarenta e cinco recém-nascidos a termo, sem malformação congênita, admitidos na Unidade de Cuidados Intensivos Neonatal do Instituto da Criança-HCFMUSP e divididos em grupos 1 e 2. O grupo 1 consistiu em 27 recém-nascidos com diagnóstico clínico e laboratorial de sepse tardia enquanto que o grupo 2 foi composto por 18 recém-nascidos sem quadro séptico vigente. As citocinas foram determinadas por teste de CBA em sangue periférico. A expressão e MFI dos TLR-2 e TLR-4 foi determinado por imunofenotipagem em APCs e linfócitos no sangue periférico total através de análise pelo citômetro de fluxo BD FACSDiva. RESULTADOS: Os dados clínicos foram semelhantes entre os grupos 1 e 2, exceto para o estado infeccioso. Microrganismos foram identificados em 37 % no grupo 1 e estes tiveram níveis mais elevados de citocinas pró-inflamatórias (IL-8, IL-6, IL-1beta) e de citocina anti-inflamatória (IL-10). Nas células dendríticas, a expressão de TLR-2 e 4 foi semelhante entre os grupos enquanto que houve menor expressão nos pacientes infectados da molécula co-estimuladora CD86 (p < 0,05) e expressão semelhante de CD1a e CD80 em relação aos RN não infectados. No monócito, o MFI para TLR-2 e a freqüência de expressão do TLR-4 foi maior no grupo 1 (p = 0,01). Apesar da frequência de linfócitos totais ter sido mais baixa no grupo 1 (p = 0,002), não foi observada diferença quanto as suas subpopulações exceto em relação a maior frequência de LT efetor no grupo infectado com menor expressão da molécula CD28. Houve maior frequência de LB ativados no grupo 1 enquanto que a população total e as demais subpopulações foram semelhantes em número, moléculas de ativação e na expressão dos TLR-2 e 4 em ambos os grupos. CONCLUSÃO: Este estudo analisou a resposta imune inata no recém-nascido com e sem sepse. As IL-6, IL-8 e IL-10 foram bons indicadores desta doença. Recém-nascidos sépticos, que dependem quase exclusivamente do sistema imune inato, apresentaram pouca resposta in vivo na ativação de células dendríticas e monócitos propiciando uma resposta imune deficiente e maior susceptibilidade à infecção / INTRODUCTION: Despite continuous progress in the clinical treatment and other supportive care therapies, sepsis remains a leading cause of morbidity and mortality in the intensive care unit with similar outcome throughout the past 50 years. The susceptibility to severe infection is partially due to newborn immature innate immune system associated to minimal in utero antigen exposure and effector T and B cell impaired function. Although the importance of pattern recognition domains such as Toll-like receptors (TLR) in the innate immune system activation has been fully acknowledged within the last few years its behavior in front of an in vivo infection scenario is still not completely understood. Here we analyzed the TLR-2 and TLR-4 expression in antigen-presenting cell in healthy and septic newborns. PATIENTS AND METHODS: This prospective study was conducted during the period from February 2011 until January 2013 at Sao Paulo University, Sao Paulo, Brazil. Forty-five term newborns without congenital malformation were included from the Newborn Intensive Care Unit at Children\'s Hospital. As group 1, 27 newborns who had clinical and laboratory diagnostic of late onset sepsis were included while 18 newborns were evaluated in a non-septic status and were included at group 2. Cytokines were measured by cytometric bead array in peripheral blood. TLR-2 and TLR-4 expression and MFI were determined by immunophenotyping at peripheral whole blood in APC cells and lymphocytes and analyzed on a BD FACSDiva flow cytometer. RESULTS: Clinical data was similar between septic and non-septic groups except for the infectious status. Group 1 had microorganisms identified in 37 % septic newborns associated with higher levels of pro-inflammatory (IL-8, IL-6, IL-1beta) and anti-inflammatory interleukins (IL-10). When it comes to dendritic cells, the expression of TLR-2 and 4 was similar between groups whereas there was lower expression of co-molecule CD86 (p < 0,05) and similar expression of CD1a and CD80 between infected and non-infected patients. At monocytes, the MFI for TLR-2 and the frequency of TLR-4 expression was higher in infected newborn (p=0,01). There were lower levels of total lymphocytes in infected patients (p=0,002) but no difference was observed in T cells subtypes frequency except for higher levels of effector T cell in infected group with lower expression of CD28 molecule. Group 1 had higher levels of activated B cell whereas total population and the other subsets were similar in number, activation molecules and TLR-2 and 4 expressions in both groups. CONCLUSION: This study investigated the innate immune response in septic and non-septic newborn. Interleukin levels 6, 8 and 10 were good indicators of sepsis. Septic newborns, which count most exclusively with innate immune system, had little in vivo response at dendritic cell and monocyte activation leading to an impaired immune response and increased susceptibility to infection

INTRODUÇÃO: Apesar do contínuo progresso no tratamento e suporte clínico a sepse continua sendo uma das principais causas de morbidade e mortalidade nas unidades de terapia intensiva, com desfechos semelhantes ao longo dos últimos 50 anos. A suscetibilidade à infecção grave no recém-nascido é parcialmente devida à imaturidade do sistema imune inato associado à mínima em exposição antigênica in utero e à ação ineficaz das células T efetoras e das célula B. Embora a ativação do sistema imune inato por padrões de reconhecimento (PRR) como os dos receptores Toll-like (TLR) tenham sua importância amplamente reconhecida nos últimos anos, seu comportamento frente a uma infecção in vivo ainda não foi completamente compreendido. Neste trabalho nós analisamos a expressão dos TLR-2 e TLR-4 em células apresentadoras de antígeno em recém-nascidos com e sem sepse. CAUSUÍSTICA E MÉTODO: Trata-se de um estudo prospectivo realizado no período entre fevereiro de 2011 e janeiro de 2013 onde foram incluídos quarenta e cinco recém-nascidos a termo, sem malformação congênita, admitidos na Unidade de Cuidados Intensivos Neonatal do Instituto da Criança-HCFMUSP e divididos em grupos 1 e 2. O grupo 1 consistiu em 27 recém-nascidos com diagnóstico clínico e laboratorial de sepse tardia enquanto que o grupo 2 foi composto por 18 recém-nascidos sem quadro séptico vigente. As citocinas foram determinadas por teste de CBA em sangue periférico. A expressão e MFI dos TLR-2 e TLR-4 foi determinado por imunofenotipagem em APCs e linfócitos no sangue periférico total através de análise pelo citômetro de fluxo BD FACSDiva. RESULTADOS: Os dados clínicos foram semelhantes entre os grupos 1 e 2, exceto para o estado infeccioso. Microrganismos foram identificados em 37 % no grupo 1 e estes tiveram níveis mais elevados de citocinas pró-inflamatórias (IL-8, IL-6, IL-1beta) e de citocina anti-inflamatória (IL-10). Nas células dendríticas, a expressão de TLR-2 e 4 foi semelhante entre os grupos enquanto que houve menor expressão nos pacientes infectados da molécula co-estimuladora CD86 (p < 0,05) e expressão semelhante de CD1a e CD80 em relação aos RN não infectados. No monócito, o MFI para TLR-2 e a freqüência de expressão do TLR-4 foi maior no grupo 1 (p = 0,01). Apesar da frequência de linfócitos totais ter sido mais baixa no grupo 1 (p = 0,002), não foi observada diferença quanto as suas subpopulações exceto em relação a maior frequência de LT efetor no grupo infectado com menor expressão da molécula CD28. Houve maior frequência de LB ativados no grupo 1 enquanto que a população total e as demais subpopulações foram semelhantes em número, moléculas de ativação e na expressão dos TLR-2 e 4 em ambos os grupos. CONCLUSÃO: Este estudo analisou a resposta imune inata no recém-nascido com e sem sepse. As IL-6, IL-8 e IL-10 foram bons indicadores desta doença. Recém-nascidos sépticos, que dependem quase exclusivamente do sistema imune inato, apresentaram pouca resposta in vivo na ativação de células dendríticas e monócitos propiciando uma resposta imune deficiente e maior susceptibilidade à infecção / INTRODUCTION: Despite continuous progress in the clinical treatment and other supportive care therapies, sepsis remains a leading cause of morbidity and mortality in the intensive care unit with similar outcome throughout the past 50 years. The susceptibility to severe infection is partially due to newborn immature innate immune system associated to minimal in utero antigen exposure and effector T and B cell impaired function. Although the importance of pattern recognition domains such as Toll-like receptors (TLR) in the innate immune system activation has been fully acknowledged within the last few years its behavior in front of an in vivo infection scenario is still not completely understood. Here we analyzed the TLR-2 and TLR-4 expression in antigen-presenting cell in healthy and septic newborns. PATIENTS AND METHODS: This prospective study was conducted during the period from February 2011 until January 2013 at Sao Paulo University, Sao Paulo, Brazil. Forty-five term newborns without congenital malformation were included from the Newborn Intensive Care Unit at Children\'s Hospital. As group 1, 27 newborns who had clinical and laboratory diagnostic of late onset sepsis were included while 18 newborns were evaluated in a non-septic status and were included at group 2. Cytokines were measured by cytometric bead array in peripheral blood. TLR-2 and TLR-4 expression and MFI were determined by immunophenotyping at peripheral whole blood in APC cells and lymphocytes and analyzed on a BD FACSDiva flow cytometer. RESULTS: Clinical data was similar between septic and non-septic groups except for the infectious status. Group 1 had microorganisms identified in 37 % septic newborns associated with higher levels of pro-inflammatory (IL-8, IL-6, IL-1beta) and anti-inflammatory interleukins (IL-10). When it comes to dendritic cells, the expression of TLR-2 and 4 was similar between groups whereas there was lower expression of co-molecule CD86 (p < 0,05) and similar expression of CD1a and CD80 between infected and non-infected patients. At monocytes, the MFI for TLR-2 and the frequency of TLR-4 expression was higher in infected newborn (p=0,01). There were lower levels of total lymphocytes in infected patients (p=0,002) but no difference was observed in T cells subtypes frequency except for higher levels of effector T cell in infected group with lower expression of CD28 molecule. Group 1 had higher levels of activated B cell whereas total population and the other subsets were similar in number, activation molecules and TLR-2 and 4 expressions in both groups. CONCLUSION: This study investigated the innate immune response in septic and non-septic newborn. Interleukin levels 6, 8 and 10 were good indicators of sepsis. Septic newborns, which count most exclusively with innate immune system, had little in vivo response at dendritic cell and monocyte activation leading to an impaired immune response and increased susceptibility to infection

Os peptídeos antimicrobianos desempenham papéis protetores críticos em uma gama de doenças humanas, incluindo o câncer. Vários estudos demonstraram funções - tais como proliferação, angiogênese, apoptose e imunomodulação - desses peptídeos em vias cancerígenas cruciais. Investigamos o papel do Peptídeo antimicrobiano LL-37 sobre stemness em câncer de mama (SKBR3) e células de melanoma (A375). Análise por PCR array da expressão diferencial de genes em SKBR3 e A375 com knockdown por siRNA para o mRNA de LL-37 revelou uma regulação negativa de genes relacionados com stemness, incluindo transcriptase reversa da telomerase, forkhead box D3 e para o fator indiferenciado de transcrição de células embrionárias 1, notavelmente em células de câncer de mama.Além disso, as células SKBR3 com knockdown para a expressão de LL-37 mostraram uma diminuição da produção de oncosferas em comparação com controles negativos, enquanto as células A375 exibiram uma produção aumentada. Tomados em conjunto, nossos achados indicam um papel para LL- 37 em stemness, dependendo do tipo de celular analisado / Antimicrobial peptides play critical protective roles in a range of human diseases, including cancer. Multiple studies have demonstrated functions -- such as proliferation, angiogenesis, apoptosis and immunomodulation -- of these peptides in crucial cancer pathways. We investigated the role of the antimicrobial peptide LL-37 on stemness in breast cancer (SKBR3) and melanoma cells (A375). PCR array analysis of differential gene expression in SKBR3 and A375 cancer cell lines downregulated for LL-37 expression by siRNA revealed downregulation of genes related to stemness, including telomerase reverse transcriptase, forkhead box D3 and undifferentiated embryonic cell transcription factor 1, remarkably in breast cancer cells. Furthermore, SKBR3 cells knocked down for LL-37 expression showed a decreased production of oncospheres in comparison with negative controls, while A375 cells exhibited increased production. Taken collectively, our findings indicate a role for LL-37 in cancer cell stemness depending on the cell type

Yersinia pestis (Y. pestis), as the causative agent of plague, has caused deaths estimated to more than 200 million people in three historical plague pandemics, including the infamous Black Death in medieval Europe. Although infection with Yersinia pestis can mostly be limited by antibiotics and only 2000-5000 cases are observed worldwide each year, this bacterium is still a concern for bioterrorism and recognized as a category A select agent by the Centers for Disease Control and Prevention (CDC). The investigation into the host-pathogen interactions during Y. pestis infection is important to advance and broaden our knowledge about plague pathogenesis for the development of better vaccines and treatments. Y. pestis is an expert at evading innate immune surveillance through multiple strategies, several mediated by its type three secretion system (T3SS). It is known that the bacterium induces rapid and robust cell death in host macrophages and dendritic cells. Although the T3SS effector YopJ has been determined to be the factor inducing cytotoxicity, the specific host cellular pathways which are targeted by YopJ and responsible for cell death remain poorly defined. This thesis research has established the critical roles of caspase-8 and RIP kinases in Y. pestis-induced macrophage cell death. Y. pestis-induced cytotoxicity is completely inhibited in RIP1-/- or RIP3-/-caspase-8-/- macrophages or by specific chemical inhibitors. Strikingly, this work also indicates that macrophages deficient in either RIP1, or caspase-8 and RIP3, have significantly reduced infection-induced production of IL-1β, IL-18, TNFα and IL-6 cytokines; impaired activation of NF-κB signaling pathway and greatly compromised caspase-1 processing; all of which are critical for innate immune responses and contribute to fight against pathogen infection. Y. pestis infection causes severe and often rapid fatal disease before the development of adaptive immunity to the V bacterium, thus the innate immune responses are critical to control Y. pestis infection. Our group has previously established the important roles of key molecules of the innate immune system: TLR4, MyD88, NLRP12, NLRP3, IL-18 and IL-1β, in host responses against Y. pestis and attenuated strains. Yersinia has proven to be a good model for evaluating the innate immune responses during bacterial infection. Using this model, the role of caspase-8 and RIP3 in counteracting bacterial infection has been determined in this thesis work. Mice deficient in caspase-8 and RIP3 are very susceptible to Y. pestis infection and display reduced levels of pro-inflammatory cytokines in spleen and serum, and decreased myeloid cell death. Thus, both in vitro and in vivo results indicate that caspase-8 and RIP kinases are key regulators of macrophage cell death, NF-κB and caspase-1 activation in Yersinia infection. This thesis work defines novel roles for caspase-8 and RIP kinases as the central components in innate immune responses against Y. pestis infection, and provides further insights to the host-pathogen interaction during bacterial challenge.