Browsing by Author "Resende, Daniela de Melo"

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    An assessment on epitope prediction methods for protozoa genomes.
    (2012) Resende, Daniela de Melo; Rezende, Antonio Mauro; Oliveira, Nesley Jesus Daher de; Batista, Izabella Cristina Andrade; Oliveira, Rodrigo Corrêa de; Reis, Alexandre Barbosa; Ruiz, Jeronimo Conceição
    Background: Epitope prediction using computational methods represents one of the most promising approaches to vaccine development. Reduction of time, cost, and the availability of completely sequenced genomes are key points and highly motivating regarding the use of reverse vaccinology. Parasites of genus Leishmania are widely spread and they are the etiologic agents of leishmaniasis. Currently, there is no efficient vaccine against this pathogen and the drug treatment is highly toxic. The lack of sufficiently large datasets of experimentally validated parasites epitopes represents a serious limitation, especially for trypanomatids genomes. In this work we highlight the predictive performances of several algorithms that were evaluated through the development of a MySQL database built with the purpose of: a) evaluating individual algorithms prediction performances and their combination for CD8+ T cell epitopes, B-cell epitopes and subcellular localization by means of AUC (Area Under Curve) performance and a threshold dependent method that employs a confusion matrix; b) integrating data from experimentally validated and in silico predicted epitopes; and c) integrating the subcellular localization predictions and experimental data. NetCTL, NetMHC, BepiPred, BCPred12, and AAP12 algorithms were used for in silico epitope prediction and WoLF PSORT, Sigcleave and TargetP for in silico subcellular localization prediction against trypanosomatid genomes. Results: A database-driven epitope prediction method was developed with built-in functions that were capable of: a) removing experimental data redundancy; b) parsing algorithms predictions and storage experimental validated and predict data; and c) evaluating algorithm performances. Results show that a better performance is achieved when the combined prediction is considered. This is particularly true for B cell epitope predictors, where the combined prediction of AAP12 and BCPred12 reached an AUC value of 0.77. For T CD8+ epitope predictors, the combined prediction of NetCTL and NetMHC reached an AUC value of 0.64. Finally, regarding the subcellular localization prediction, the best performance is achieved when the combined prediction of Sigcleave, TargetP and WoLF PSORT is used. Conclusions: Our study indicates that the combination of B cells epitope predictors is the best tool for predicting epitopes on protozoan parasites proteins. Regarding subcellular localization, the best result was obtained when the three algorithms predictions were combined. The developed pipeline is available upon request to authors.
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    A chimeric vaccine combined with adjuvant system induces immunogenicity and protection against visceral leishmaniasis in BALB/c mice.
    (2021) Ostolin, Thais Lopes Valentim Di Paschoale; Gusmão, Miriã Rodrigues; Mathias, Fernando Augusto Siqueira; Cardoso, Jamille Mirelle de Oliveira; Roatt, Bruno Mendes; Soares, Rodrigo Dian de Oliveira Aguiar; Ruiz, Jeronimo Conceição; Resende, Daniela de Melo; Brito, Rory Cristiane Fortes de; Reis, Alexandre Barbosa
    In Brazil, canine visceral leishmaniasis is an important public health problem due to its alarming growth. The high prevalence of infected dogs reinforces the need for a vaccine for use in prophylactic vaccination campaigns. In the present study, we evaluate the immunogenicity and protection of the best dose of Chimera A selected through the screening of cytokines production important in disease. BALB/c mice were vaccinated subcutaneously with three doses and challenged intravenously with 1 107 L. infantum promastigotes. Spleen samples were collected to assess the intracellular cytokine profile production, T cell proliferation and parasite load. At first, three different doses of Chimera A (5 lg, 10 lg and 20 lg) were evaluated through the production of IFN-c and IL-10 cytokines. Since the dose of 20 lg showed the best results, it was chosen to continue the study. Secondarily, Chimera A at dose of 20 lg was formulated with Saponin plus Monophosphoryl lipid A. Vaccination with Chimera A alone and formulated with SM adjuvant system was able to increase the percentage of the proliferation of specific T lymphocytes and stimulated a Th1 response with increased levels of IFN-c, TNF-a and IL-2, and decreased of IL-4 and IL-10. The vaccine efficacy through real-time PCR demonstrated a reduction in the splenic parasite load in animals that received Chimera A formulated with the SM adjuvant system (92%). Additionally, we observed increased levels of nitric oxide in stimulated-culture supernatants. The Chimera A formulated with the SM adjuvant system was potentially immunogenic, being able to induce immunoprotective mechanisms and reduce parasite load. Therefore, the use of T-cell multi-epitope vaccine is promising against visceral leishmaniasis.
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    Chimeric vaccines designed by immunoinformatics-activated polyfunctional and memory T cells that trigger protection against experimental visceral leishmaniasis.
    (2020) Brito, Rory Cristiane Fortes de; Ruiz, Jeronimo Conceição; Cardoso, Jamille Mirelle de Oliveira; Ostolin, Thais Lopes Valentim Di Paschoale; Reis, Levi Eduardo Soares; Mathias, Fernando Augusto Siqueira; Soares, Rodrigo Dian de Oliveira Aguiar; Roatt, Bruno Mendes; Oliveira, Rodrigo Corrêa de; Resende, Daniela de Melo; Reis, Alexandre Barbosa
    Many vaccine candidates against visceral leishmaniasis (VL) have been proposed; however, to date, none of them have been efficacious for the human or canine disease. On this basis, the design of leishmaniasis vaccines has been constantly changing, and the use of approaches to select specific epitopes seems to be crucial in this scenario. The ability to predict T cell-specific epitopes makes immunoinformatics an even more necessary approach, as in VL an efficient immune response against the parasite is triggered by T lymphocytes in response to Leishmania spp. immunogenic antigens. Moreover, the success of vaccines depends on the capacity to generate long-lasting memory and polyfunctional cells that are able to eliminate the parasite. In this sense, our study used a combination of different approaches to develop potential chimera candidate vaccines against VL. The first point was to identify the most immunogenic epitopes of Leishmania infantum proteins and construct chimeras composed of Major histocompatibility complex (MHC) class I and II epitopes. For this, we used immunoinformatics features. Following this, we validated these chimeras in a murine model in a thorough memory study and multifunctionality of T cells that contribute to a better elucidation of the immunological protective mechanisms of polyepitope vaccines (chimera A and B) using multicolor flow cytometry. Our results showed that in silico-designed chimeras can elicit polyfunctional T cells producing T helper (Th)1 cytokines, a strong immune response against Leishmania antigen, and the generation of central and effector memory T cells in the spleen cells of vaccinated animals that was able to reduce the parasite burden in this organ. These findings contribute two potential candidate vaccines against VL that can be used in further studies, and help in this complex field of vaccine development against this challenging parasite.
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    Emprego da vacinologia reversa para a identificação, triagem e avaliação de peptídeos de L. infantum para o desenho e desenvolvimento de vacinas poliepítopos e de coquetel de peptídeos contra a leishmaniose visceral.
    (2018) Brito, Rory Cristiane Fortes de; Reis, Alexandre Barbosa; Resende, Daniela de Melo; Luca, Paula Mello de; Guimarães, Ana Carolina Ramos; Afonso, Luís Carlos Crocco; Reis, Alexandre Barbosa
    No contexto de desenvolvimento de vacinas, a vacinologia reversa, ou imunoinformática, é uma abordagem que integra diferentes metodologias computacionais para a busca de alvos e o desenho de vacinas. Assim, a imunoinformática vem se destacando ao permitir o uso de programas para a predição de epítopos imunogênicos in silico. Essa estratégia tem o potencial de buscar alvos para o desenvolvimento de vacinas em todo o proteoma predito de organismos patogênicos. Até a presente data, não existe uma vacina eficaz contra a leishmaniose visceral empregada em campanhas de vacinação. Diante desse cenário, este projeto propõe a utilização da imunoinformática para selecionar epítopos e construir vacinas quiméricas poliepítopos e/ou coquetel de peptídeos a serem testadas contra leishmaniose visceral. No capítulo II desta tese foi apresentado um sistema de predição de epítopos de células T e B, além de vias de sinalização de proteínas. Este sistema foi validado utilizando dados experimentais de proteínas imunogênicas já descritas na literatura, comprovando a existência de uma correlação e associação entre o número de epítopos preditos para células T/B e os resultados experimentais relatados. Em seguida, no capítulo III encontram-se os dados relacionados a duas quimeras poliepítopos que foram desenhadas a partir da abordagem proposta em proteínas imunogênicas já escritas na literatura. Tais quimeras formuladas deram origem a duas vacinas, VAC-1 (quimera A) e VAC-2 (quimera B) ambas associadas ao adjuvante saponina. Assim, foi avaliada a imunogenicidade, a geração de memória imunológica e eficácia das vacinas em camundongos BALB/c submetidos ao protocolo de imunização e desafio com promastigotas de Leishmania infantum. Essas vacinas apresentaram imunogenicidade e capacidade para induzir linfócitos T de memória além de promoverem redução da carga parasitária no baço. Finalmente, no capítulo IV, são mostrados os resultados obtidos de peptídeos imunogênicos identificados através da abordagem de imunoinformática no proteoma predito de L. infantum. Para a seleção destes peptídeos foi realizada uma triagem em cães naturalmente infectados por L. infantum. Estes testes permitiram selecionar os peptídeos que obtiveram melhor performance após o inóculo intradérmico. Assim, foram constituídas as vacinas VAC-3 (coquetel 1) e VAC-4 (coquetel 2) ambas associadas à saponina que foram avaliadas em relação a imunogenicidade, a ativação de células T de memória e a eficácia frente ao desafio com L. infantum. Os resultados obtidos demostraram que a VAC-3 apresentou-se promissora no que se refere a imunogenicidade, indução de memória imunológica de células T e diminuição da carga parasitária no tecido esplênico. Este estudo permitiu certificar e ratificar o potencial da imunoinformática como ferramenta a ser empregada no desenvolvimento de vacinas contra a leishmaniose visceral. Assim sendo, torna-se relevante a realização de maiores estudos para comprovar a real eficácia das vacinas propostas em cães.
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    Epitope mapping and protective immunity elicited by adenovirus expressing the Leishmania amastigote specific A2 antigen : correlation with IFN- and cytolytic activity by CD8+ T cells.
    (2008) Resende, Daniela de Melo; Caetano, Bráulia Costa; Dutra, Míriam Santos; Abrantes, Christiane de Freitas; Verly, Rodrigo Moreira; Resende, Jarbas Magalhães; Veloso, Dorila Piló; Rezende, Simone Aparecida; Romero, Oscar Bruna; Fernandes, Ana Paula; Gazzinelli, Ricardo Tostes
    A2was identified as an amastigote virulence factor of Leishmania (Leishmania) donovani and as a candidate antigen for vaccine development against visceral leishmaniasis. Here, predicted hydrophilic, class I and II MHC-binding synthetic peptides were used to define epitopes recognized by A2-specific antibodies, CD8+ T and CD4+ T cells, respectively. Immunization of BALB/c mice with adenovirus expressing A2 (AdA2) resulted in lowantibody response, contrasting with high levels of IFN-_ producing CD4+ T and CD8+ T cells specific for A2. Further, A2-specific CD8+ T cells from immunized mice were capable of lysing sensitized target cells in vivo. Finally, we demonstrated an association of A2-specific T cell responses and reduced parasitism in both liver and spleen from mice immunized with AdA2 and challenged with L. (L.) chagasi.
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    Identificação de novos antígenos candidatos vacinais contra leishmaniose visceral canina no genoma de L. infantum utilizando a bioinformática como ferramenta.
    (2014) Brito, Rory Cristiane Fortes de; Reis, Alexandre Barbosa; Resende, Daniela de Melo; Reis, Cristina Helena dos Santos; Marinho, Flávia Dias Marques; Souza, Jacqueline de
    A leishmaniose visceral canina (LVC) é uma zoonose na América Latina, e o cão possui um papel central como reservatório do parasito e na transmissão da infecção para o vetor no ciclo urbano da Leishmania infantum. A vacinologia reversa permite realizar a predição de epítopos in silico de células B e T, que são importantes na resposta imune, permitindo o desenho de vacinas com tempo reduzido. O objetivo deste trabalho foi selecionar genes do protozoário L. infantum candidatos à vacina contra LVC. Esse objetivo foi divido em duas etapas, sendo a primeira a seleção de antígenos utilizando ferramentas de bioinformática e a segunda a clonagem e expressão dos antígenos selecionados em um sistema eucarioto. Na ETAPA I foi realizado o download do proteoma predito da espécie L. infantum, com 8.241 proteínas, que foi usado em todas as análises subsequentes. As predições foram feitas utilizando-se os seguintes algoritmos: a) para MHC-I, NetCTL e NetMHC; b) para MHC-II, NetMHCII; c) para células B, BepiPred, AAP12 e BCPred12 enquanto que para a predição da localização subcelular das proteínas foram utilizados Sigcleave, TargetP e WoLF PSORT. Foram analisados 12 alelos MHC-I humanos e sete alelos MHC-I de camundongos, e no contexto de MHC-II, foram analisados 14 alelos humanos e três de camundongos. Após a realização das predições, foi necessário o desenvolvimento de um Banco de Dados relacional em um Sistema Gerenciador de Banco de Dados (SGBD), o MySQL, para a integração dos resultados e pré-seleção das proteínas baseado nos seguintes critérios: proteínas secretadas/excretadas ou de membrana plasmática, com epítopos preditos com afinidade pelos 19 alelos de MHC-I utilizados e epítopos preditos com afinidade por no mínimo 14 alelos de MHC-II, além de epítopos preditos para células B. Em seguida, foi feita uma busca por similaridade de sequências com os proteomas preditos de humano, de cão e de camundongo a fim de evitar reações autoimunes no ato da vacinação, para isso foi utilizado o algoritmo BLASTp, do pacote Blastall. Após o alinhamento de sequências, as proteínas com pouca similaridade foram confrontadas com a rede predita de interação proteínaproteína do parasito, desenvolvida pelo grupo de pesquisa. Na ETAPA II, as proteínas selecionadas foram clonadas no vetor de clonagem pGEM T easy, seguido da clonagem no vetor de expressão pPICZα-A, onde os clones foram confirmados pela PCR e digestão enzimática. Após essa etapa, os plasmídeos pPICZα-A recombinantes foram linearizados e transformados na levedura Pichia pastoris, integrando-se no gemona da levedura. Os clones recombinantes foram selecionados por PCR. Através das ferramentas de bioinformática, foram selecionadas quatro proteínas candidatas a uma vacina contra LVC. Neste trabalho foi mostrado o resultado de clonagem e expressão de dois genes que codificam duas proteínas.
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    Immunoinformatics features linked to leishmania vaccine development : data integration of experimental and in silico studies.
    (2017) Brito, Rory Cristiane Fortes de; Guimarães, Frederico Gonçalves; Velloso, João Paulo Linhares; Oliveira, Rodrigo Corrêa de; Ruiz, Jeronimo Conceição; Reis, Alexandre Barbosa; Resende, Daniela de Melo
    Leishmaniasis is a wide-spectrum disease caused by parasites from Leishmania genus. There is no human vaccine available and it is considered by many studies as apotential effective tool for disease control. To discover novel antigens, computational programs have been used in reverse vaccinology strategies. In this work, we developed a validation antigen approach that integrates prediction of B and T cell epitopes, analysis of Protein-Protein Interaction (PPI) networks and metabolic pathways. We selected twenty candidate proteins from Leishmania tested in murine model, with experimental outcome published in the literature. The predictions for CD4+ and CD8+ T cell epitopes were correlated with protection in experimental outcomes. We also mapped immunogenic proteins on PPI networks in order to find Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with them. Our results suggest that non-protective antigens have lowest frequency of predicted T CD4+ and T CD8+ epitopes, compared with protective ones. T CD4+ and T CD8+ cells are more related to leishmaniasis protection in experimental outcomes than B cell predicted epitopes. Considering KEGG analysis, the proteins considered protective are connected to nodes with few pathways, including those associated with ribosome biosynthesis and purine metabolism.
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    Molecular diagnosis of canine visceral leishmaniasis : a comparative study of three methods using skin and spleen from dogs with natural Leishmania infantum infection.
    (2013) Reis, Levi Eduardo Soares; Vital, Wendel Coura; Roatt, Bruno Mendes; Bouillet, Leoneide Érica Maduro; Ker, Henrique Gama; Brito, Rory Cristiane Fortes de; Resende, Daniela de Melo; Carneiro, Cláudia Martins; Reis, Alexandre Barbosa
    Polymerase chain reaction (PCR) and its variations represent highly sensitive and specificmethods for Leishmania DNA detection and subsequent canine visceral leishmaniasis (CVL)diagnosis. The aim of this work was to compare three different molecular diagnosis tech-niques (conventional PCR [cPCR], seminested PCR [snPCR], and quantitative PCR [qPCR])in samples of skin and spleen from 60 seropositive dogs by immunofluorescence antibodytest and enzyme-linked immunosorbent assay. Parasitological analysis was conducted byculture of bone marrow aspirate and optical microscopic assessment of ear skin and spleensamples stained with Giemsa, the standard tests for CVL diagnosis. The primers L150/L152and LINR4/LIN17/LIN19 were used to amplify the conserved region of the Leishmania kDNAminicircle in the cPCR, and snPCR and qPCR were performed using the DNA polymerasegene (DNA pol _) primers from Leishmania infantum. The parasitological analysis revealedparasites in 61.7% of the samples. Sensitivities were 89.2%, 86.5%, and 97.3% in the skin and81.1%, 94.6%, and 100.0% in spleen samples used for cPCR, snPCR, and qPCR, respectively.We demonstrated that the qPCR method was the best technique to detect L. infantum inboth skin and spleen samples. However, we recommend the use of skin due to the highsensitivity and sampling being less invasive.
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    Peptide vaccines for leishmaniasis.
    (2018) Brito, Rory Cristiane Fortes de; Cardoso, Jamille Mirelle de Oliveira; Reis, Levi Eduardo Soares; Vieira, João Filipe Pereira; Mathias, Fernando Augusto Siqueira; Roatt, Bruno Mendes; Soares, Rodrigo Dian de Oliveira Aguiar; Ruiz, Jeronimo Conceição; Resende, Daniela de Melo; Reis, Alexandre Barbosa
    Due to an increase in the incidence of leishmaniases worldwide, the development of new strategies such as prophylactic vaccines to prevent infection and decrease the disease have become a high priority. Classic vaccines against leishmaniases were based on live or attenuated parasites or their subunits. Nevertheless, the use of whole parasite or their subunits for vaccine production has numerous disadvantages. Therefore, the use of Leishmania peptides to design more specific vaccines against leishmaniases seems promising. Moreover, peptides have several benefits in comparison with other kinds of antigens, for instance, good stability, absence of potentially damaging materials, antigen low complexity, and low-cost to scale up. By contrast, peptides are poor immunogenic alone, and they need to be delivered correctly. In this context, several approaches described in this review are useful to solve these drawbacks. Approaches, such as, peptides in combination with potent adjuvants, cellular vaccinations, adenovirus, polyepitopes, or DNA vaccines have been used to develop peptide-based vaccines. Recent advancements in peptide vaccine design, chimeric, or polypeptide vaccines and nanovaccines based on particles attached or formulated with antigenic components or peptides have been increasingly employed to drive a specific immune response. In this review, we briefly summarize the old, current, and future stands on peptide-based vaccines, describing the disadvantages and benefits associated with them. We also propose possible approaches to overcome the related weaknesses of synthetic vaccines and suggest future guidelines for their development.
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    Shotgun proteomics to unravel the complexity of the leishmania infantum exoproteome and the relative abundance of its constituents.
    (2014) Braga, Micheline Soares; Neves, Leandro Xavier; Campos, Jonatan Marques; Roatt, Bruno Mendes; Soares, Rodrigo Dian de Oliveira Aguiar; Braga, Samuel Leôncio; Resende, Daniela de Melo; Reis, Alexandre Barbosa; Borges, William de Castro
    The exoproteome of some Leishmania species has revealed important insights into host–parasite inter-action, paving the way for the proposal of novel disease-oriented interventions. The focus of the presentinvestigation constituted the molecular profile of the L. infantum exoproteome revealed by a shotgunproteomic approach. Promastigotes under logarithmic phase of growth were obtained and harvestedby centrifugation at different time points. Cell integrity was evaluated through the counting of viableparasites using propidium iodide labeling, followed by flow cytometry analysis. The 6 h culture super-natant, operationally defined here as exoproteome, was then conditioned to in solution digestion andthe resulting peptides submitted to mass spectrometry. A total of 102 proteins were identified and cat-egorized according to their cellular function. Their relative abundance index (emPAI) allowed inferencethat the L. infantum exoproteome is a complex mixture dominated by molecules particularly involved innucleotide metabolism and antioxidant activity. Bioinformatic analyses support that approximately 60%of the identified proteins are secreted, of which, 85% possibly reach the extracellular milieu by means ofnon-classic pathways. At last, sera from naturally infected animals, carriers of differing clinical forms ofCanine Visceral Leishmaniasis (CVL), were used to test the immunogenicity associated to the L. infantumexoproteome. Western blotting experiments revealed that this sub-proteome was useful at discrimi-nating symptomatic animals from those exhibiting other clinical forms of the disease. Collectively, themolecular characterization of the L. infantum exoproteome and the preliminary immunoproteomic assaysopened up new research avenues related to treatment, prognosis and diagnosis of CVL.
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    Synthetic peptides elicit strong cellular immunity in Visceral Leishmaniasis natural reservoir and contribute to long-lasting polyfunctional T-cells in BALB/c mice.
    (2019) Brito, Rory Cristiane Fortes de; Cardoso, Jamille Mirelle de Oliveira; Reis, Levi Eduardo Soares; Mathias, Fernando Augusto Siqueira; Soares, Rodrigo Dian de Oliveira Aguiar; Carvalho, Andréa Teixeira de; Roatt, Bruno Mendes; Oliveira, Rodrigo Corrêa de; Ruiz, Jeronimo Conceição; Resende, Daniela de Melo; Reis, Alexandre Barbosa
    Reverse vaccinology or immunoinformatics is a computational methodology which integrates data from in silico epitope prediction, associated to other important information as, for example, the predicted subcellular location of the proteins used in the design of the context of vaccine development. This approach has the potential to search for new targets for vaccine development in the predicted proteome of pathogenic organisms. To date, there is no effective vaccine employed in vaccination campaigns against visceral leishmaniasis (VL). For the first time, herein, an in silico, in vitro, and in vivo peptide screening was performed, and immunogenic peptides were selected to constitute VL peptide-based vaccines. Firstly, the screening of in silico potential peptides using dogs naturally infected by L. infantum was conducted and the peptides with the best performance were selected. The mentioned peptides were used to compose Cockt-1 (cocktail 1) and Cockt-2 (cocktail 2) in combination with saponin as the adjuvant. Therefore, tests for immunogenicity, polyfunctional T-cells, and the ability to induce central and effector memory in T-lymphocytes capacity in reducing the parasite load on the spleen for Cockt-1 and Cockt-2 were performed. Among the vaccines under study, Cockt-1 showed the best results, eliciting CD4+ and CD8+ polyfunctional T-cells, with a reduction in spleen parasitism that correlates to the generation of T CD4+ central memory and T CD8+ effector memory cells. In this way, our findings corroborate the use of immunoinformatics as a tool for the development of future vaccines against VL.