The aim of this project is to design an algorithm that identifies the Area of Interest (AOI) in ELISpot and FluoroSpot images. ELISpot and FluoroSpot are two varieties of a biochemical test used to analyze immune responses by quantifying the amount of cytokine secreted by cells. ELISpot and FluoroSpot images show a well that contains the cytokinesecreting cells which appear as scattered spots. Prior to counting the number of spots, it is required to detect the area in which to count the spots, i.e. the area delimited by the contour of the well. We propose to use the Circle Hough Transform together with filtering and the Laplacian of Gaussian edge detector in order to accurately detect such area. Furthermore we develop an outlier removal method that contributes to increase the robustness of the proposed detection method. Finally we compare our algorithm with another algorithm already in use. A Swedish biotech company called Mabtech has implemented an AOI identifier in the same field. Our proposed algorithm proves to be more robust and provides consistent results for all the images in the dataset.

L’infection primaire au VZV et la réactivation du VZV latent sont fréquemment observées à la suite d’une GMO ou d’une GSCO, ce qui cause de sérieuses complications chez le patient. Pour prévenir ces infections, une prophylaxie antivirale est administrée systématiquement chez tous les greffés de MO ou de SCO, alors qu’il n’existe aucun consensus sur la durée optimale d’une telle prophylaxie. Pour résoudre ce problème, notre objectif est de développer et valider une méthode ELISpot-VZV-IFN- qui permettra de suivre la reconstitution de l’immunité à médiation cellulaire anti-VZV chez les receveurs de GMO ou de GSCO et ainsi déterminer le moment opportun pour réduire ou interrompe la prophylaxie chez les receveurs de greffes de CSH. Dans un premier temps, des valeurs-seuil de la réponse à médiation cellulaire anti-VZV chez la population pédiatrique saine ont dû être générées. À la lumière de nos résultats, un enfant avec un résultat ELISpot-VZV-IFN- > 190.0 SFU/106 PBMC devrait être protégé contre une possible infection à VZV. Pour valider cette étude, une étude prospective de la reconstitution immunitaire anti-VZV a été effectuée chez 9 enfants greffés de MO ou de SCO. Nos résultats préliminaires ont montré qu’il n’y avait eu aucune reconstitution significative de l’immunité à médiation cellulaire anti-VZV dans les 18 premiers mois post-transplantation chez 8 de ces 9 enfants. Les résultats de ces expériences vont fournir d’importantes informations quant à la reconstitution de l’immunité anti-VZV à la suite d’une GMO ou d’une GSCO et pourraient permettre l’amélioration des soins apportés aux receveurs de GMO ou de GSCO. / Primary infection with VZV and reactivation of latent VZV are commonly observed following BMT and UCBT, leading to serious complications in patients. As a result, antiviral prophylaxis is systematically administered to BMT and UCBT recipients, yet there is no consensus that defines its optimal duration. To resolve this problem, our objective was to develop and validate a VZV-IFN--ELISpot with which reconstitution of VZV immunity can be followed in BMT and UCBT recipients, providing clinicians a practical tool to gauge the need for and adjust antiviral prophylaxis in individual HSCT recipients. First of all, threshold values for anti-VZV immunity in healthy pediatric subjects were generated. Based on our results, a child exhibiting > 190.0 VZV-specific SFU /106 PBMC should be protected against a possible VZV infection. To validate these results, a prospective study on the recovery of VZV-specific T cell immunity was performed on 9 children following BMT or UCBT. Preliminary results demonstrated that there was no significant recovery of VZV-specific T cell immunity in the first 18 months post-transplantation in 8 of 9 cases. Results of these experiments will yield important new information regarding reconstitution of anti-VZV immunity following BMT and UCBT and could lead to improvements in clinical management of BMT and UCBT recipients.

L’infection primaire au VZV et la réactivation du VZV latent sont fréquemment observées à la suite d’une GMO ou d’une GSCO, ce qui cause de sérieuses complications chez le patient. Pour prévenir ces infections, une prophylaxie antivirale est administrée systématiquement chez tous les greffés de MO ou de SCO, alors qu’il n’existe aucun consensus sur la durée optimale d’une telle prophylaxie. Pour résoudre ce problème, notre objectif est de développer et valider une méthode ELISpot-VZV-IFN- qui permettra de suivre la reconstitution de l’immunité à médiation cellulaire anti-VZV chez les receveurs de GMO ou de GSCO et ainsi déterminer le moment opportun pour réduire ou interrompe la prophylaxie chez les receveurs de greffes de CSH. Dans un premier temps, des valeurs-seuil de la réponse à médiation cellulaire anti-VZV chez la population pédiatrique saine ont dû être générées. À la lumière de nos résultats, un enfant avec un résultat ELISpot-VZV-IFN- > 190.0 SFU/106 PBMC devrait être protégé contre une possible infection à VZV. Pour valider cette étude, une étude prospective de la reconstitution immunitaire anti-VZV a été effectuée chez 9 enfants greffés de MO ou de SCO. Nos résultats préliminaires ont montré qu’il n’y avait eu aucune reconstitution significative de l’immunité à médiation cellulaire anti-VZV dans les 18 premiers mois post-transplantation chez 8 de ces 9 enfants. Les résultats de ces expériences vont fournir d’importantes informations quant à la reconstitution de l’immunité anti-VZV à la suite d’une GMO ou d’une GSCO et pourraient permettre l’amélioration des soins apportés aux receveurs de GMO ou de GSCO. / Primary infection with VZV and reactivation of latent VZV are commonly observed following BMT and UCBT, leading to serious complications in patients. As a result, antiviral prophylaxis is systematically administered to BMT and UCBT recipients, yet there is no consensus that defines its optimal duration. To resolve this problem, our objective was to develop and validate a VZV-IFN--ELISpot with which reconstitution of VZV immunity can be followed in BMT and UCBT recipients, providing clinicians a practical tool to gauge the need for and adjust antiviral prophylaxis in individual HSCT recipients. First of all, threshold values for anti-VZV immunity in healthy pediatric subjects were generated. Based on our results, a child exhibiting > 190.0 VZV-specific SFU /106 PBMC should be protected against a possible VZV infection. To validate these results, a prospective study on the recovery of VZV-specific T cell immunity was performed on 9 children following BMT or UCBT. Preliminary results demonstrated that there was no significant recovery of VZV-specific T cell immunity in the first 18 months post-transplantation in 8 of 9 cases. Results of these experiments will yield important new information regarding reconstitution of anti-VZV immunity following BMT and UCBT and could lead to improvements in clinical management of BMT and UCBT recipients.

B cells have a central role in the pathogenesis of collagen-induced arthritis (CIA), an animal model of the autoimmune disease rheumatoid arthritis. In this report, a specific subset of an innate type of B cells, B-1 B cells, have been studied for the involvement in CIA. The B-1 B cells were shown to produce small amounts of collagen-specific antibodies upon stimulation in vitro, suggesting that they play a minor role in the development of CIA. This report also includes how marginal zone B cells, another innate type of B cells with natural collagen-reactivity, can be identified in the medullary sinuses of lymph nodes of collagen-immunized mice, implying involvement in auto antigen trapping.

In dieser Promotionsarbeit wird der Quad-Color FluoroSpot (QCF) vorgestellt, welcher die Bestimmung der Frequenz von DENV-Serotyp-spezifischen und DENV- Serotyp-kreuzreaktiven B-Zellen auf Einzelzellbasis ermöglicht. Das vorgestellte Verfahren erlaubt die umfassende Analyse der spezifischen B-Zellantwort, so wie sie sich während einer primären oder sekundären DENV-Infektion bzw. nach einer Dengueimpfung entwickelt. Außerdem ermöglicht der QCF die Beurteilung, ob die DENV-Serotypspezifität bzw. -kreuzreaktivität von B-Zellen als Surrogatmarker für Immunschutz bei DENV-Infizierten bzw. in Studien, welche Dengueimpfstoff- kandidaten testen, relevant ist. Außerdem kann das Verfahren durch die Anpassung des verwendeten Antigens auch zur Beurteilung der B-Zellantwort, so wie sie sich nach einer Infektion mit anderen Erregern wie HIV oder Influenzavirus entwickelt, Anwendung finden. / Dengue is a major public health problem globally. It is caused by four antigenically distinct serotypes of dengue virus (DENV1-4), and although serotype-specific and strongly neutralizing cross-reactive immune responses against the four DENV serotypes are thought to be protective, subneutralizing Abs can contribute to increased disease severity upon secondary infection with a different DENV serotype. Understanding the breadth of the immune response in natural DENV infections and in vaccinees is crucial for determining the correlates of protection or disease severity. Transformation of B cell populations to generate mAbs and ELISPOT assays have been used to determine B cell and Ab specificity to DENV; however, both methods have technical limitations. We therefore modified the conventional ELISPOT to develop a Quad-Color FluoroSpot to provide a means of examining B cell/Ab serotype specificity and cross-reactivity on a single-cell basis. Abs secreted by B cells are captured by an Fc-specific Ab on a filter plate. Subsequently, standardized concentrations of all four DENV serotypes are added to allow equal stoichiometry for Ag binding. After washing, the spots, representing individual B cells, are visualized using four fluorescently labeled DENV serotype-specific detection mAbs. This method can be used to better understand the breadth and magnitude of B cell responses following primary and secondary DENV infection or vaccination and their role as immune correlates of protection from subsequent DENV infections. Furthermore, the Quad-Color FluoroSpot assay can be applied to other diseases caused by multiple pathogen serotypes in which determining the serotype or subtype-specific B cell response is important.

Streptococcus pneumoniae is a significant cause of mortality and morbidity in both children and older adults, with infection resulting in invasive disease, pneumonia and otitis media. The inclusion of pneumococcal conjugate vaccines in routine infant immunisation programmes has had a major impact on disease rates. Vaccine-induced protection against pneumococcal infection is thought to be mediated by the generation of persistent serotype-specific functional antibodies and antigen-specific memory B cells, the latter capable of generating a rapid secondary antibody response on re-exposure to antigen. Although many studies have investigated the immunogenicity of pneumococcal vaccines in different age groups by measuring serotype-specific antibodies, there is more limited information about the B cells underlying such an immune response. Important areas to investigate include the identity of the B cell subsets involved in antibody production and the potential link between memory B cells (B_MEM) and persistent antibody production by long-lived plasma cells. In this thesis I have investigated in detail the immune response to pneumococcal vaccines given to children and adults by a variety of different methods. By examining the variability of a B_MEM ELISpot method, it was shown that this assay is robust and reproducible and can be performed on fresh or frozen samples and in different laboratories. Using this technique, in a study of pre-school children, it was demonstrated for the first time that the level of pre-existing serotype 3-specific antibody is negatively correlated with, and may directly impair the B_MEM response to a booster dose of 13-valent pneumococcal conjugate vaccine (PCV-13) containing serotype 3 glycoconjugate. In the same study, it was shown that antibody persistence against most vaccine serotypes can be expected until the age of 3.5 years. A novel antigen-labelling technique was used in a detailed kinetics study of antigen-specific B cell subsets in response to either PCV-13 or 23-valent pneumococcal polysaccharide vaccine in adults. The results of this study revealed distinct B cell subset response patterns that were observed in all study participants indicating that IgM B_MEM seem to play a major role in the immune response to pneumococcal vaccines. In addition, in the same study, genome wide analysis of gene expression was performed and it was shown that vaccination with either a pneumococcal conjugate or polysaccharide vaccine results in a marked difference in numbers of differentially expressed genes 8 days following vaccination. A further tool likely to be of use in investigating B cell responses is the analysis of the antibody repertoire using next-generation sequencing techniques. In order to test the ability of these methods to detect vaccine responses, a large dataset of high-throughput B cell receptor sequences was analysed and revealed convergence of antigen-specific complementary-determining region (CDR)₃ amino acid (AA) sequences following vaccination and identified antigen-specific sequences. It was further demonstrated that for sequences directed against the H. influenzae type b (Hib) polysaccharide, diversity of immunoglobulin gene rearrangements is much greater than previously recognised. Frequencies of Hib-specific CDR₃ AA sequences were linked with anti-Hib avidity indices highlighting the potential of this method as an alternative (functional) measure of vaccine immunogenicity. These data suggest that studying the B cells and antibody repertoire post-vaccination can give novel insights into the biology that underlies the immune responses.

La transmission mère-enfant (TME) du VIH-1 est un des enjeux majeurs de la pandémie. Une meilleure compréhension de la réponse des lymphocytes T cytotoxiques CD8+ (LTC) VIH-spécifiques lors de la grossesse facilitera le design de stratégies optimales pour diminuer la TME. Notre objectif est donc de caractériser l’amplitude et la diversité de la reconnaissance antigénique des LTC VIH-spécifiques avant, pendant et après la grossesse chez des femmes infectées par le VIH-1. Nos résultats montrent pour la première fois que l’initiation et la progression de la grossesse, à elles seules, n'ont que peu d’influence sur l’amplitude et la diversité de la reconnaissance antigénique des réponses LTC en termes de production d’IFN‐. Ces résultats indiquent que les femmes infectées par le VIH conservent une immunocompétence durant leur grossesse, du moins dans le contexte d’un traitement antirétroviral efficace. Ceci pourrait éventuellement aider à promouvoir l’immunisation comme stratégie pour prévenir la TME du VIH‐1. / Mother-to-child transmission (MTCT) of HIV-1 is one of the major issues of the pandemic. Characterization of HIV-specific immunity during pregnancy, especially cytotoxic CD8+ T lymphocytes (CTL), will lead to a better understanding of HIV pathogenesis and facilitate design of optimal strategies to prevent MTCT. Our objective is to describe the magnitude and the breadth of antigen recognition of HIV-specific CTL responses before, throughout and after pregnancy in a group of HIV-infected women. Our results revealed for the first time that initiation of pregnancy by itself doesn’t change the magnitude of CTL responses in terms of IFN- production. These findings support the fact that HIV-infected women maintain immunocompetence throughout gestation, at least in the context of effective antiretroviral treatment. These results provide a novel understanding of the dynamics of HIV-specific CTL responses during pregnancy and may help to promote maternal immunization as a strategy to prevent MTCT of HIV-1.

Objetivo: Retrovirus Endógeno Humano (HERV) compreende ao redor de 8% do genoma humano. Apesar do fato de que em sua maioria são genes não-funcionais devido a processos de mutação ou perda de material genético no processo de retrotransposição, existem evidências do aumento da expressão de HERVs em tecido de câncer de próstata. Nós estudamos e comparamos a imunogenicidade de peptídeos da família HERV em 2 coortes de pacientes com câncer de próstata. Posteriormente examinamos o estado de ativação e senescência linfocitária nestas coortes. Desenho Experimental: Células Mononucleares de Sangue Periférico (CMSP) de 65 pacientes com câncer localizado da próstata em situação de hormônio-sensibilidade e de 24 pacientes com câncer de próstata metastático e em situação de resistência à castração, comparados a um grupo controle de 12 indivíduos normais foram avaliados em relação ao seu estado de resposta imune pela técnica de ELISPOT contra um conjunto de peptídeos derivados dos exons gag e env do gene da família HERV-K HML-2. Como parte de nosso estudo, foi realizado de forma preliminar uma análise genômica in silico de 500 pacientes com câncer de próstata sequenciados e disponíveis para análise pública do banco de dados TCGA, com o objetivo de reforçar o racional de nossa interrogação científica. Além disso , como estudo de correlação, fizemos uma análise por citometria de fluxo da ativação celular de linfócitos T de nossas coortes para determinarmos a imunofenotipagem e ontogenia linfocitária em nossos indivíduos investigados, no momento de nossa pesquisa de sua resposta imune. Resultados: Nossa análise da resposta imune contra peptídeos de HERV-K HML-2 por ELISPOT-Interferon Gama não mostrou nenhum resultado significativo. Nenhum paciente apresentou dados significativos de resposta de acordo com nossos critérios, apesar de nossos dados preliminares de expressão gênica terem mostrado expressão gênica em torno de 17% em pacientes com doença localizada. Nossos dados de ativação linfocitária mostraram maior ativação e senescência nos pacientes com doença disseminada e resistente à castração. Conclusões: Este parece ser o primeiro estudo a interrogar a presença de resposta celular imune contra peptídeos de HERV-K em pacientes com câncer de próstata. Nosso achados não mostraram resposta imune relevante em doença localizada ou disseminada e em diferentes estados de ativação linfocitária ou status de integridade hormonal. Apesar destes resultados, pesquisa posterior poderia utilizar diferente metodologia, como por exemplo a utilização de citometria de fluxo bem como a busca de diferentes citoquinas envolvidas, tais como as relacionadas a resposta Th2, ao invés de Th1 / Purpose: Human Endogenous Retrovirus (HERV) comprises 8% of human genome. Despite the fact that most of it is non-functional due to mutations or loss of genetic material in the process of retrotransposition, there are some evidence of increased expression of HERV in prostate cancer tissue. We studied the cellular immunogenicity of peptides from HERV-K family in 2 cohorts of prostate cancer patients. Experimental Design: PBMCs from 65 patients with hormone-intact localized prostate cancer and 24 patients with castrate-metastatic disease, matched with 12 normal controls were evaluated for cellular immune response by ELLISPOT against a pool of gag and env peptides from HERV-K family of HML-2 type. As an independent supportive study we did in silico genomic analysis of 500 prostate cancer patients from TCGA database to give another evidence of the prevalence of HERV-K gene expression in prostate cancer genome, reinforcing the rational of our questions. Results: Our analysis of cellular immune response against HERV-K HML-2 peptides by Interferon-gama ELISPOT did not show any meaningful results. No patient showed any minimal criteria of response, despite the fact that in our preliminary genomic analysis we obtained HERV expression in about 17% of a cohort of 500 patients with localized prostate cancer. In regards to the flow cytometry data of the lymphocytes we showed stronger activation and senescence status in the cohort of patients with castration sensitive and resistant disseminated disease, compared to the localized disease cohort. Conclusions: To the authors\'s knowledge this is the first study to look for cellular immune response against peptides derived from coding HERV-K transcripts in prostate cancer patients. Our findings did not show relevant immune response in neither localized nor metastatic castrate prostate cancer patients. Despite those results, further research could continue using different methodology, like flow cytometry as well as looking for different cytokines involved, such as those related to a Th2 response, instead of Th1

La transmission mère-enfant (TME) du VIH-1 est un des enjeux majeurs de la pandémie. Une meilleure compréhension de la réponse des lymphocytes T cytotoxiques CD8+ (LTC) VIH-spécifiques lors de la grossesse facilitera le design de stratégies optimales pour diminuer la TME. Notre objectif est donc de caractériser l’amplitude et la diversité de la reconnaissance antigénique des LTC VIH-spécifiques avant, pendant et après la grossesse chez des femmes infectées par le VIH-1. Nos résultats montrent pour la première fois que l’initiation et la progression de la grossesse, à elles seules, n'ont que peu d’influence sur l’amplitude et la diversité de la reconnaissance antigénique des réponses LTC en termes de production d’IFN‐. Ces résultats indiquent que les femmes infectées par le VIH conservent une immunocompétence durant leur grossesse, du moins dans le contexte d’un traitement antirétroviral efficace. Ceci pourrait éventuellement aider à promouvoir l’immunisation comme stratégie pour prévenir la TME du VIH‐1. / Mother-to-child transmission (MTCT) of HIV-1 is one of the major issues of the pandemic. Characterization of HIV-specific immunity during pregnancy, especially cytotoxic CD8+ T lymphocytes (CTL), will lead to a better understanding of HIV pathogenesis and facilitate design of optimal strategies to prevent MTCT. Our objective is to describe the magnitude and the breadth of antigen recognition of HIV-specific CTL responses before, throughout and after pregnancy in a group of HIV-infected women. Our results revealed for the first time that initiation of pregnancy by itself doesn’t change the magnitude of CTL responses in terms of IFN- production. These findings support the fact that HIV-infected women maintain immunocompetence throughout gestation, at least in the context of effective antiretroviral treatment. These results provide a novel understanding of the dynamics of HIV-specific CTL responses during pregnancy and may help to promote maternal immunization as a strategy to prevent MTCT of HIV-1.

Objetivo: Retrovirus Endógeno Humano (HERV) compreende ao redor de 8% do genoma humano. Apesar do fato de que em sua maioria são genes não-funcionais devido a processos de mutação ou perda de material genético no processo de retrotransposição, existem evidências do aumento da expressão de HERVs em tecido de câncer de próstata. Nós estudamos e comparamos a imunogenicidade de peptídeos da família HERV em 2 coortes de pacientes com câncer de próstata. Posteriormente examinamos o estado de ativação e senescência linfocitária nestas coortes. Desenho Experimental: Células Mononucleares de Sangue Periférico (CMSP) de 65 pacientes com câncer localizado da próstata em situação de hormônio-sensibilidade e de 24 pacientes com câncer de próstata metastático e em situação de resistência à castração, comparados a um grupo controle de 12 indivíduos normais foram avaliados em relação ao seu estado de resposta imune pela técnica de ELISPOT contra um conjunto de peptídeos derivados dos exons gag e env do gene da família HERV-K HML-2. Como parte de nosso estudo, foi realizado de forma preliminar uma análise genômica in silico de 500 pacientes com câncer de próstata sequenciados e disponíveis para análise pública do banco de dados TCGA, com o objetivo de reforçar o racional de nossa interrogação científica. Além disso , como estudo de correlação, fizemos uma análise por citometria de fluxo da ativação celular de linfócitos T de nossas coortes para determinarmos a imunofenotipagem e ontogenia linfocitária em nossos indivíduos investigados, no momento de nossa pesquisa de sua resposta imune. Resultados: Nossa análise da resposta imune contra peptídeos de HERV-K HML-2 por ELISPOT-Interferon Gama não mostrou nenhum resultado significativo. Nenhum paciente apresentou dados significativos de resposta de acordo com nossos critérios, apesar de nossos dados preliminares de expressão gênica terem mostrado expressão gênica em torno de 17% em pacientes com doença localizada. Nossos dados de ativação linfocitária mostraram maior ativação e senescência nos pacientes com doença disseminada e resistente à castração. Conclusões: Este parece ser o primeiro estudo a interrogar a presença de resposta celular imune contra peptídeos de HERV-K em pacientes com câncer de próstata. Nosso achados não mostraram resposta imune relevante em doença localizada ou disseminada e em diferentes estados de ativação linfocitária ou status de integridade hormonal. Apesar destes resultados, pesquisa posterior poderia utilizar diferente metodologia, como por exemplo a utilização de citometria de fluxo bem como a busca de diferentes citoquinas envolvidas, tais como as relacionadas a resposta Th2, ao invés de Th1 / Purpose: Human Endogenous Retrovirus (HERV) comprises 8% of human genome. Despite the fact that most of it is non-functional due to mutations or loss of genetic material in the process of retrotransposition, there are some evidence of increased expression of HERV in prostate cancer tissue. We studied the cellular immunogenicity of peptides from HERV-K family in 2 cohorts of prostate cancer patients. Experimental Design: PBMCs from 65 patients with hormone-intact localized prostate cancer and 24 patients with castrate-metastatic disease, matched with 12 normal controls were evaluated for cellular immune response by ELLISPOT against a pool of gag and env peptides from HERV-K family of HML-2 type. As an independent supportive study we did in silico genomic analysis of 500 prostate cancer patients from TCGA database to give another evidence of the prevalence of HERV-K gene expression in prostate cancer genome, reinforcing the rational of our questions. Results: Our analysis of cellular immune response against HERV-K HML-2 peptides by Interferon-gama ELISPOT did not show any meaningful results. No patient showed any minimal criteria of response, despite the fact that in our preliminary genomic analysis we obtained HERV expression in about 17% of a cohort of 500 patients with localized prostate cancer. In regards to the flow cytometry data of the lymphocytes we showed stronger activation and senescence status in the cohort of patients with castration sensitive and resistant disseminated disease, compared to the localized disease cohort. Conclusions: To the authors\'s knowledge this is the first study to look for cellular immune response against peptides derived from coding HERV-K transcripts in prostate cancer patients. Our findings did not show relevant immune response in neither localized nor metastatic castrate prostate cancer patients. Despite those results, further research could continue using different methodology, like flow cytometry as well as looking for different cytokines involved, such as those related to a Th2 response, instead of Th1