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.

The envelope glycoprotein (Env) of Human Immunodeficiency Virus 1 (HIV-1) has developed several immune-evasion mechanisms to avoid the induction of neutralising antibodies, including immunodominant non-neutralising epitopes, conformational flexibility of conserved epitopes, and spontaneous subunit dissociation, thus impeding vaccine development. Here, chemical modification of Env-based vaccine antigens is explored to overcome these obstacles. Firstly, covalent fixation of Env by chemical cross-linking was used to stabilise the conformationally flexible structure and prevent subunit dissociation. Cross-linked Env constructs showed reduced binding of many non-neutralising antibodies whilst largely maintaining antibody recognition by broadly neutralising antibodies. Compared to unmodified material, immunisation with some of these cross-linked proteins led to the induction of significantly increased antibody titres targeting the conserved CD4 binding site of Env despite similar overall antibody titres. These refocused antibody responses resulted in increased serum neutralising titres compared to animals receiving unmodified protein. Secondly, an epitope masking strategy was developed to reduce or eliminate the immunogenicity of neutralisation-irrelevant surfaces. This was achieved using site-selective addition of theoretically immunosilent glycoconjugates to lysine residues. Masking of model protein hen egg lysozyme (HEL) led to site-selective loss of antibody binding to the modification sites in vitro, which translated into refocusing of antibody responses from masked to unmasked epitopes in vivo. Mutant HIV-1 and influenza virus surface glycoproteins were designed that had lysine residues removed from close proximity to the respective broadly neutralising epitopes, but added throughout the remaining surface. Masking of these mutant proteins with second-generation glycoconjugates led to predictable perturbations of antibody binding in vitro. However, administration of these modified glycoproteins revealed unexpectedly that the masking glycans were highly immunogenic in vivo. Thus, this strategy may well prove useful if truly non-immunogenic glycoconjugates can be identified. Taken together, these chemical modifications of vaccine antigens may allow focused targeting of specific antigenic regions for increased B cell recognition, and may thus be a valuable tool for vaccine antigen design.

A bovinocultura brasileira possui grande ênfase no mercado nacional. Doenças que acometem rebanhos comprometem o mercado além de gerarem grandes prejuízos econômicos. O Clostridium novyi tipo B provoca necrose hepática em bovinos através da produção da alfa toxina, uma potente exotoxina que reduz a produtividade através de alterações como hemoglobinúria, redução do apetite, febre, letargia, diminuição da produção de leite e sangue nas fezes. Conter o microrganismo causador torna-se uma busca necessária tanto do ponto de vista econômico quanto social. Entretanto, o controle da doença ainda é realizado por vacinas formuladas com múltiplos antígenos. A emulsão pode ser uma alternativa promissora para a melhoria da adsorção de antígenos nas formulações vacinais. Camundongos da linhagem Swiss foram utilizados a fim de se avaliar aspectos clínicos e validar resultados referentes a composição de uma nova formulação vacinal contendo adjuvante Montanide ISA 61 VG e antígeno inativado de C. novyi. Os testes de caracterização e antigenicidade indicaram a presença da proteína alfa toxina na composição avaliada. A imunogenicidade do antígeno inativado em emulsão W/O (água/óleo) foi verificada e a proporção empregada (40/60) mostrou ser ideal no uso de múltiplos antígenos, apresentando inocuidade, estabilidade do produto, liberação controlada e estímulo da resposta imune. A determinação da concentração de antígeno foi averiguada pela relação antígeno ativo e inativado com soros de animais doentes, visto a eficácia vacinal de 40%. A adequação da concentração de alfa toxina inativada na emulsão mostrou ser necessária para atingir melhores valores de proteção animal. Análises de hemograma, bioquímicas e morfologia de fígado, baço e coxa contribuíram para elucidar os efeitos da emulsão e comprovar necrose hepática nos grupos não imunizados, além de sugerir avanços na adsorção de vacinas. Os resultados possibilitaram o estabelecimento de um modelo murino de infecção de C. novyi com futuras aplicações relacionadas à produção vacinal com múltiplos antígenos emulsificados para controle das clostridioses. / Brazilian cattle breeding has great emphasis on the national market. Diseases that affect herds compromise the market as well as generate great economic losses. Clostridium novyi type B causes hepatic necrosis in cattle through the production of alpha toxin, a potent exotoxin that reduces productivity through changes such as hemoglobinuria, reduced appetite, fever, lethargy, decreased milk and stool production. Containing the causative micro-organism becomes a necessary quest both economically and socially. However, control of the disease is still performed by vaccines formulated with multiple antigens. The emulsion may be a promising alternative for the improvement of antigen adsorption in vaccine formulations. Swiss strain mice were used to evaluate clinical aspects and validate results regarding the composition of a new vaccine formulation containing Montanide ISA 61 VG adjuvant and C. novyi inactivated antigen. Characterization and antigenicity tests indicated the presence of the alpha toxin protein in the evaluated composition. The immunogenicity of antigen inactivated in W / O emulsion (water / oil) was verified and the ratio employed (40/60) showed to be ideal in the use of multiple antigens, presenting innocuousness, product stability, controlled release and stimulation of the immune response. The determination of the antigen concentration was investigated by the active antigen ratio and inactivated with sera from sick animals, since the vaccine efficacy was 40%. The suitability of the inactivated alpha toxin concentration in the emulsion was shown to be necessary to achieve better animal protection values. Hemogram, biochemical and liver, spleen and thigh morphology contributed to elucidate the effects of the emulsion and to verify hepatic necrosis in the nonimmunized groups, in addition to suggesting advances in the adsorption of vaccines. The results allowed the establishment of a murine model of C. novyi infection with future applications related to the vaccine production with multiple emulsified antigens to control clostridia.

INTRODUÇÃO: Pacientes infectados pelo HIV apresentam maior risco de doença pneumocócica invasiva com maior mortalidade que a população geral. Estratégias para redução da carga de doença pneumocócica são importantes. A vacina antipneumocócica polissacarídica 23-valente é recomendada para adultos infectados pelo HIV, entretanto, a imunogenicidade desta vacina nessa população ainda é discutível. A vacina antipneumocócica ideal e o regime vacinal de maior eficácia ainda são controversos na literatura. Os poucos estudos publicados com vacina antipneumocócica conjugada 7-valente em adultos infectados pelo HIV apresentam resultados discrepantes. Esse estudo visa comparar a resposta de anticorpos e a reatogenicidade de três esquemas diferentes de vacina antipneumocócica, em adultos infectados pelo HIV; e avaliar o impacto da vacinação no estado de colonização da nasofaringe. MÉTODOS: ensaio clínico randomizado e duplo-cego, envolvendo 331 pacientes infectados pelo HIV, de 18 a 60 anos de idade, com contagem de linfócitos T-CD4 acima de 200 cél/mm3. Os pacientes foram alocados em grupos de duas intervenções com intervalos de 60 dias entre elas: a) vacina antipneumocócica polissacarídica 23-valente + placebo; b) vacina antipneumocócica conjugada 7-valente + placebo; c) vacina antipneumocócica conjugada 7-valente + vacina antipneumocócica polissacarídica 23-valente. A imunogenicidade das vacinas foi determinada através da reação de ELISA para sorotipos 6B, 9V e 14, realizadas no momento pré-vacinal, 60 dias e 180 dias após a primeira intervenção. A reatogenicidade foi avaliada através de entrevista após cada vacinação. A colonização da nasofaringe foi avaliada antes do início da vacinação e 180 dias após. RESULTADOS: Os grupos foram similares nas características demográficas e condições associadas à infecção pelo HIV. Nos três grupos foi observado um aumento significativo dos níveis de anticorpo-IgG para todos os três sorotipos avaliados. Foi observada uma maior proporção de indivíduos que sustentaram aumento de quatro vezes ou mais na concentração de anticorpos para sorotipos 6B e 9V nos grupos que receberam PC7V na primeira vacinação. A combinação das vacinas conjugada 7-valente seguida da vacina polissacarídica 23-valente não aumentou a imunogenicidade para nenhum dos sorotipos avaliados. Ambas as vacinas foram bem toleradas, entretanto, eventos adversos sistêmicos foram mais frequentes após aplicação da vacina conjugada 7-valente. Nenhum evento grave foi reportado. O uso da vacina polissacarídica 23- valente após a aplicação da vacina conjugada 7-valente não aumentou a reatogenicidade. A colonização da nasofaringe por S.pneumoniae foi significantemente menor 180 dias após a vacinação, embora não tenha sido observada diferença entre os três grupos. CONCLUSÃO: nesse ensaio clínico conduzido em adultos brasileiros infectados pelo HIV, observamos que as vacinas antipneumocócicas polissacarídica 23-valente e conjugada 7- valente foram seguras e imunogênicas. As evidências sugerem que a vacina conjugada 7-valente foi mais imunogênica que a polissacarídica 23-valente para os sorotipos 6B e 9V. Não houve benefício da aplicação da vacina antipneumocócica polissacarídica 23-valente após vacina conjugada 7- valente. A vacinação antipneumocócica reduziu a colonização da nasofaringe por S.pneumoniae, independentemente do esquema vacinal aplicado / BACKGROUND: The risk and the mortality of invasive pneumococcal disease are higher in HIV-infected patients than in uninfected individuals. Strategy to reduce the burden of invasive pneumococcal disease is crucial. Pneumococcal polysaccharide vaccine 23-valent is recommended for HIV- adults, but its immunogenicity is still controversial. The ideal antipneumococcal vaccine and effective vaccination regimen remain controversial. Few trials with 7-valent pneumococcal conjugate vaccine in HIV-adults revealed disparate results. This study aims to compare antibody response and reactogenicity to three different pneumococcal vaccine schedules in HIV-infected adults, and impact of vaccine in nasopharyngeal carriage of Streptococcus pneumoniae. METHODS: a randomized, blinded clinical trial was conducted in Brazil with 331 HIV-patients aged 18 to 60 years with CD4+ T-lymphocytes count >=200 cells/mm3. Two interventions 60 days apart were done in three schedules: a) 23-valent pneumococcal polysaccharide vaccine + placebo; b) 7-valent pneumococcal conjugate vaccine + placebo; and c) 7-valent pneumococcal conjugate vaccine + pneumococcal polysaccharide vaccine 23-valent. Immunogenicity was assessed by an IgG enzyme-linked immunosorbent assay to S. pneumoniae serotypes 6B, 9V and 14, performed at baseline, 60 and 180 days after first intervention. Reactogenicity was evaluated by individual interview. Nasopharyngeal colonization was evaluated before first dose and 180 days after. RESULTS: Demographic and HIV conditions were similar between all groups. Significant increase in IgG-antibodies was observed to all serotypes evaluated. A greater proportion of individuals who reached and sustained IgG antibody concentrations at least four times as high as those at baseline, for serotypes 6B and 9V received PC7V at first vaccination. A pneumococcal polysaccharide vaccine 23-valent dose after 7-valent pneumococcal conjugate vaccine did not enhance immunogenicity. Both vaccines were well tolerated across vaccine groups; however, more systemic adverse events were reported after 7-valent pneumococcal conjugate vaccine despite none severe events were described. Pneumococcal polysaccharide vaccine 23- valent after 7-valent pneumococcal conjugate vaccine did not increased reactogenicity. Nasopharyngeal colonization of S. pneumoniae 180 days after vaccination was statistically significant lower than pre-vaccination, although none difference was been observed between three groups. CONCLUSIONS: In this clinical trial conducted in Brazilian HIV-infected adults, both pneumococcal polysaccharide vaccine 23-valent and 7-valent pneumococcal conjugate vaccine were safe and immunogenic. Evidence suggesting 7-valent pneumococcal conjugate vaccine was more immunogenic than pneumococcal polysaccharide vaccine 23-valent, as it elicited higher and persistent >=4-fold increase of antibodies for serotypes 6B and 9V in a greater proportion of HIV-patients, is noteworthy. No benefit of a pneumococcal polysaccharide vaccine 23-valent dose following 7-valent pneumococcal conjugate vaccine was observed. Pneumococcal vaccination reduced nasopharyngeal colonization of S.pneumoniae in this population, without statistical difference between groups

INTRODUÇÃO: Pacientes infectados pelo HIV apresentam maior risco de doença pneumocócica invasiva com maior mortalidade que a população geral. Estratégias para redução da carga de doença pneumocócica são importantes. A vacina antipneumocócica polissacarídica 23-valente é recomendada para adultos infectados pelo HIV, entretanto, a imunogenicidade desta vacina nessa população ainda é discutível. A vacina antipneumocócica ideal e o regime vacinal de maior eficácia ainda são controversos na literatura. Os poucos estudos publicados com vacina antipneumocócica conjugada 7-valente em adultos infectados pelo HIV apresentam resultados discrepantes. Esse estudo visa comparar a resposta de anticorpos e a reatogenicidade de três esquemas diferentes de vacina antipneumocócica, em adultos infectados pelo HIV; e avaliar o impacto da vacinação no estado de colonização da nasofaringe. MÉTODOS: ensaio clínico randomizado e duplo-cego, envolvendo 331 pacientes infectados pelo HIV, de 18 a 60 anos de idade, com contagem de linfócitos T-CD4 acima de 200 cél/mm3. Os pacientes foram alocados em grupos de duas intervenções com intervalos de 60 dias entre elas: a) vacina antipneumocócica polissacarídica 23-valente + placebo; b) vacina antipneumocócica conjugada 7-valente + placebo; c) vacina antipneumocócica conjugada 7-valente + vacina antipneumocócica polissacarídica 23-valente. A imunogenicidade das vacinas foi determinada através da reação de ELISA para sorotipos 6B, 9V e 14, realizadas no momento pré-vacinal, 60 dias e 180 dias após a primeira intervenção. A reatogenicidade foi avaliada através de entrevista após cada vacinação. A colonização da nasofaringe foi avaliada antes do início da vacinação e 180 dias após. RESULTADOS: Os grupos foram similares nas características demográficas e condições associadas à infecção pelo HIV. Nos três grupos foi observado um aumento significativo dos níveis de anticorpo-IgG para todos os três sorotipos avaliados. Foi observada uma maior proporção de indivíduos que sustentaram aumento de quatro vezes ou mais na concentração de anticorpos para sorotipos 6B e 9V nos grupos que receberam PC7V na primeira vacinação. A combinação das vacinas conjugada 7-valente seguida da vacina polissacarídica 23-valente não aumentou a imunogenicidade para nenhum dos sorotipos avaliados. Ambas as vacinas foram bem toleradas, entretanto, eventos adversos sistêmicos foram mais frequentes após aplicação da vacina conjugada 7-valente. Nenhum evento grave foi reportado. O uso da vacina polissacarídica 23- valente após a aplicação da vacina conjugada 7-valente não aumentou a reatogenicidade. A colonização da nasofaringe por S.pneumoniae foi significantemente menor 180 dias após a vacinação, embora não tenha sido observada diferença entre os três grupos. CONCLUSÃO: nesse ensaio clínico conduzido em adultos brasileiros infectados pelo HIV, observamos que as vacinas antipneumocócicas polissacarídica 23-valente e conjugada 7- valente foram seguras e imunogênicas. As evidências sugerem que a vacina conjugada 7-valente foi mais imunogênica que a polissacarídica 23-valente para os sorotipos 6B e 9V. Não houve benefício da aplicação da vacina antipneumocócica polissacarídica 23-valente após vacina conjugada 7- valente. A vacinação antipneumocócica reduziu a colonização da nasofaringe por S.pneumoniae, independentemente do esquema vacinal aplicado / BACKGROUND: The risk and the mortality of invasive pneumococcal disease are higher in HIV-infected patients than in uninfected individuals. Strategy to reduce the burden of invasive pneumococcal disease is crucial. Pneumococcal polysaccharide vaccine 23-valent is recommended for HIV- adults, but its immunogenicity is still controversial. The ideal antipneumococcal vaccine and effective vaccination regimen remain controversial. Few trials with 7-valent pneumococcal conjugate vaccine in HIV-adults revealed disparate results. This study aims to compare antibody response and reactogenicity to three different pneumococcal vaccine schedules in HIV-infected adults, and impact of vaccine in nasopharyngeal carriage of Streptococcus pneumoniae. METHODS: a randomized, blinded clinical trial was conducted in Brazil with 331 HIV-patients aged 18 to 60 years with CD4+ T-lymphocytes count >=200 cells/mm3. Two interventions 60 days apart were done in three schedules: a) 23-valent pneumococcal polysaccharide vaccine + placebo; b) 7-valent pneumococcal conjugate vaccine + placebo; and c) 7-valent pneumococcal conjugate vaccine + pneumococcal polysaccharide vaccine 23-valent. Immunogenicity was assessed by an IgG enzyme-linked immunosorbent assay to S. pneumoniae serotypes 6B, 9V and 14, performed at baseline, 60 and 180 days after first intervention. Reactogenicity was evaluated by individual interview. Nasopharyngeal colonization was evaluated before first dose and 180 days after. RESULTS: Demographic and HIV conditions were similar between all groups. Significant increase in IgG-antibodies was observed to all serotypes evaluated. A greater proportion of individuals who reached and sustained IgG antibody concentrations at least four times as high as those at baseline, for serotypes 6B and 9V received PC7V at first vaccination. A pneumococcal polysaccharide vaccine 23-valent dose after 7-valent pneumococcal conjugate vaccine did not enhance immunogenicity. Both vaccines were well tolerated across vaccine groups; however, more systemic adverse events were reported after 7-valent pneumococcal conjugate vaccine despite none severe events were described. Pneumococcal polysaccharide vaccine 23- valent after 7-valent pneumococcal conjugate vaccine did not increased reactogenicity. Nasopharyngeal colonization of S. pneumoniae 180 days after vaccination was statistically significant lower than pre-vaccination, although none difference was been observed between three groups. CONCLUSIONS: In this clinical trial conducted in Brazilian HIV-infected adults, both pneumococcal polysaccharide vaccine 23-valent and 7-valent pneumococcal conjugate vaccine were safe and immunogenic. Evidence suggesting 7-valent pneumococcal conjugate vaccine was more immunogenic than pneumococcal polysaccharide vaccine 23-valent, as it elicited higher and persistent >=4-fold increase of antibodies for serotypes 6B and 9V in a greater proportion of HIV-patients, is noteworthy. No benefit of a pneumococcal polysaccharide vaccine 23-valent dose following 7-valent pneumococcal conjugate vaccine was observed. Pneumococcal vaccination reduced nasopharyngeal colonization of S.pneumoniae in this population, without statistical difference between groups

No description available.

More human lives have been lost to tuberculosis than to any other disease and despite the availability of effective short course chemotherapy (DOTS) as well as the Bacilli Calmette Guerin (BCG) vaccine, tuberculosis continues to claim more than a million lives annually. Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis, is one of the most successful and scientifically challenging pathogens of all time. However in the last two decades, the ability to perform molecular genetic analysis of M. tuberculosis has resulted in powerful new research tools, while the availability of the complete genome sequence has provided us with a wealth of new information and understanding of the biology of this major pathogen. One of the major challenges, however, is to analyze the properties and functions of those genes that are unique to M. tuberculosis genome. The identification and characterization of such genes which impart various survival strategies employed by M. tuberculosis for successful infection will be of particular significance. One of the important outcomes from the complete genome sequence of M. tuberculosis is the discovery of two multigene families designated PE (99 members) and PPE (69 members) named respectively for the Pro-Glu (PE) and Pro-Pro-Glu (PPE) motifs near the N-terminus of their gene products. In addition to these motifs, proteins of the PE family possess highly homologous N-terminal domains of approximately 100 amino acids (PE domain), whereas the PPE proteins possess a highly homologous N-terminal domain of about 180 amino acids (PPE domain). Although the PE and PPE families of mycobacterial proteins are the focus of intense research, no precise function has so far been unraveled for any member of these families. The current study focuses on Rv3097c gene of M. tuberculosis, a PE family gene that was bioinformatically predicted to be a triacylglycerol hydrolase (lipase). In order to decipher the role of the PE domain, we have carried out functional characterization of the Rv3097c gene (also named lipY) as it was, initially, the only known PE protein for which an enzymatic function (i.e. lipase activity) had been predicted. Further, to understand the function of PE family proteins, an important question that needs to be answered is; whether the PE domain of different PE family proteins has similar or different functions? In this context, our studies were focused on studying the functional role of the PE domain in LipY, as outlined below. In general, the in vivo function and subcellular localization of any protein are integrally connected. PE domain has been reported to be essential for cell wall localization of PE_PGRS33, another PE family protein. Therefore we investigated the subcellular localization of LipY and the influence of the PE domain on subcellular localization of LipY. LipY and a truncated form of LipY lacking the PE domain [LipY(ΔPE)] were expressed in mycobacteria(M. smegmatis and M. bovis BCG). Subcellular fractionation and western blot demonstrated that both LipY and LipY(ΔPE) were predominantly detected in the cell wall fraction, indicating that LipY is localized to the cell wall and the PE domain of LipY was not required for translocation of LipY to cell wall. This result is in contrast to the findings for PE_PGRS33, where the absence of the PE domain caused the cell wall associated protein to localize to the cytosol. Furthermore, immuno-electron microscopy of M. bovis BCG expressing LipY(ΔPE) clearly showed a cell surface localization of LipY(ΔPE). These results signify that the function of the PE domain might not always be similar amongst different PE family proteins. In order to further investigate the role of the PE domain in LipY, we studied the lipase activity of LipY and the influence of the PE domain on lipase activity. Bioinformatic analysis confirmed the presence of a lipase domain containing a GDSAG active site motif characteristic of lipases. Overexpression of LipY in mycobacteria (M. smegmatis and M. bovis BCG) resulted in a significant reduction in the pool of triacylglycerols (TAG), consistent with the lipase activity of this enzyme. Interestingly, this reduction was more pronounced in mycobacteria overexpressing LipY(ΔPE), suggesting that the presence of the PE domain diminishes the lipase activity of LipY. In vitro lipase assays also confirmed LipY(ΔPE) as a more efficient lipase compared to the wild-type LipY. Together these results suggest that the PE domain of LipY might be involved in the modulation of lipase activity. Surprisingly, M. marinum, another pathogenic mycobacteria, possesses a protein homologous to LipY, termed LipYmar, in which the PE domain is substituted by a PPE domain. The overexpression of LipYmar in M. smegmatis significantly reduced the TAG pool suggesting that it is a triacylglycerol hydrolase/lipase. Interestingly, similar to the removal of the PE domain of LipY, this reduction in the TAG pool was further pronounced when the PPE domain of LipYmar was removed. This suggests that PE and PPE domains might share similar functional roles in modulating the enzymatic activities of these lipase homologs. In order to assess the in vivo relevance of LipY expression during M. tuberculosis infection, we examined the humoral immune responses against LipY in sera derived from various clinical categories of tuberculosis patients. The presence of specific antibodies against any protein is suggestive of expression of the protein during infection and could potentially be used to differentiate between healthy individuals and infected patients (serodiagnosis of tuberculosis). The cell wall localization suggested that LipY may be accessible for interaction with the host immune system during infection. Moreover, humoral responses were observed against LipY in mice immunized with DNA constructs expressing LipY, indicating that LipY could be an effective B-cell antigen. Accordingly, a strong humoral response against LipY and LipY(ΔPE) was observed in tuberculosis patients compared to healthy individuals, suggesting that LipY is expressed during infection by clinical strains of M. tuberculosis and might represent an immunodominant antigen of M. tuberculosis with potential use in serodiagnosis of tuberculosis.

Des données complexes sont fréquentes dans les essais cliniques récents et nécessitent des méthodes statistiques adaptées. La recherche vaccinale du VIH est un exemple d’un domaine avec des données complexes et une absence de critères de jugement validés dans les essais précoces. Cette thèse d’Université concerne des recherches méthodologiques sur la conception et les aspects statistiques des essais cliniques vaccinaux du VIH, en particulier sur les critères de jugement d’immunogénicité et les schémas d’essai de phase I-II. A l’aide des données cytokiniques multiplex, nous illustrons les aspects méthodologiques spécifiques à une technique de mesure. Nous proposons ensuite des définitions de critères de jugement et des méthodes statistiques adéquates pour l'analyse des données d'immunogénicité multidimensionnelles. En particulier, nous montrons l’intérêt des scores multivariés non-paramétriques, permettant de résumer l’information à travers différents marqueurs d’immunogénicité et de faire des comparaisons inter- et intra-groupe. Dans l’objectif de contribuer à la conception méthodologique des nouveaux essais vaccinaux, nous présentons la construction d’un schéma d’essai optimisé pour le développement clinique précoce. En imbriquant les phases I et II d’évaluation clinique, ce schéma permet d’accélerer le développement de plusieurs stratégies vaccinales en parallèle. L’intégration d’une règle d’arrêt est proposée dans des perspectives fréquentistes et Bayesiennes. Les méthodes mises en avant dans cette thèse sont transposables à d’autres domaines d’application avec des données complexes, telle que les données d’imagerie ou les essais d’autres immunothérapies. / Complex data are frequently recored in recent clinical trials and require the use of appropriate statistical methods. HIV vaccine research is an example of a domaine with complex data and a lack of validated endpoints for early-stage clinical trials. This thesis concerns methodological research with regards to the design and analysis aspects of HIV vaccine trials, in particular the definition of immunogenicity endpoints and phase I-II trial designs. Using cytokine multiplex data, we illustrate the methodological aspects specific to a given assay technique. We then propose endpoint definitions and statistical methods appropriate for the analysis of multidimensional immunogenicity data. We show in particular the value of non-parametric multivariate scores, which allow for summarizing information across different immunogenicity markers and for making statistical comparisons between and within groups. In the aim of contributing to the design of new vaccine trials, we present the construction of an optimized early-stage HIV vaccine design. Combining phase I and II assessments, the proposed design allows for accelerating the clinical development of several vaccine strategies in parallel. The integration of a stopping rule is proposed from both a frequentist and a Bayesian perspective. The methods advocated in this thesis are transposable to other research domains with complex data, such as imaging data or trials of other immune therapies.

L'obésité est un facteur de risque majeur de cancer. Il est connu qu’une adiposité élevée prédispose à un stress inflammatoire accru et potentialise la croissance tumorale. Néanmoins, les mécanismes restent mal définis. De façon intéressante, la sénescence cellulaire, ou le programme moléculaire causant l’arrêt du cycle cellulaire suite à un stress insurmontable, favorise l'inflammation chronique et délétère pendant l'obésité. Nous avons donc émis l’hypothèse que l'obésité puisse être un inducteur de sénescence protumoral qu’il est possible d’exploiter, via une stratégie sénolytique, pour ralentir ou même bloquer le développement de tumeurs. Grâce à des marquages de coupes histologiques de tumeurs métastatiques, nous avons montré que les masses malignes de patients ayant un indice de masse corporelle (IMC)>35 sont associées à des marqueurs de sénescence. Cette découverte suggère une charge élevée de cellules sénescentes chez ses patients. Alors que la sénolyse, ou l’élimination thérapeutique des cellules sénescentes, s'est révélée très prometteuse dans le traitement de plusieurs maladies liées à l'âge, son efficacité en tant que traitement du cancer est souvent mitigé et dépend des antécédents du patient. Dans notre étude, nous avons utilisé un modèle murin d'obésité induit par la diète combinée avec un modèle d’injections syngéniques de différentes lignées cancéreuses occasionnant des réponses immunogéniques faibles, légères ou hautes. Chez les souris sur une diète riche en gras, nous avons identifié des cellules cancéreuses sénescentes spécifiquement dans les tumeurs faiblement immunogènes, soit faiblement reconnue par le système immunitaire et donc difficile à traiter. Un traitement sénolytique avec l'inhibiteur de la famille BCL-2 ABT-263 abolit la réponse protumorale observée via l'ablation des cellules cancéreuses sénescentes. Ainsi, nous proposons que les thérapies combinatoires avec des agents sénolytiques devraient être envisagées pour traiter les patients cancéreux présentant une adiposité accrue. De plus, dans la même cohorte de patients où nous avons rapporté des marqueurs de sénescence dans les tissus malins, les patients obèses ont aussi montré une expression importante de Toll-like receptor 4 (TLR4). Nous avons donc émis l’hypothèse que le récepteur TLR4 joue un rôle important dans l’établissement d’un microenvironnement tumoral qui favorise la sénescence cellulaire et la croissance tumorale de souris en surplus de poids. Dans notre étude, nous rapportons que l'expression systémique de TLR4 est importante pour la croissance tumorale induite par l'obésité. Nous montrons également que l’induction d’un stress du réticulum endoplasmique médié par Inositol requiring enzyme 1a (IRE1ɑ) dans les cellules myéloïdes associées à une tumeur, favorise la sénescence des cellules cancéreuses, dans un contexte de faible immunogénicité, via TLR4. Ce travail établit les fondements d’une compréhension moléculaire du lien entre les régimes à forte teneur calorique et l'immunité protumorale. / Obesity is a major risk factor for cancer. High adiposity predisposes to increased inflammatory stress, which potentiates tumor growth. However, the mechanisms remain poorly defined. Interestingly, cellular senescence, or the molecular program causing cell cycle arrest following insurmountable stress, is known to promote chronic and deleterious inflammation during obesity. We therefore hypothesized that obesity could be an inducer of a protumoral senescence that can be exploited, via a senolytic strategy, to slow down or even block tumor development. Through histological sections of metastatic tumor, we show that malignant masses from patients with a body mass index (BMI)>35 are associated with markers of senescence, suggesting a high burden of senescent cells in these patients. While senolysis, or the therapeutic elimination of senescent cells, has shown great promises in the treatment of several age-related diseases, its efficacy as a treatment for cancer is often elusive and depends on patients’ history. In our study, we used a mouse model of diet-induced obesity (DIO) combined with a model of syngeneic injections of different cancer cell lines causing low, mild, or high immunogenic responses. In mice under a DIO, we have identified senescent cancer cells specifically in weakly immunogenic tumors, or tumors poorly recognized by the immune system, and therefore difficult to treat. Moreover, a senolytic treatment with the BCL-2 family inhibitor ABT-263 abolishes the protumor response seen in these mice via the ablation of senescent cancer cells. Thus, combination therapies using senolytic agents should fall into consideration to treat cancer patients with increased adiposity. In addition, in the same cohort of patients where we reported markers of senescence in malignant tissues, obese patients also showed significant expression of TLR4. We therefore hypothesized that the TLR4 receptor plays an important role in establishing a tumor microenvironment that promotes cellular senescence and tumor growth in mice subjected to experimental obesity. In our second study, we report that systemic expression of TLR4 is important for obesity-induced tumor growth. Moreover, we show that the induction of an IRE1ɑ-mediated endoplasmic reticulum stress, in tumor-associated myeloid cells, promotes the senescence of cancer cells, in a context of low immunogenicity, via TLR4. This work lays the foundation for a molecular understanding of the link between high-calorie diets and protumoral immunity.

Chronisches Nierenversagen kann zu einem endgültigen Funktionsverlust der Nieren führen. Nierenersatztherapien bleiben dabei die einzigen lebensrettenden Behandlungsmaßnahmen. Der globale Bedarf an Nierenorganen übersteigt jedoch bei weitem die Anzahl verfügbarer Spenderorgane. Humane induzierte pluripotente Stammzellen (hiPSC) stellen eine vielversprechende Quelle für die Generierung funktioneller Nierenzellen dar. Die hiPSC-abgeleiteten Nierenzellen könnten zukünftig für zelluläre Ersatztherapien verwendet werden. Innerhalb dieser Arbeit sollten die aus hiPSC-abgeleiteten Nierenzellen auf ihre Immunogenität überprüft werden. Dafür wurden hiPSC-Linien, reprogrammiert aus primären Urinzellen gesunder Spender, generiert. Die hiPSC wurden daraufhin in renale Vorläuferzellen (IM-Zellen) und proximale Tubuluszellen (PT-Zellen) differenziert. Die immunphänotypische Analyse ergab eine generell verminderte Expression immun-relevanter Gene verglichen zu adulten Urinzellen. Für die Immunigenitätsbestimmung wurden die Nierenzellen jeweils mit autologen oder allogenen Zellen des peripheren Blutes (PBMCs) kokultiviert. Die IM- sowie PT-Zell-Kokulturen mit PBMC gesunder Spender sowie von Patienten mit diabetischer Nephropathie ergaben keine Proliferation autoreaktiver sowie allogener T-Zellen, im Vergleich zu primäre Urinzellen mit gleichen HLA-Merkmalen. Des Weiteren wiesen IM- und PT-Zellen aktive immunsupprimierende Eigenschaften auf. Diese konnten in langzeit-kultivierten PT-Zellen nicht mehr beobachtet werden. Zusätzlich zeigten die hiPSC-abgeleiteten Nierenzellen eine Anfälligkeit gegenüber autologe sowie allogene natürliche Killerzellen (NK-Zellen). Diese Studie ergab erstmalig Einblicke in die Dynamiken der T- und NK-Zell-Antworten renal differenzierter hiPSC. Die hier gewonnenen Erkenntnisse können für die Entwicklung zukünftiger Therapien beitragen, um eine sichere Transplantation von hiPSC-abgeleiteten Nierenzellen, selbst im allogenen System, zu ermöglichen. / Kidneys are essential for numerous vital processes. Chronic damage can lead to end stage renal disease with the requirement of kidney replacement therapies. Kidneys are nowadays the most frequently transplanted human organs, however, the transplant demand is far exceeding the number of available donations. Human induced pluripotent stem cells (hiPSC) represent a promising alternative approach for the generation of functional renal differentiated cells suitable for autologous cell replacement therapies (CRT). Yet, the immunogenic potential of hiPSC and their progenies are among the major concerns. This study aimed to analyze immunogenic effects of hiPSC-derived renal cells in autologous and allogeneic settings in vitro. Therefor, primary urinary cells (pUC) from healthy donors were reprogrammed into hiPSC, which were differentiated into renal progenitors (IMC) and into proximal tubular cells (PTC). Immune-phenotypic characterization revealed overall reduced expression of immune-relevant genes in hiPSC and renal derivatives compared to pUC. Co-culture experiments of IMC or PTC with either autologous or allogeneic peripheral blood mononuclear cells of healthy donors or patients with diabetic nephropathy revealed no induction of T cell proliferation in comparison to pUC cells with the same HLA-types. IMC and PTC showed immunomodulatory effects on allogeneic T cell proliferation. These immunosuppressive capacities were lost in long-term cultivated PTC. hiPSC-derived renal cells showed to elicit autologous as well as for allogeneic natural killer cells (NK cells). This study provided insights about the immunogenic properties of hiPSC-derived renal cells. In vitro experiments revealed new hints about the dynamics of T- and NK cell responses dependent on the differentiation status of hiPSC-derived renal cells. These data show translational potential for the development of future CRT strategies aiming safe transplantation of hiPSC-derived renal cells across HLA barriers.