O CD30 solúvel (CD30s) é uma glicoproteína transmembrana da família do fator de necrose tumoral expressa na superfície das células T. Quando este marcador é clivado ele torna-se solúvel, sendo detectado na circulação. Atualmente, o valor de CD30s pré-transplante vem sido demonstrado como um bom preditor de rejeição aguda (RA) e perda do enxerto. Poucos estudos foram realizados para sua avaliação no pós-transplante e sua correlação com sobrevida e TFG. Avaliar a eficácia da determinação dos marcadores laboratoriais CD30 solúvel (CD30s) e anticorpos reativos contra painel HLA (PRA) em seis meses, um ano e seis anos pós-transplante renal em receptores de doadores vivos, correlacionando estes marcadores com episódios de rejeição aguda, eventos infecciosos no pós-transplante, perda do enxerto e óbito do paciente transplantado. E, avaliar a correlação destes marcadores com a sobrevida do enxerto renal nestes períodos. Os pacientes estudados foram transplantados renais com doadores vivos no Hospital Federal de Bonsucesso (HFB) do Rio de Janeiro no ano de 2006 e do período de agosto de 2010 a maio de 2011, sendo uma extensão de um trabalho realizado previamente. CD30s e PRA foram analisados nas amostras coletadas no pré-transplante e com 7, 14, 21 dias, 1, 3, 6, 12 meses após o transplante e nos pacientes transplantados em 2006 amostras após 6 anos de transplante. A taxa de filtração glomerular (TFG) foi estimada utilizando MDRD e CKD-epi e 6 meses, 1 ano e 6 anos após o transplante. Os pacientes foram agrupados em 5 grupos: sem eventos, com perda do enxerto, óbito, rejeição aguda e pacientes com quadros infecciosos. Estes grupos foram avaliados com relação ao CD30s, PRA I e II e comparados dois a dois. O teste qui quadrado foi utilizado. Quando necessário aplicou-se a correção de Yates, o teste de Fisher, o teste de Kruskal-wallis. Foi considerado estatisticamente significante p<0,05. As análises foram feitas pelo programa EPI-Info (versão 3.5.3). Setenta e seis pacientes com doadores vivos foram incluídos no estudo 47 pacientes não tiveram nenhum evento (grupo 1), 7 pacientes perderam o enxerto (grupo 2), 3 pacientes faleceram (grupo 3), 11 pacientes ficaram no grupo de rejeição aguda (grupo 4) e oito pacientes tiveram infecção por CMV e herpes (grupo 5). Os pacientes do grupo de RA tiveram correlação positiva com os valores tanto de CD30s Pré-transplante (p=0,01), quanto do CD30s pós-transplante (p=0,002) e PRA I e II (p<0,001), respectivamente, quando comparados com pacientes sem eventos. A TFG tanto com MDRD e CKD-Epi não mostrou correlação com CD30s pré e pós-transplante e nem PRA I e II. A TFG com as duas fórmulas foi menor no grupo com RA comparado com o grupo sem evento após 6 anos de transplante (p=0,006). CD30s é um bom preditor de RA, assim como PRAI e II. E, também mais uma ferramenta que pode ser utilizada no acompanhamento pós-transplante Renal. A RA é um preditor isolado para diminuição de TFG no transplante.

Tolerance-based stem cell transplantation using sub-lethal conditioning is being considered for the treatment of human disease, but safety and efficacy remain to be established. In order to study these two issues, we first established that mouse bone marrow recipients treated with sub-lethal irradiation plus transient blockade of the CD40-CD154 costimulatory pathway develop permanent hematopoietic chimerism across allogeneic barriers. Our conditioning regimen of 6 Gy irradiation, a short course of anti-CD154 mAb and 25 million fully allogeneic BALB/c bone marrow cells consistently produced long-term, stable, and multilineage chimerism in C57BL/6 recipients. Furthermore, chimeric mice displayed donor-specific transplantation tolerance, as BALB/c skin allografts were permanently accepted while third-party CBA/JCr skin allografts were promptly rejected. We next determined both the safety and efficacy of this protocol by infecting chimeric mice with lymphocytic choriomeningitis virus (LCMV) either at the time of transplantation or at several time points afterwards. Infection with LCMV at the time of transplantation prevented engraftment of allogeneic, but not syngeneic, bone marrow in similarly treated mice. Surprisingly, infected allograft recipients also failed to clear the virus and died. Post-mortem study revealed hypoplastic bone marrow and spleens. Hypoplasia and death in these mice required the combination of 6 Gy irradiation, LCMV infection on the day of transplantation, and an allogeneic bone marrow transplant but did not require the presence of anti-CDl54 mAb. Allochimeric mice infected with LCMV 15 days after transplantation were able to survive and maintain their bone marrow graft, indicating that the deleterious effects of LCMV infection on host and graft survival are confined to a narrow window of time during the tolerization and transplantation process. The final section of this thesis studied the mechanisms of graft rejection and death in sublethally irradiated recipients of allogeneic bone marrow and infection with LCMV at the time of bone marrow transplantation. Infection of interferon-α/β receptor knockout mice at the time of transplantation prevented the engraftment of allogeneic bone marrow, but the mice survived. Therefore, IFN-αβ is involved in the development of marrow hypoplasia and death, whereas a second mechanism is involved in blocking the development of chimerism in these mice. Through the use of depleting mAb's and knockout mice we demonstrate that three types of recipients survived and became chimeric after being given sublethal irradiation, anti-CD154 mAb, an allogeneic bone marrow transplant and a day 0 LCMV infection: mice depleted of CD8+ T cells, CD8 knockout mice, and TCR-αβ knockout mice. Our data indicate that the mediator of bone marrow allograft destruction in LCMV-infected mice treated with costimulatory blockade is a radioresistant CD8+ NK1.1- TCRαβ+ T cell. We conclude that a non-cytopathic viral infection at the time of transplantation can prevent engraftment of allogeneic bone marrow and result in the death of sub-lethally irradiated mice treated with costimulation blockade. The abrogation of allogeneic bone marrow engraftment is mediated by a population of CD8+ NK1.1- TCRαβ+ T cells and the mediator of hypoplasia and death is viral induction of IFN-αβ.

O CD30 solúvel (CD30s) é uma glicoproteína transmembrana da família do fator de necrose tumoral expressa na superfície das células T. Quando este marcador é clivado ele torna-se solúvel, sendo detectado na circulação. Atualmente, o valor de CD30s pré-transplante vem sido demonstrado como um bom preditor de rejeição aguda (RA) e perda do enxerto. Poucos estudos foram realizados para sua avaliação no pós-transplante e sua correlação com sobrevida e TFG. Avaliar a eficácia da determinação dos marcadores laboratoriais CD30 solúvel (CD30s) e anticorpos reativos contra painel HLA (PRA) em seis meses, um ano e seis anos pós-transplante renal em receptores de doadores vivos, correlacionando estes marcadores com episódios de rejeição aguda, eventos infecciosos no pós-transplante, perda do enxerto e óbito do paciente transplantado. E, avaliar a correlação destes marcadores com a sobrevida do enxerto renal nestes períodos. Os pacientes estudados foram transplantados renais com doadores vivos no Hospital Federal de Bonsucesso (HFB) do Rio de Janeiro no ano de 2006 e do período de agosto de 2010 a maio de 2011, sendo uma extensão de um trabalho realizado previamente. CD30s e PRA foram analisados nas amostras coletadas no pré-transplante e com 7, 14, 21 dias, 1, 3, 6, 12 meses após o transplante e nos pacientes transplantados em 2006 amostras após 6 anos de transplante. A taxa de filtração glomerular (TFG) foi estimada utilizando MDRD e CKD-epi e 6 meses, 1 ano e 6 anos após o transplante. Os pacientes foram agrupados em 5 grupos: sem eventos, com perda do enxerto, óbito, rejeição aguda e pacientes com quadros infecciosos. Estes grupos foram avaliados com relação ao CD30s, PRA I e II e comparados dois a dois. O teste qui quadrado foi utilizado. Quando necessário aplicou-se a correção de Yates, o teste de Fisher, o teste de Kruskal-wallis. Foi considerado estatisticamente significante p<0,05. As análises foram feitas pelo programa EPI-Info (versão 3.5.3). Setenta e seis pacientes com doadores vivos foram incluídos no estudo 47 pacientes não tiveram nenhum evento (grupo 1), 7 pacientes perderam o enxerto (grupo 2), 3 pacientes faleceram (grupo 3), 11 pacientes ficaram no grupo de rejeição aguda (grupo 4) e oito pacientes tiveram infecção por CMV e herpes (grupo 5). Os pacientes do grupo de RA tiveram correlação positiva com os valores tanto de CD30s Pré-transplante (p=0,01), quanto do CD30s pós-transplante (p=0,002) e PRA I e II (p<0,001), respectivamente, quando comparados com pacientes sem eventos. A TFG tanto com MDRD e CKD-Epi não mostrou correlação com CD30s pré e pós-transplante e nem PRA I e II. A TFG com as duas fórmulas foi menor no grupo com RA comparado com o grupo sem evento após 6 anos de transplante (p=0,006). CD30s é um bom preditor de RA, assim como PRAI e II. E, também mais uma ferramenta que pode ser utilizada no acompanhamento pós-transplante Renal. A RA é um preditor isolado para diminuição de TFG no transplante.

Orientadores: Cármino Antonio de Souza, Jeane Eliete Laguila Visentainer / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-22T17:20:39Z (GMT). No. of bitstreams: 1 Cardozo_DanielaMaira_D.pdf: 3033896 bytes, checksum: b4696b2dc5fc0ec422091c74289aed9f (MD5) Previous issue date: 2013 / Resumo: No organismo humano, as moléculas HLA (Human Leukocyte Antigens) são proteínas expressas na superfície da maioria das células nucleadas e são codificadas por genes localizados no braço curto do cromossomo 6 na região do Complexo Principal de Histocompatibilidade (CPH). Essas proteínas são caracterizadas pelo alto grau de polimorfismo, e também faz a ligação com receptores KIR (Immunoglobulin-like Receptors), expressos nas células Natural Killer. Os receptores KIR, que reconhecem moléculas do complexo HLA de classe I, estão entre os principais receptores inibidores dos linfócitos NK. Células infectadas por vírus e células tumorais perdem ou têm diminuída a expressão de moléculas HLA de classe I e, por isso, são eliminadas pela ausência de ligação entre moléculas HLA e receptores KIR inibitórios. Atualmente, muitos estudos têm destacado a importância dos genes KIR e HLA no Transplante de Células Progenitoras Hematopoiéticas (TCPH). O TCPH é o tratamento de escolha para muitas doenças hematológicas e dependem de vários fatores incluindo o estágio da doença, o regime de condicionamento, a fonte de células, o grau de identidade HLA entre doador e receptor e o desenvolvimento da doença do enxerto contra o hospedeiro (DECH). Estudos recentes indicam que a presença de células NK alorreativas no enxerto representa um fator favorável à recuperação de pacientes, uma vez que essas células têm a capacidade de eliminar células tumorais residuais pela ausência ou diminuição da expressão de moléculas HLA e sem a indução da DECH. Também outros fatores podem estar envolvidos na resposta pós-transplante, como a presença e ausência de determinados alelos HLA e genes KIR, os quais podem estar ligados à melhor ou pior resposta pós-transplante. O primeiro ensaio investigou a associação entre HLA e a ocorrência da DECH aguda e crônica em pacientes que receberam transplante de células progenitoras hematopoiéticas HLA-idêntico, aparentados. No total, foram 176 pacientes que receberam o primeiro transplante entre 1997 e 2009. DECH aguda foi positivamente associada ao HLA-A10 (P = 0.0007), HLA-A26 (P = 0.002), B55 (P = 0.001), DRB1*15 (P = 0.0211) e DQB1*05 (P = 0.038), enquanto que HLA-B16 (P = 0.0333) foi mais frequente em pacientes sem DECH aguda. DECH crônica foi positivamente associada com HLA-A9 (P = 0.01) e A23 (P = 0.0292) e negativamente associada com HLA-A2 (P = 0.0031) e B53 (P = 0.0116). HLA-B35 (P = 0.0373), B49 (P = 0.0155) e B55 (P = 0.0024) foi alta em pacientes com DECH aguda grau 3 ou mais, do que os outros pacientes. Nos pacientes com DECH crônica extensa, HLA-A9 (P = 0.0004), A24 (P = 0.0059) e A26 (P = 0.0411) foi maior do que nos outros pacientes, enquanto HLA-A2 foi baixo (P = 0.0097). O objetivo do segundo ensaio foi avaliar as possíveis interações dos genes KIR e HLA com o curso clínico do transplante HLA compatível, aparentado e não depletado de linfócitos T, particularmente na doença do enxerto contra o hospedeiro (DECH) aguda e crônica, recaída, sobrevida global e sobrevida livre de evento. A maioria dos doadores (78%) apresentaram o haplótipo B do KIR enquanto que 22% apresentaram o haplótipo A. Dos pacientes que receberam o haplótipo A do doador, 90% tiveram DECH, aguda ou crônica, comparados com os que receberam o haplótipo B (58%) (dados não estatisticamente significantes). Não houve diferença significativa para recaída entre pacientes que receberam os haplótipo A ou B (27% vs 23%). Não houve diferença no desenvolvimento da DECH e recaída para os pacientes homozigotos (C1C1 ou C2C2) e heterozigotos (C1C2) e nem para aqueles com HLA-Bw4 presente e ausente. Também, a sobrevida global não foi diferente para os grupos de pacientes analisados. No entanto, houve forte correlação entre o grupo de pacientes heterozigotos para HLA-C (C1C2) e a incidência de DECH aguda e recaída. A SLE foi maior nos pacientes heterozigotos que não desenvolveram DECHa (p<0,0001). Resultados mostraram que as variantes de HLA podem influenciar na ocorrência de DECH em transplante alogênico, com doadores relacionados, HLA-idênticos, tanto como fatores de proteção, quanto como fatores de susceptibilidade. Ainda, a interação KIR/HLA tem impacto significante no resultado dos transplantes relacionados, HLA compatível, sem depleção de linfócitos T, influenciando na incidência de recaída e na ocorrência da DECH. Resultados mostraram que para o grupo heterozigoto (C1C2) a maioria dos pacientes não desenvolveu DECH aguda e apresentou maior SLE, sugerindo um possível efeito protetor para esse grupo / Abstract: In the human organism, the HLA (human leukocyte antigens) are proteins expressed on the surface of most nucleated cells and are encoded by genes located on the short arm of chromosome 6 in the region of the Major Histocompatibility Complex (MHC). These proteins are characterized by a high degree of polymorphism, and also make the connection with KIR (Immunoglobulin-like Receptors), expressed in Natural Killer cells. KIR receptors that recognize HLA molecules of class I are among the major inhibitory receptors of NK-cells. Virus infected cells and tumor cells have lost or diminished expression of HLA class I molecules and therefore are eliminated by the absence of binding between HLA molecules and inhibitory KIR receptors. Currently, many studies have highlighted the importance of KIR and HLA genes in Hematopoietic Stem Cell Transplantation (HSCT). HPCT is the treatment of choice for many hematological malignancies and depends on various factors including stage of disease, the conditioning regimen, the source of cells, the degree of identity between donor and recipient HLA and development of chronic graft-versus-host (GVHD). Recent studies indicate that the presence of alloreactive NK cells in the graft is a factor aiding the recovery of patients, since these cells have the ability to eliminate residual tumor cells by the absence or diminution of expression of HLA molecules and without inducing GVHD. Also other factors may be involved in response post-transplant, as the presence or absence of certain HLA genes and KIR, which can be connected to a better or worse response after transplantation. The first trial investigated the association between HLA and the occurrence of acute and chronic GVHD in patients receiving hematopoietic stem cell transplant HLA-identical related. In total, 176 patients who received a first transplant between 1997 and 2009. GVHD was positively associated with HLA-A10 (P = 0.0007), HLA-A26 (P = 0.002), B55 (P = 0.001), DRB1 * 15 (P = 0.0211) and DQB1 * 05 (P = 0.038), while that HLA-B16 (P = 0.0333) was more frequent in patients without acute GVHD. Chronic GVHD was positively associated with HLA-A9 (P = 0.01) and A23 (P = 0.0292) and negatively associated with HLA-A2 (P = 0.0031) and B53 (P = 0.0116). HLA-B35 (P = 0.0373), B49 (P = 0.0155) and B55 (P = 0.0024) was high in patients with acute GVHD grade 3 or more, than the other patients. In patients with extensive chronic GvHD, HLA-A9 (P = 0.0004), A24 (P = 0.0059) and A26 (P = 0.0411) was greater than in the other patients, whereas HLA-A2 was low (P = 0.0097). The objective of the second test was to evaluate the possible interactions of KIR and HLA genes with the clinical course of the transplant HLA compatible related and not depleted of T lymphocytes, particularly in chronic graft versus host disease (GVHD) acute and chronic relapse, survival overall and event-free survival. Most donors (78%) presented the KIR B haplotype while 22% were haplotype A. Of the patients who received the donor haplotype A, 90% had GvHD, acute or chronic, compared with those who received the haplotype B (58%) (data not statistically significant). There was no significant difference in relapse between patients who received the haplotype A or B (27% vs 23%). There was no difference in the development of GVHD and relapse for patients homozygous (C1C1 or C2C2) and heterozygous (C1C2) and not for those with HLA-Bw4 present and absent. Also, the overall survival was not different for the groups of patients studied. However, there was strong correlation between the group of patients heterozygous for HLA-C (C1C2) and the incidence of acute GVHD and relapse. The SLE was higher in patients who did not develop GVHD heterozygotes (p <0.0001). Results showed that the HLA variants may influence the occurrence of GVHD in allogeneic transplantation with related donors, HLA-identical, both as protective factors, such as susceptibility factors. Furthermore, the interaction KIR / HLA has a significant impact on the outcome of transplantation related HLA-compatible, without depletion of T cells, influencing the incidence of relapse and the occurrence of GVHD. Results showed that for the heterozygous group (C1C2) most patients did not develop acute GVHD and showed higher SLE, suggesting a possible protective effect for this group / Doutorado / Clinica Medica / Doutora em Clínica Médica

Le traitement des leucémies myéloïdes et lymphoblastiques aiguës a connu des avancées importantes dans la dernière décennie. Malgré ces progrès, le taux de rechutes reste élevé et le besoin médical est réel. Ces leucémies sont caractérisées par une expression aberrante d’antigènes qui peuvent provenir de protéines mutées, mais aussi de séquences rapportées comme non codantes. Les réponses contre ces néoantigènes tumoraux « cryptiques » demeurent non caractérisées. Afin de définir l’existence d’un répertoire varié de récepteurs des lymphocytes T (TCR) qui reconnaitraient ces néoantigènes, des cellules mononuclées du sang périphérique de patients sains sont isolées puis enrichies en cellules T CD8+ naïves. L’expansion et l’activation de ces cellules sont ensuite réalisées avec des cellules dendritiques autologues chargées avec l’antigène d’intérêt puis triées à l’aide de multimères HLA-peptides spécifiques. L’ARN des cellules avec TCR spécifiques aux antigènes spécifiques des tumeurs (TSA) leucémiques est isolé afin de réaliser un séquençage du TCR-bêta. L’expansion cellulaire a été réalisée de façon suffisante pour effectuer le séquençage des cellules identifiées comme positives par le marquage avec dextramères. Une réponse T est obtenue pour 50% des néoantigènes testés avec une réactivité montrée par ELISpot et se traduisant par une sécrétion de cytokines inflammatoires. Des lymphocytes T spécifiques aux TSA d’intérêt sont donc présents dans le sang périphérique de donneurs sains. Le séquençage de ces cellules a permis d’identifier les clonotypes pour lesquels une réponse anti-leucémique forte est possible. Il serait intéressant d’utiliser ces clonotypes spécifiques aux tumeurs cryptiques dans le développement de nouveaux traitements d’immunothérapie adoptive. / The treatment of acute myeloid and lymphoblastic leukemia has seen significant advances in the past decade. Despite this progress, the relapse rate remains high and the medical need is real. These leukemias are characterized by an aberrant expression of antigens, some from mutated proteins but also from sequences of DNA that were reported as non-coding. Responses against these “cryptic” neoantigens remains uncharacterized. In order to verify whether a diverse repertoire of T cell receptors (TCR) does recognize these neoantigens, mononuclear cells from peripheral blood of healthy patients are isolated and enriched with naive CD8+ T cells. The expansion and activation of these cells are then carried out with autologous dendritic cells loaded with the antigen of interest and then sorted using HLA-peptide specific multimers. RNA from cells with TCR specific for leukemic tumor-specific antigens (TSA) is isolated in order to perform TCR-beta sequencing. Cell expansion was sufficient to perform the sequencing of cells identified as positive by staining with dextramers. A T-cell response is obtained for 50% of the neoantigens tested with reactivity shown by ELISpot and resulting in a secretion of inflammatory cytokines. T lymphocytes specific to the TSA of interest are therefore present in the peripheral blood of healthy donors. Sequencing of these cells made it possible to identify clonotypes for which a strong anti-leukemic response can be expected. It would be interesting to use these cryptic tumor-specific clonotypes in the development of new adoptive immunotherapy treatments.

Increasing evidence of non-canonical protein translation has sparked interest in their identification and characterization for use in immunotherapy. In addition, recent studies on the repertoire of major histocompatibility complex class I (MHC-I) associated peptides (MAPs or immunopeptidome), have suggested that MAPs derived from these translations are potential targets for cancer immunotherapy. Therefore, the aim of this study was to assess the impact of these MAPs in cancer by developing methods to facilitate their identification and their validation as potential targets for immunotherapy. To facilitate the identification of non-canonical proteins, we developed Ribo-db, a proteogenomic approach that combines RNA sequencing, ribosome profiling and mass spectrometry. This approach enables the generation of specific databases aimed at including protein diversity. The use of Ribo-db to analyze diffuse large B-cell lymphoma (DLBCL) samples revealed that approximately 10% of MAPs were derived from non-canonical proteins. These proteins had distinct properties compared to those derived from canonical proteins. They had shorter lengths and lower stability, but greater efficiency in generating MAPs. Importantly, we found limited overlap between the non-canonical proteins detected in the immunopeptidome and those detected in the whole proteome suggesting the existence of two distinct non-canonical protein repertoires. Knowing that non-canonical MAPs can be effective targets for cancer immunotherapy, we developed BamQuery, a tool to assess their expression in tissues to determine whether they can be used in a vaccine. BamQuery aims to predict the probability of MHC-I presentation of each peptide in different tissues based on its RNA expression. Using BamQuery, we found that previously identified tumor antigens (TA) would be highly expressed in healthy tissues, making them poor candidates for immunotherapy. In addition, we also identified highly potential immunotherapeutic targets in DLBCL that were derived from non-canonical translations. These targets showed promising as they were poorly expressed in normal tissues but highly expressed and shared in tumor samples. Thus, BamQuery proved to be a useful tool for identifying and prioritizing potential immunotherapeutic targets. Overall, our research indicated that non-canonical regions of the genome increase the diversity of MAPs that can be recognized by T cells. Furthermore, the expression of MAPs in tissues can be used as a predictor of their presentation to MHC I to identify reliable targets for immunotherapy, for which BamQuery is an effective tool. / Les preuves de plus en plus nombreuses de la traduction des protéines non canonique ont suscité l'intérêt pour leur identification et leur caractérisation en vue de leur utilisation dans les immunothérapies. En outre, des études récentes sur le répertoire des peptides associés au complexe majeur d'histocompatibilité de classe I (CMH-I, connus sous le nom de MAPs ou immunopeptidome), ont suggéré que les MAPs dérivés de ces traductions sont des cibles potentielles pour l'immunothérapie du cancer. L'objectif de cette étude était donc d'évaluer l'impact de ces MAP dans le cancer en développant des méthodes pour faciliter leur identification et leur validation en tant que cibles potentielles pour l'immunothérapie. Afin de faciliter l'identification des protéines non canoniques, nous avons développé Ribodb, une approche protéogénomique qui combine le séquençage de l'ARN, le profilage ribosomal et la spectrométrie de masse. Cette approche permet de générer des bases de données spécifiques visant à inclure la diversité des protéines. Notre analyse avec Ribo-db d'échantillons de lymphome diffus à grandes cellules B (DLBCL) a révélé qu'environ 10% des MAP étaient dérivés de protéines non canoniques. Ces protéines avaient des propriétés distinctes par rapport à celles dérivées de protéines canoniques. Elles étaient plus courtes et avaient une stabilité plus faible, mais une plus grande efficacité dans la génération de MAPs. Fait important, nous avons constaté un chevauchement limité entre les protéines non canoniques détectées dans l'immunopeptidome et celles détectées dans le proteome entier, ce qui suggère l'existence de deux répertoires distincts de protéines non canoniques. Sachant que les MAP non canoniques peuvent être des cibles efficaces pour l'immunothérapie du cancer, nous avons développé BamQuery, un outil permettant d'évaluer leur expression dans les tissus afin de déterminer s'ils peuvent être utilisés dans un vaccin. BamQuery vise à prédire la probabilité de présentation au CMH-I de chaque MAP dans différents tissus sur la base de son expression ARN. En utilisant BamQuery, nous avons découvert que des antigènes tumoraux (TA) précédemment identifiés seraient fortement exprimés dans les tissus sains, ce qui en fait de mauvais candidats pour l'immunothérapie. En outre, nous avons également ii identifié des cibles immunothérapeutiques très potentielles dans DLBCL qui étaient dérivées de traductions non canoniques. Ces cibles se sont révélées prometteuses car elles étaient peu exprimées dans les tissus normaux mais fortement exprimées et partagées dans les échantillons tumoraux. Ainsi, BamQuery s'est avéré être un outil utile pour identifier et hiérarchiser les cibles immunothérapeutiques potentielles. Dans l'ensemble, nos recherches ont indiqué que les régions non canonique du génome augmentent la diversité des MAPs qui peuvent être reconnues par les cellules T. De plus, l'expression des MAPs dans les tissus peut être utilisée comme un prédicteur de leur présentation au CMH I afin d'identifier des cibles fiables pour l'immunothérapie, ce pour quoi BamQuery est un outil efficace.

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Streptococcus suis est un important pathogène porcin et humain, causant méningites et septicémies. Des études suggèrent que S. suis dispose de facteurs de virulence, notamment sa capsule polysaccharidique (CPS), qui lui permettent de moduler les fonctions des cellules dendritiques (DCs), situées à l’interface entre l’immunité innée et adaptative. Les difficultés à développer un vaccin efficace suggèrent aussi une altération de la voie T dépendante. L’objectif général du projet était d’évaluer l’effet de S. suis sur l’activation des cellules T CD4+ ainsi que sur la capacité de présentation antigénique des DCs. Nous avons étudié dans un modèle murin in vivo la réponse T CD4+ mémoire lors d’infections primaire et secondaire. Une faible réponse mémoire centrale a été obtenue, suggérant que la réponse adaptative générée contre S. suis est limitée. Étant donné l’importance du complexe majeur d’histocompatibilité (MHC) de classe II dans la présentation antigénique, nous avons évalué in vitro et in vivo l’expression de ces molécules chez les DCs. Une modulation de l’expression du MHC-II par S. suis a été observée. L’analyse de la transcription de gènes impliqués dans la régulation transcriptionnelle et post-transcriptionnelle du MHC-II nous permet de suggérer que S. suis régule à la baisse la synthèse de nouvelles molécules et favorise leur dégradation lysosomale. Cette stratégie, dans laquelle la CPS ne jouerait qu’un rôle partiel, permettrait à S. suis d’échapper à la réponse adaptative T dépendante. Les résultats de cette étude fourniront de nouvelles perspectives dans la compréhension de la réponse adaptative lors de l’infection par S. suis. / Streptococcus suis is an important swine and human pathogen causing meningitis and septicemia. Recent studies suggest that S. suis possesses several virulence factors, including the capsular polysaccharide, which enable this pathogen to modulate dendritic cell (DCs) functions. DCs are key immune cells that bridge innate and adaptive immunity. Moreover, the difficulties in developing an effective vaccine suggest that S. suis interferes with the T-cell dependent response. The main objective of the project was to evaluate the effect of S. suis on CD4+ T-cell activation, as well as on the antigen presentation ability of DCs. We investigated the CD4+ T-cell memory response in an in vivo mouse model. A poor central memory response was obtained following primary and secondary infections with S. suis, thus suggesting that the adaptive immune response against this pathogen is limited. The major histocompatibility complex (MHC) class II is central to the antigen presentation pathway. We thus investigated in vitro and in vivo the expression of these molecules on DCs. We observed a modulation in the expression of MHC-II by S. suis. Transcriptional analysis of genes involved in transcriptional and post-transcriptional regulation of MHC-II suggests that S. suis downregulates synthesis of MHC-II molecules and promotes their lysosomal degradation. This strategy, in which the CPS would play only a partial role, might allow S. suis to evade the T-cell dependent adaptive response. Overall, these results provide new insights into the comprehension of the adaptive immune response during the infection by S. suis.

La présentation d'antigène par les molécules d'histocompatibilité majeure de classe I (CMHI) permet au système immunitaire adaptatif de détecter et éliminer les agents pathogènes intracellulaires et des cellules anormales. La surveillance immunitaire est effectuée par les lymphocytes T CD8 qui interagissent avec le répertoire de peptides associés au CMHI présentés à la surface de toutes cellules nucléées. Les principaux gènes humains de CMHI, HLA-A et HLA-B, sont très polymorphes et par conséquent montrent des différences dans la présentation des antigènes. Nous avons étudié les différences qualitatives et quantitatives dans l'expression et la liaison peptidique de plusieurs allotypes HLA. Utilisant la technique de cytométrie de flux quantitative nous avons établi une hiérarchie d'expression pour les quatre HLA-A, B allotypes enquête. Nos résultats sont compatibles avec une corrélation inverse entre l'expression allotypique et la diversité des peptides bien que d'autres études soient nécessaires pour consolider cette hypothèse. Les origines mondiales du répertoire de peptides associés au CMHI restent une question centrale à la fois fondamentalement et dans la recherche de cibles immunothérapeutiques. Utilisant des techniques protéogénomiques, nous avons identifié et analysé 25,172 peptides CMHI isolées à partir des lymphocytes B de 18 personnes qui exprime collectivement 27 allotypes HLA-A,B. Alors que 58% des gènes ont été la source de 1-64 peptides CMHI par gène, 42% des gènes ne sont pas représentés dans l'immunopeptidome. Dans l'ensemble, l’immunopeptidome présenté par 27 allotypes HLA-A,B ne couvrent que 17% des séquences exomiques exprimées dans les cellules des sujets. Nous avons identifié plusieurs caractéristiques des transcrits et des protéines qui améliorent la production des peptides CMHI. Avec ces données, nous avons construit un modèle de régression logistique qui prédit avec une grande précision si un gène de notre ensemble de données ou à partir d'ensembles de données indépendants génèrerait des peptides CMHI. Nos résultats montrent la sélection préférentielle des peptides CMHI à partir d'un répertoire limité de produits de gènes avec des caractéristiques distinctes. L'idée que le système immunitaire peut surveiller des peptides CMHI couvrant seulement une fraction du génome codant des protéines a des implications profondes dans l'auto-immunité et l'immunologie du cancer. / Antigen presentation by major histocompatibility complex class I (MHCI) molecules allows the adaptive immune system to detect and eliminate intracellular pathogens or abnormal cells. Immune surveillance is executed by CD8 T cells that monitor the repertoire of MHCI-associated peptides (MAPs) presented at the surface of all nucleated cells. The primary human MHCI genes, HLA-A and HLA-B, are highly polymorphic and consequentially demonstrate differences in antigen presentation. We investigated qualitative and quantitative differences in expression and peptide binding. Using quantitative flow cytometry we establish clear hierarchy of expression for the four HLA-A,B allotypes investigated. Our results are consistent with an inverse correlation between expression and peptide diversity although further work is necessary to solidify this hypothesis. The global origins of the MAP repertoire remains a central question both fundamentally and in the search for immunotherapeutic targets. Using proteogenomics, we identified and analyzed 25,172 MAPs isolated from B lymphocytes of 18 individuals who collectively expressed 27 HLA-A,B allotypes. While 58% of genes were the source of 1-64 MAPs per gene, 42% of genes were not represented in the immunopeptidome. Overall, we estimate the immunopeptidome presented by 27 HLA-A,B allotypes covered only 17% of exomic sequences expressed in subjects’ cells. We identified several features of transcripts and proteins that enhance MAP production. From these data we built a logistic regression model that predicts with high accuracy whether a gene from our dataset or from independent datasets would generate MAPs. Our results show preferential selection of MAPs from a limited repertoire of gene products with distinct features. The notion that the immune system can monitor MAPs covering only a fraction of the protein coding genome has profound implications in autoimmunity and cancer immunology.

Intrdodução: As terapias com anticonvulsivantes de anel aromático (ACA) são freqüentemente associadas a reações adversas. No entanto, reações de hipersensibilidade (RH) não-imediatas (tardias) a estes fármacos são raras, imprevisíveis e geralmente relacionadas à alta morbidade e mortalidade. Foi demonstrado que estas RH aos ACA estão fortemente associadas ao Antígenio de Leucócitos Humanos (HLA)-B*1502 em pacientes chineses e ao HLA-A*3101 em caucasianos. Polimorfismos de genes do metabolismo do Citocromo P450 (CYP)2C9 foram mais associados a estas reações em pacientes orientais. Objetivo: Nosso objetivo é analisar a associação das reações de hipersensibilidade a anticonvulsivantes de anel aromático com os polimorfismos descritos e de interesse, bem como realizar a tipificação de HLA em uma população de São Paulo, Brasil. Métodos: Estudo tipo caso-controle com genotipagem dos polimorfismos de interesse por reação em cadeia da polimerase (PCR) em tempo real e tificação de HLA A, B, C, DRB, DQA, DQB por PCR seguido de deteção utilizando método LuminexR. A avaliação fenotípica se baseou em sistemas de escores padronizados, utilizando um questionário adaptado da ENDA (Rede Européia de Alergia a Medicamentos), em registros médicos e no acompanhamento clínico. O teste de contato com o medicamento suspeito foi realizado de acordo com as recomendações da ENDA, nos pacientes que apresentaram reação. Resultados: Foram estudados 506 pacientes, 65% do gênero feminino e a idade média foi de 43,6 anos. Oitenta por cento era de etnia mista. Polimorfismos de HLA-A*3101, HLA-B*1502, CYP2C9, CYP2C19 e CYP3A5 foram analisados de 55 indivíduos com reações de hipersensibilidade (RH) a antiepilépticos, de 85 tolerantes e de 366 controles sadios. Dos 55 casos foram validados como RH, 32 apresentaram Reação a Drogas com eosinofilia e sintomas sistêmicos (DRESS), 12 Síndrome de Stevens-Johnson (SSJ) e 11 exantema maculo-papular. De todos os 46 testes de contato com medicamento, 29 (63%) foram positivos, tanto em SSJ como em DRESS. Houve associação significativa entre polimorfismo de HLA-A*1502 e casos. Nenhum de nossos grupos de estudo apresentou associação positiva com polimorfismos de HLAA* 3101. Verificamos uma forte associação entre a atividade normal do CYP3A5 e indivíduos tolerantes quando comparado com casos (p = 0,0002, OR = 4,8). A tipificação de HLA demonstrou associação significante de HLA-A*31, HLA-A*74, HLA-B*35 e HLA-B*53 com reações graves aos ACA e de HLA-B*44 e HLA-C*03 com indivíduos tolerantes. Conclusão: Estes resultados sugere fortemente a existência de fatores genéticos de risco e/ou de proteção a RH a ACA em indivíduos brasileiros, mas não devem ser considerados de forma isolada. Assim, a relevância deste estudo extrapola o objetivo de estudo caso-controle e sugere um modelo como forma de prevenção primária às RH aos ACA. / Background: Antiepileptics with aromatic ring (AAR) therapies are frequently associated with adverse reactions. Nevertheless non-immediate (late) hypersensitivity reactions (HR) to these drugs are rare, unpredictable and usually related with high morbidity and mortality. A strong pharmacogenetic association has been reported in Chinese patients with these HR and Human Leukocyte Antigen (HLA)-B*1502 and with HLA- A*3101 in caucasians. Polymorphism of genes of P450 Cytocrome (CYP)2C9 has been related to these reactions in patients of oriental origin. Objective: Our aim is to analyze the association between hypersensitivity reactions due to AAR and the described polymorphisms, as well as perform the typification of HLA in a population of São Paulo, Brazil. Methods: Case-control study genotyping the polymorphisms of interest by polymerase chain reaction (PCR) real time and typifying HLA A, B, C, DRB, DQA, DQB by PCR followed by LuminexR .The phenotype evaluation was based on standardized scoring systems using an adapted ENDA (European Network of Drug Allergy) questionnaire, medical records and on the clinical follow-up in our Allergy Clinic. The patch test with the culprit drug was performed in patients who experienced HR according to the ENDA recommendations. Results: We studied 506 subjects, 65% female and mean age was 43,6 years. Eighty percent had mixed ethnicity. Polymorphisms of HLA-B*1502, HLA- A*3101, CYP2C9, CYP2C19 e CYP3A5 were studied in 55 subjects with antiepileptics HR, 85 tolerants, and 366 control subjects. Of 55 cases were validated as AHR, 32 presented Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS), 12 Stevens-Johnson Syndrome (SJS) and 11 maculopapular exanthema. Of all 46 drug patch tests, 29 (63%) were positive, in both SJS and DRESS. A significant association between polymorphism of HLA-A*1502 and cases was found. None of our study groups presented positive association with HLA-A*3101 polymorphisms. We found a strong association between the normal activity of CYP3A5 and tolerants subjects when compared to HR (p=0.0002, OR=4.8). The HLA typification showed a significant association between HLA-A*31, HLA-A*74, HLAB* 35 e HLA-B*53 and severe AAR reactions and HLA-B*44 and HLA-C*03 in tolerants subjects. Conclusion: These results strongly suggests the existence of genetic risk and/or protective factors to the development of HR to AAR AAR in Brazilian subjects, but it should not be considered in a isolated manner. So, the relevance of this study extrapolates the aim of a case-control study and suggests a system of primary prevention to HR due to AAR