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Identification des peptides du complexe majeur d’histocompatibilité de classe I par spectrométrie de masseBramoullé, Alexandre 12 1900 (has links)
L’immunité adaptive et la discrimination entre le soi et le non-soi chez les vertébrés à mâchoire reposent sur la présentation de peptides par les récepteurs d’histocompatibilité majeur de classe I. Les peptides antigéniques, présentés par les molécules du complexe d’histocompatibilité (CMH), sont scrutés par les lymphocytes T CD8 pour une réponse immunitaire appropriée. Le répertoire des peptides du CMH de classe I, aussi appelé immunopeptidome, est généré par la dégradation protéosomale des protéines endogènes, et a un rôle essentiel dans la régulation de l’immunité cellulaire. La composition de l’immunopeptidome dépend du type de cellule et peut présenter des caractéristiques liées à des maladies comme le cancer. Les peptides antigéniques peuvent être utilisés à des fins immunothérapeutiques notamment dans le traitement voire la prévention de certains cancers. La spectrométrie de masse est un outil de choix pour l’identification, le séquençage et la caractérisation de ces peptides. Cependant, la composition en acides aminés, la faible abondance et la diversité de ces peptides compliquent leur détection et leur séquençage. Nous avons développé un programme appelé StatPeaks qui permet de calculer un certains nombres de statistiques relatives à la fragmentation des peptides. À l’aide de ce programme, nous montrons sans équivoque que les peptides du CMH classe I, en mode de fragmentation par dissociation induite par collision (CID), fragmentent très différemment des peptides trypsiques communément utilisés en protéomique. Néanmoins, la fragmentation par décomposition induite par collision à plus haute énergie (HCD) proposée par le spectromètre LTQ-Orbitrap Velos améliore la fragmentation et fournit une haute résolution qui permet d’obtenir une meilleure confiance dans l’identification des peptides du CMH de classe I. Cet avantage permet d’effectuer le séquençage de novo pour identifier les variants polymorphes qui ne sont normalement pas identifiés par les recherches utilisant des bases de données. La comparaison des programmes de séquençage Lutefisk, pepNovo, pNovo, Vonode et Peaks met en évidence que le dernier permet d’identifier un plus grand nombre de peptides du CMH de classe I. Ce programme est intégré dans une chaîne de traitement de recherche d’antigènes mineurs d’histocompatibilité. Enfin, une base de données contenant les informations spectrales de plusieurs centaines de peptides du CMH de classe I accessible par Internet a été développée. / Adaptive immunity and discrimination between self and nonself in jawed vertebrates relies on the presentation of peptides by the major histocompatibility (MHC) class I receptors. Foreign or self peptide antigens presented by the MHC molecules are probed by CD8 T-cell lymphocyte for proper immune response. The repertoire of MHC I peptides collectively referred to as the immunopeptidome is generated through the proteasomal degradation of endogenous proteins and plays an important role in the regulation of cellular immunity. The composition of the immunopeptidome is cell specific and can harbor important hallmark of human diseases including cancer. Antigenic peptides can also be used in immunotherapy to mount an appropriate immune response against cancer cells displaying these peptides. Mass spectrometry is a tool of choice for the identification, sequencing and characterization of these peptides. However, the amino acid composition, the low abundance and diversity of these peptides make their detection and sequencing more challenging. We developed a software, called StatPeaks, that calculates statistics relative to the fragmentation of peptides. Using this software, we demonstrate that under collision induced dissociation (CID) MHC class I peptides fragment in a very different fashion than tryptic peptides, commonly used in proteomics. However, the higher-energy collisional dissociation (HCD) mode available on the LTQ-Orbitrap Velos enhances peptide fragmentation and provides high resolution fragment information that significantly improves the confidence in MHC class I peptide identification. This inherent advantage confers the ability to perform de novo sequencing to identify polymorphic variants that would normally elude conventional database searches. The comparison of de novo peptide sequencing software Lutefisk, pepNovo, pNovo, Vonode and Peaks indicated that the later software enabled higher rates of correct identification for MHC class I peptides. This software was integrated into a data analysis pipeline for the identification minor histocompatibility antigens (MiHAs). A web-based library that stores spectral information of hundreds of synthetic MHC class I peptides was developed in support to the needs of the immunopeptidome discovery program.
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L’immunoprotéasome : producteur de peptides-CMH I et régulateur de l’expression géniquede Verteuil, Danielle Angeline 01 1900 (has links)
Le système ubiquitine-protéasome est le principal mécanisme par lequel les protéines intracellulaires sont dégradées. Le protéasome dit constitutif (PC) est donc essentiel à l’homéostasie mais aussi à la régulation de la majorité des processus cellulaires importants. La découverte d’un deuxième type de protéasome, appelé immunoprotéasome (IP), soulève toutefois de nouvelles questions. Pourquoi existe-t-il plus d’un type de protéasome ? L’IP a-t-il des rôles redondants ou complémentaires avec le PC ? L’IP étant présent principalement dans les cellules immunitaires ou stimulées par des cytokines, plusieurs groupes ont tenté de définir son rôle dans la réponse immunitaire. Or, l’implication de son homologue constitutif dans un éventail de processus non spécifiquement immunitaires nous laisse croire que l’IP pourrait lui aussi avoir un impact beaucoup plus large. L’objectif de cette thèse était donc de caractériser certains rôles cellulaires de l’IP dans les cellules dendritiques. Nous avons d’abord étudié l’impact global de l’IP sur la présentation antigénique de classe I. Ce faisant, nous avons pu déterminer ses deux contributions principales, soit l’augmentation drastique du nombre et de la diversité des peptides présentés sur les complexes majeurs d’histocompatibilité de classe I. Les différences de clivage entre le PC et l’IP pourraient expliquer en partie cette diversité du répertoire peptidique, notamment par l’affinité apparente de l’IP pour les régions protéiques non structurées. Dans un deuxième temps, nous avons dévoilé un nouveau rôle de l’IP sur un processus dépassant le cadre immunitaire : la transcription. Nous avons découvert que l’IP modifie l’abondance des ARNm en agissant principalement au niveau de leur synthèse. L’impact de l’IP sur le transcriptome est majeur et serait dû en partie à une dégradation différente de facteurs de transcription des familles IRF, STAT et NF-kB. Les cellules dendritiques IP-déficientes activent moins efficacement les lymphocytes T CD8+ et nous croyons que cette défaillance est causée (du moins en partie) par la perturbation transcriptomique provoquée par l’absence d’IP. Il importe donc de comprendre les différents rôles moléculaires de l’IP afin de mieux définir sa contribution globale au fonctionnement de la cellule et comprendre l’avantage évolutif, au niveau de l’organisme, procuré par une telle plasticité du système ubiquitine-protéasome. / The ubiquitin-proteasome system is the major mechanism by which intracellular proteins get degraded. Constitutive proteasomes (CPs) are thus essential for cellular homeostasis but also to regulate the majority of important cellular processes. However, the discovery of a second type of proteasome, named immunoproteasome (IP), raises new questions. Why are there more than one type of proteasome? Does the IP perform redundant or complementary roles with the CP? The IP is predominantly expressed in immune or cytokine-stimulated cells and several groups worked at defining its role during the immune response. Yet, the implication of its constitutive homolog in a variety of processes suggests that the IP may also have a much broader impact. The objective was to characterize cellular roles of the IP in dendritic cells. We first studied the global impact of the IP on class I antigen presentation. We discovered that the IP drastically increases the number and the diversity of peptide presented by class I major histocompatibility complexes. Cleavage differences between the CP and the IP are likely part of the explanation for this peptide repertoire diversity, notably due to IP’s apparent affinity for unstructured protein regions. Second, we discovered a new role for the IP in a process unrestricted to the immune system: transcription. We found that the IP affects transcript abundance mostly at the level of mRNA synthesis. The impact of IPs on the transcriptome is major and would be partly based on a different degradation of IRF, STAT and NF-kB transcription factor family members by the two types of proteasomes. IP-deficient dendritic cells are less potent activators of CD8+ T cells and we believe that this defect is at least partly caused by the transcriptome alterations induced by the absence of IPs. It is therefore important to understand the different molecular roles of the IP in order to better define its global contribution to cellular functions and to understand the evolutionary advantage, at the level of the organism, brought by such plasticity of the ubiquitin- proteasome system.
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Rôle des Pioneer Translation Products (PTPs) dans la réponse immunitaire anti-tumorale. / Role of Pioneer Translation Products (PTPs) in the immune response against cancer.Pierson, Alison 20 December 2017 (has links)
Les vaccins thérapeutiques anti-tumoraux reposent sur l’activation du système immunitaire adaptatif et sont basés sur la reconnaissance des antigènes tumoraux (AT) par les lymphocytes T auxiliaires et cytotoxiques spécifiques. Leur efficacité nécessite une sélection méticuleuse des antigènes cibles ainsi qu’une présentation antigéniques par le CMH de classe I (CMH-I) dans les tumeurs non modifiée. Alors que l’attention s’est d’abord portées uniquement sur les AT dérivés de séquences exoniques, ceux dérivés d’évènements de traduction alternatifs ont été montrés comme ayant un fort potentiel en tant que cibles. Ces derniers peuvent dérivés d’une traduction de séquences dîtes « non traduites », initiée par des codons alternatifs ou dans un cadre de lecture non canonique. Une telle traduction alternative des ARN épissés dans le noyau et donnant naissance aux Pioneer Translation Products (PTPs) a été décrite. Ces derniers ont été montrés comme source de peptides pour la voie de présentation des antigènes par le CMH-I. Récemment, nous avons montré que les antigènes dérivés des PTPs et présentés par les tumeurs sont capables d’entrainer une réponse lymphocytaire T cytotoxique in vivo et de contrôler la croissance tumorale. Lors de ma thèse, nous avons identifié la molécule inhibitrice de l’épissage isoginkgetin comme modulateur positif de cette présentation dans les cellules cancéreuses. De plus, nous avons observé qu’un de ses dérivées, l’IP2, qui est soluble dans l’eau et moins toxique que l’isoginkgetin, est de même capable d’augmenter la présentation des antigènes dérivés des PTPs dans les tumeurs in vitro, ainsi que de réduire la croissance tumorale in vivo de manière dépendante de la réponse immunitaire. Ainsi, le composé IP2 se révèle être un immunomodulateur de la réponse anti-tumorale efficace et prometteur pour le développement de nouvelles stratégies thérapeutiques. / Anti-tumoral therapeutic vaccines rely on the activation of the adaptative immune system and are based on the recognition of tumor antigens (TA) by specific helper and cytotoxic T lymphocytes (CTL). Their efficacy requires a careful selection of the targeted antigens as well as an unaltered MHC class I (MHC-I) antigenic presentation in tumors. While the focus was first put on exome-derived TA, evidences highlighted the ones derived from alternative translations as having a high potential as T-cells targets. These can be derived from translation of allegedly non coding sequences, initiated at alternative codons or performed in non-canonical open reading frames. Such an alternative translation occurring from pre-spliced mRNAs in the nucleus has been described as giving rise to the Pioneer Translation Products (PTPs), which constitute a source of polypeptides for the MHC-I pathway. Recently, we showed that PTPs-derived antigens presented by tumors are able to elicit a CTL response in vivo that controls tumor growth. Here, we identified one positive modulator of PTPs-derived antigenic presentation in cancer cells: the splicing inhibitor isoginkgetin. Then, we provided one of its derivatives, the IP2, which is water soluble and less toxic than the isoginkgetin, and showed that IP2 treatment increases PTPs-derived antigenic presentation of cancer cells in vitro and reduces tumor growth in vivo in an immune-dependent manner. Hence we describe here the IP2 as a new efficient immunomodulator of the antitumor response, promising for the development of innovative therapeutic strategies.
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Improving anti-cancer therapies through a better identification and characterization of non-canonical MHC-I associated peptidesRuiz Cuevas, Maria Virginia 12 1900 (has links)
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
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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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La tagatose-1,6-bisphosphate aldolase et la fructose-1,6-bisphosphate aldolase de classe I : mécanisme et stéréospécificitéLow-Kam, Clotilde Jeanne M. 08 1900 (has links)
La tagatose-1,6-biphosphate aldolase de Streptococcus pyogenes est une aldolase qui fait preuve d'un remarquable manque de spécificité vis à vis de ses substrats. En effet, elle catalyse le clivage réversible du tagatose-1,6-bisphosphate (TBP), mais également du fructose-1,6-bisphosphate (FBP), du sorbose-1,6-bisphosphate et du psicose-1,6-bisphosphate, quatre stéréoisomères, en dihydroxyacétone phosphate (DHAP) et en glycéraldéhyde-3-phosphate (G3P). Aldolase de classe I, qui donc catalyse sa réaction en formant un intermédiaire covalent obligatoire, ou base de Schiff, avec son susbtrat, la TBP aldolase de S. pyogenes partage 14 % d’identité avec l’enzyme modèle de cette famille, la FBP aldolase de muscle de mammifère. Bien que le mécanime catalytique de la FBP aldolase des mammifères ait été examiné en détails et qu’il soit approprié d’en tirer des renseignements quant à celui de la TBP aldolase, le manque singulier de stéréospécificité de cette dernière tant dans le sens du clivage que celui de la condensation n’est toujours pas éclairci. Afin de mettre à jour les caractéristiques du mécanisme enzymatique, une étude structurale de la TBP aldolase de S. pyogenes, un pathogène humain extrêmement versatile, a été entreprise. Elle a permis la résolution des structures de l’enzyme native et mutée, en complexe avec des subtrats et des inhibiteurs compétitifs, à des résolutions comprises entre 1.8 Å et 2.5 Å. Le trempage des cristaux de TBP aldolase native et mutante dans une solution saturante de FBP ou TBP a en outre permis de piéger un authentique intermédiaire covalent lié à la Lys205, la lysine catalytique. La determination des profils pH de la TBP aldolase native et mutée, entreprise afin d'évaluer l’influence du pH sur la réaction de clivage du FBP et TBP et ìdentifier le(s) résidu(s) impliqué(s), en conjonction avec les données structurales apportées par la cristallographie, ont permis d’identifier sans équivoque Glu163 comme résidu responsable du clivage. En effet, le mode de liaison sensiblement différent des ligands utilisés selon la stéréochimie en leur C3 et C4 permet à Glu163, équivalent à Glu187 dans la FBP aldolase de classe I, d’abstraire le proton sur l’hydroxyle du C4 et ainsi d’amorcer le clivage du lien C3-C4. L’étude du mécanimse inverse, celui de la condensation, grâce par exemple à la structure de l’enzyme native en complexe avec ses substrats à trois carbones le DHAP et le G3P, a en outre permis d’identifier un isomérisme du substrat G3P comme possible cause de la synthèse des isomères en C4 par cette enzyme. Ce résultat, ainsi que la decouverte d’un possible isomérisme cis-trans autour du lien C2-C3 de la base de Schiff formée avec le DHAP, identifié précedemment, permet de cerner presque complètement les particularités du mécanisme de cette enzyme et d’expliquer comment elle est capable de synthétiser les quatres stéréoisomères 3(S/R), 4(S/R). De plus, la résolution de ces structures a permis de mettre en évidence trois régions très mobiles de la protéine, ce qui pourrait être relié au rôle postulé de son isozyme chez S. pyogenes dans la régulation de l’expression génétique et de la virulence de la bactérie.
Enfin, la résolution de la structure du mutant Lys229→Met de la FBP aldolase de muscle en complexe avec la forme cyclique du FBP, de même que des études cristallographiques sur le mutant équivalent Lys205→Met de la TBP aldolase de S. pyogenes et des expériences de calorimétrie ont permis d’identifier deux résidus particuliers, Ala31 et Asp33 chez la FBP aldolase, comme possible cause de la discrimination de cette enzyme contre les substrats 3(R) et 4(S), et ce par encombrement stérique des substrats cycliques.
La cristallographie par rayons X et la cinétique enzymatique ont ainsi permis d'avancer dans l'élucidation du mécanisme et des propriétés structurales de cette enzyme aux caractéristiques particulières. / Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes is a class I aldolase that shows a lack of stereospecificity that is rare in enzymes in general, and in aldolases in particular. This aldolase catalyzes the reversible cleavage of tagatose-1,6-bisphosphate (TBP), fructose-1,6-bisphosphate (FBP), sorbose-1,6-bisphosphate and psicose-1,6-bisphosphate, four stereoisomers, in dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P). A class I aldolase, the aldolase TBP S. pyogenes shares 14 % identity with the model enzyme of this family, mammalian FBP aldolase. Although the catalytic mechanism of the class I FBP aldolase has been examined in detail and it is appropriate to infer information as to the class I TBP aldolase, the singular lack of specificity of the latter enzyme both in the direction of cleavage and condensation is still not elucidated. To better comprehend the characteristics of the enzymatic mechanism, a structural study of the TBP aldolase of S. pyogenes, an extremely versatile human pathogen, has been undertaken. It has allowed the resolution of high resolution structures of the native and mutated enzyme in complex with subtrates and competitive inhibitors. These same structures allowed us to gain information as to the active site of the enzyme in general and the catalytic residues in particular. TBP aldolase native and mutated soaked in a saturated solution of FBP or TBP also trapped an iminium intermediate covalenty bound to Lys205, the Schiff base-forming lysine. The determination of the pH profiles of the native and mutated enzyme, carried out to assess the influence of pH on FBP and TBP cleavage and identify the residue(s) involved, in conjunction with the structural data provided by crystallography, identified unequivocally Glu163, corresponding to Glu187 in FBP aldolase, as the residue responsible for substrate cleavage. The substantially different binding mode of the ligands, according to the stereochemistry of their C3 and C4 carbons, indeed allows Glu163 to abstract the proton in C3-OH and thus initiate C3-C4 bond cleavage. The study of the inverse mechanism, the condensation one, using for instance the crystallographic structure of native TBP aldolase in complex with DHAP and G3P, its three carbons substrates, has led us to believe that a possible isomerism of the G3P substrate was the reason for the synthesis of both C4 isomers by this enzyme. This result, as well as the discovery of a possible cis-trans isomerism around the C2-C3 bond of the Schiff base formed with DHAP, identified previously, almost completely elucidated the features of this enzyme`s mechanism. In addition, these structures have highlighted three highly mobile regions of the protein, which may be related to the role of its isozyme in the regulation of gene expression and virulence in S. pyogenes.
Lastly, the resolution of the structure of the FBP aldolase mutant Lys229 → Met in complex with the cyclic form of FBP, as well as crystallographic studies of the corresponding mutant in TBP aldolase, Lys205→Met and ITC experiments, allowed the identification of two particular residues, Ala31 and Asp33 in FBP aldolase, as responsible for this enzyme discrimination against 3(R) 4(S) substrates, by steric hindrance of the cyclic substrates.
X-ray crystallography, enzyme kinetics and isothermal calorimetry thus enabled advances in the elucidation of the mechanism and structural properties of this enzyme with singular characteristics.
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Studies of MHC class I antigen presentation & the origins of the immunopeptidomePearson, Hillary 04 1900 (has links)
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.
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Estudo da associação entre antígenos de histocompatibilidade leucocitária (HLA) e pênfigo vulgar em pacientes brasileiros / Study of the association between HLA antigens and Pemphigus Vulgaris in brazilian patientsWeber, Raimar 09 December 2010 (has links)
INTRODUÇÃO: O Pênfigo Vulgar é uma doença bolhosa crônica que acomente pele e mucosas. A perda de adesão epitelial ocorre por agressão autoimune às desmogleínas presentes nos desmossomos, mediada por anticorpos IgG. Estudos sobre a gênese da autoimunidade no pênfigo indicam associação entre alelos do sistema HLA, especialmente dos loci DR e DQ. A população brasileira apresenta características favoráveis a estudos exploratórios em genética decorrente de sua origem mista e intensa miscigenação. PACIENTES E MÉTODO: O grupo em estudo incluiu trinta e seis pacientes não consanguíneos com diagnóstico de Pênfigo Vulgar comprovado por imunopatologia provenientes do estado de São Paulo, Brasil. Foram tipados para os loci HLA-A, HLA-B e HLA-DR utilizando-se oligonucleotídeos sequência-específica (PCR-SSO). As frequências alélicas e fenotípicas encontradas foram comparadas com as de um grupo controle composto de dados de 712 indivíduos doadores voluntários cadastrados no Registro Nacional de Doadores de Medula Óssea (REDOME) provenientes de São Paulo e tipados pelo mesmo método. O valor de P crítico foi corrigido utilizando-se o método False Discovery Rate. RESULTADOS: Os alelos HLA-DRB1*04:02, DRB1*08:04 e DRB1*14 estiveram associados à doença com riscos relativos de 44,6, 18,6 e 4,8, respectivamente (p<0,001). Não houve diferença estatisticamente significante entre as frequências de nenhum alelo dos loci HLA-A ou HLA-B entre os grupos. DISCUSSÃO: O alelo DRB1*04:02, diretamente, e o alelo DRB1*14, indiretamente por desequilíbrio de ligação com DQB1*05:03, estão associados com Pênfigo Vulgar em diversas populações ao redor do mundo, porém nenhum estudo semelhante observou associação com o alelo DRB1*08:04 em tamanha magnitude. Acreditamos que as associações encontradas em nosso estudo não sejam decorrentes de viés de estratificação populacional. É necessária, no entanto, a tipagem de loci adjascentes ao HLA-DR dos indivíduos do grupo em estudo para diferenciar se o risco à doença é inerente a estes alelos ou a algum outro nas proximidades, com o qual estariam em desequilíbrio de ligação. CONCLUSÕES: Os alelos HLA-DRB1*04:02, DRB1*08:04 e DRB1*14 estiveram associados ao Pênfigo Vulgar em pacientes brasileiros. / BACKGROUND: Pemphigus vulgaris is a chronic blistering disease affecting skin and mucous membranes. Autoimmune aggression to desmoglein in desmosomes, mediated by IgG antibodies, leads to loss of epithelial cell adhesion. Studies indicate association between some alleles of the HLA system and pemphigus vulgaris, mainly at the DR and DQ loci. Brazilian population characteristics are conducive to genetic exploratory studies because of its various origins and intense ethnically admixture. PATIENTS AND METHODS: The study group consisted of thirty-six unrelated patients with clinical and immunopathological diagnosis of pemphigus vulgaris from a tertiary hospital in Sao Paulo - Brazil. HLA allele typing at the A, B and DR loci was performed after DNA extraction using polymerase chain reaction and sequence-specific oligonucleotide probes (PCR-SSO). Allele and phenotypic frequencies were compared to those from a control group composed by 712 individuals volunteer donors registered in a national registry of bone marrow donors (REDOME) from Sao Paulo, typed using the same method. False Discovery Rate method was used to adjust level of critical P values. RESULTS: The HLADRB1* 04:02, DRB1*08:04 and DRB1*14 were associated with pemphigus vulgaris with relative risks of 44.6, 18.6 and 4.8, respectively (p <0.001). There was no significant difference between the frequencies of any allele of loci HLAA or HLA-B among the groups. DISCUSSION: The alleles DRB1*04:02 and DRB1*14 (indirectly through linkage disequilibrium with the DQB1*05:03) are associated with pemphigus vulgaris in several populations worldwide, however, no similar study reported such magnitude of association between pemphigus vulgaris and DRB1*08:04 allele. We consider that the association is not secondary to population stratification bias. HLA typing of nearby loci is required to differentiate if the association with pemphigus vulgaris is inherent to the HLA-DRB1*08:04 allele or to another gene which is in linkage disequilibrium. CONCLUSIONS: The HLA-DRB1*04:02, DRB1*08:04 and DRB1*14 were associated with pemphigus vulgaris in Brazilian patients
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Estudo da associação entre os alelos DR e DQ de antígenos de histocompatibilidade leucocitária (HLA) e pênfigo vulgar em pacientes brasileiros / Study of the association between human leukocyte antigens (HLA) - DR and DQ - and pemphigus vulgaris in Brazilian patientsGil, Julio Miranda 18 October 2016 (has links)
INTRODUÇÃO: Pênfigo Vulgar é uma doença bolhosa mucocutânea autoimune caracterizada pela formação de bolhas ou ulcerações dolorosas que afetam as superfícies cutâneas e/ou mucosas. A perda do contato célulacélula entre os queratinócitos do epitélio (acantólise) resulta na manifestação clínica do Pênfigo Vulgar. Autoanticorpos IgG se ligam às desmogleínas - anti-desmogleína 3 (Dsg3) e/ou anti-desmogleína 1 (Dsg1) -e são críticos na patogênese da doença. A predisposição genética ao PV, principalmente com alelos HLA DR e DQ, foi revelada desde a década de 80 e foi comprovada por análises genéticas e sorológicas, repetidas vezes. As características singulares da população brasileira favorecem estudos genéticos exploratórios. PACIENTES E MÉTODO: O grupo em estudo incluiu 51 pacientes com diagnóstico confirmado de Pênfigo Vulgar de um hospital terciário da cidade de São Paulo, estado de São Paulo, sudeste do Brasil. Foi realizada a extração de DNA e a tipificação de HLA A, B, C, DR e DQ por meio de kits QIagen (QIAamp DNA Mini Kit®). O grupo controle foi composto a partir de um banco de dados de 297 doadores falecidos não relacionados da cidade de São Paulo, que foram tipados pelo mesmo método. Este banco faz parte do Sistema Estadual de Transplantes da Secretaria de Saúde do Governo do Estado de São Paulo e contém a idade do paciente na coleta. O nível de significância dos testes estatísticos foi ajustado pela correção de Bonferroni, dependendo da quantidade de frequências fenotípicas avaliadas para o HLA A, HLA B, HLA C, HLA DRB1 e HLA DQB1. RESULTADOS: Os alelos HLAB* 57, HLA-C*15, HLA-DRB1*04:02, HLA-DRB1*08:04, HLA-DRB1*14:01, DQA1*03:01, DQB1*03:02 e o DQB1*05:03 estiveram associados com a susceptibilidade. Ambos os alelos HLA DRB1*04:02 e HLA-DRB1*14:01 e seus respectivos haplótipos DRB1*04-DQA1*03:01-DQB1*03:02 e DRB1*14- DQA1*01:01-DQB1*05:03 conferiram risco à doença. DISCUSSÃO: Os alelos DRB1*04:02 e DQB1*05:03 estão associados com o Pênfigo Vulgar no presente estudo, bem como a diversas populações do mundo. A associação aqui estudada com o DRB1*08:04 foi confirmada por causa deste alelo específico e não do desequilíbrio de ligação a algum gene adjacente. A associação do alelo HLA-B*57 ao pênfigo vulgar é reportada pela primeira vez pelo presente estudo. CONCLUSÕES: Os alelos HLA-B*57, HLA-C*15, HLADRB1* 04:02, HLA-DRB1*08:04, HLA-DRB1*14:01, DQA1*03:01, DQB1*03:02 e DQB1*05:03 estão associados ao Pênfigo Vulgar em pacientes brasileiros / BACKGROUND: Pemphigus vulgaris is a mucocutaneous blistering autoimune disease that manifests as painful blisters or ulcerations on the skin and/or mucosal surfaces. The loss of cell-cell adhesion among the epithelial keratinocytes (acantholisis) leads to pemphigus vulgaris clinical findings. IgG autoantibodies target desmoglein - anti-Desmoglein 3 (Dsg3) and/or 1 (Dsg1) - play a major role in the disease pathogenesis. Genetic predisposal to pemphigus vulgaris, especially the HLA DR and DQ alleles, was revealed since the 80s and has been proven through genetic and serologic analysis repeatedly. The unique constitution of the Brazilian population favours genetics exploratory studies. PATIENTS AND METHODS: The study group included fifty-one patients with confirmed diagnosis of Pemphigus Vulgaris from a tertiary hospital in Sao Paulo\'s city and state, southeast Brazil. DNA extraction and HLA A, B, C, DR and DQ typing using Qiagen kits (QIAamp DNA Mini Kit®). The control group was composed by a database of 297 unrelated deceased donors from the city of São Paulo that were typed through the same method. This database is a part of the Transplants State System of the Government\'s Health Secretary from the State of Sao Paulo. The statistical significance level was adjusted by using the Bonferroni correction depending on the phenotypic frequencies evaluated to HLA A, HLA B, HLA C, HLA DRB1 e HLA DQB1. RESULTS: The alleles HLA-B*57, HLA-C*15, HLADRB1* 04:02, HLA-DRB1*08:04, HLA-DRB1*14:01, DQA1*03:01, DQB1*03:02 and DQB1*05:03 were associated with susceptibility. Both alleles HLA DRB1*04:02 and HLA-DRB1*14:01 and their respective haplotypes DRB1*04-DQA1*03:01-DQB1*03:02 and DRB1*14-DQA1*01:01-DQB1*05:03 conferred risk to the disease. DISCUSSION: The DRB1*04:02 and DQB1*05:03 alleles are associated with Pemphigus Vulgaris in our study, as well in various populations. The association in our study with HLA-DRB1*08:04 was confirmed to be specific to this allele and not to linkage disequilibrium to any adjacent gene. The association between HLA-B*57 and pemphigus vulgaris is being reported for the first time at the present study. CONCLUSIONS: The alleles HLA-B*57, HLA-C*15, HLA-DRB1*04:02, HLADRB1* 08:04, HLA-DRB1*14:01, DQA1*03:01, DQB1*03:02 and DQB1*05:03 were associated with Pemphigus Vulgaris in Brazilian patients
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Correlações da expressão de MHC-I e II, C5b-9 e fenotipagem de células inflamatórias em tecido muscular na dermatomiosite juvenil (DMJ) / Correlations of the expression of MHC-I and II, C5b-9 and inflammatory cells phenotyping in juvenile dermatomyositis (JDM)Sallum, Adriana Maluf Elias 23 August 2005 (has links)
A presença de uma inflamação crônica no músculo, a associação com outras doenças e a presença de auto-anticorpos, sugere o envolvimento de um mecanismo autoimune na patogênese da DMJ. Trinta e sete fragmentos musculares de pacientes com o diagnóstico de DMJ foram estudados com o objetivo de avaliar a expressão de MHC classes I e II, C5b-9 e fenotipagem das células inflamatórias CD4, CD8, CD20 e CD68 em tecido muscular e correlacionar com os principais parâmetros clínicos, laboratoriais, histológicos e terapêuticos desta doença. Os achados foram comparados à expressão em oito fragmentos musculares de pacientes com polimiosite (PM), cinco de dermatomiosite (DM) e quatro de distrofia. As expressões de MHC-I, MHC-II e C5b-9 foram identificadas por imunohistoquímica, através da técnica de imunoperoxidase StreptABComplex/HRP; as células CD20 e CD68, pelo sistema LSAB+ e CD4 e CD8, pela técnica EnVision-AP. A expressão de MHC-I apresentou positividade em 97,2% dos casos, enquanto que a expressão de MHC-II foi observada em apenas 21,6% dos casos. C5b-9 (83,8% de positividade), correlacionou-se com a presença de calcinose e envolvimento cardíaco. A presença de linfócitos CD4 (81,1% de positividade), CD8 (86,5% de positividade) e CD20 (62,2 % de positividade), e CD68 (97,2% de positividade) correlacionaram-se com o grau de inflamação observada na histologia muscular. A presença de CD4 e CD68, e marcação de C5b-9 também se correlacionaram com a intensidade de fraqueza muscular, e laboratorialmente, CD4 correlacionou-se com níveis elevados de CK e CD20 com DHL. Na DMJ observou-se maior expressão de C5b-9, CD4 e CD8 e menor expressão de MHC-I e II em comparação à DM e PM. A expressão destes marcadores foi sempre menor na distrofia. A expressão de MHC-I, adjuvante ao envolvimento dos linfócitos CD4 e CD8, sugere um mecanismo inicial celular citotóxico relacionado a maior gravidade do envolvimento muscular. A concomitância da maior expressão de C5b-9 foi um fator preditivo de comprometimento sistêmico e demanda de terapêutica imunossupresssora. Os resultados deste estudo apontam para o papel do MHC-I e II, C5b-9, CD4, CD8, CD20 e CD68 na patogênese da DMJ / The presence of chronic muscle inflammation, in association with other diseases and seric autoantibodies in JDM patients, suggest the involvement of an autoimmune mechanism in the pathogenesis of this inflammatory myopathy. Thirty seven muscle biopsy specimens from patients with JDM were analyzed in order to assess the expression of MHC-I and II, C5b-9, CD4, CD8, CD20 and CD68 and to correlate with the clinical, laboratorial, histological and therapeutical parameters. These findings were compared to the expression in five dermatomyositis (DM), eight polymyositis (PM) and four dystrophy cases. Immunohistochemical reactions for MHC-I and II and C5b-9 (StreptABCcomplex/HRP), CD4, CD8 (EnVision-AP) and CD20, CD68 (LSAB+) were evaluated. MHC-I expression was positive in 97.2% of the cases, whilst MHC-II was positive in only 21.6% of the cases. C5b-9 expression (positivity of 83.8%) correlated with calcinosis and cardiac involvement. The presence of lymphocytes CD4 (positivity of 81.1%), CD8 (positivity of 86.5%), CD20 (positivity of 62.2%), and CD68 (positivity of 97.2%) correlated with inflammation in muscular histology. The presence of CD4 and CD8 and expression of C5b-9 also correlated with the severity of muscle weakness, and CD4 expression correlated with serum levels of CK and CD20 with LDH. In JDM, the expressions of C5b-9, CD4 and CD8 were statistically more significant when compared to PM and DM, while expressions of MHC-I and II were lower in JDM. All expressions were lower in dystrophy. MHC-I expression, adjuvant to the presence of CD4 and CD8 lymphocytes, corroborates the involvement of the cytotoxic cellular mechanism of muscular lesion in JDM, which correlates to severity. Concomitantly, C5b-9 expression was a predictive factor of systemic involvement and of the need for imunossupressive treatment. The results of this study indicate for the function of MHC-I and II, C5b-9, CD4, CD8, CD20 e CD68 at JDM pathogenesis
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Estudo da associação entre os alelos DR e DQ de antígenos de histocompatibilidade leucocitária (HLA) e pênfigo vulgar em pacientes brasileiros / Study of the association between human leukocyte antigens (HLA) - DR and DQ - and pemphigus vulgaris in Brazilian patientsJulio Miranda Gil 18 October 2016 (has links)
INTRODUÇÃO: Pênfigo Vulgar é uma doença bolhosa mucocutânea autoimune caracterizada pela formação de bolhas ou ulcerações dolorosas que afetam as superfícies cutâneas e/ou mucosas. A perda do contato célulacélula entre os queratinócitos do epitélio (acantólise) resulta na manifestação clínica do Pênfigo Vulgar. Autoanticorpos IgG se ligam às desmogleínas - anti-desmogleína 3 (Dsg3) e/ou anti-desmogleína 1 (Dsg1) -e são críticos na patogênese da doença. A predisposição genética ao PV, principalmente com alelos HLA DR e DQ, foi revelada desde a década de 80 e foi comprovada por análises genéticas e sorológicas, repetidas vezes. As características singulares da população brasileira favorecem estudos genéticos exploratórios. PACIENTES E MÉTODO: O grupo em estudo incluiu 51 pacientes com diagnóstico confirmado de Pênfigo Vulgar de um hospital terciário da cidade de São Paulo, estado de São Paulo, sudeste do Brasil. Foi realizada a extração de DNA e a tipificação de HLA A, B, C, DR e DQ por meio de kits QIagen (QIAamp DNA Mini Kit®). O grupo controle foi composto a partir de um banco de dados de 297 doadores falecidos não relacionados da cidade de São Paulo, que foram tipados pelo mesmo método. Este banco faz parte do Sistema Estadual de Transplantes da Secretaria de Saúde do Governo do Estado de São Paulo e contém a idade do paciente na coleta. O nível de significância dos testes estatísticos foi ajustado pela correção de Bonferroni, dependendo da quantidade de frequências fenotípicas avaliadas para o HLA A, HLA B, HLA C, HLA DRB1 e HLA DQB1. RESULTADOS: Os alelos HLAB* 57, HLA-C*15, HLA-DRB1*04:02, HLA-DRB1*08:04, HLA-DRB1*14:01, DQA1*03:01, DQB1*03:02 e o DQB1*05:03 estiveram associados com a susceptibilidade. Ambos os alelos HLA DRB1*04:02 e HLA-DRB1*14:01 e seus respectivos haplótipos DRB1*04-DQA1*03:01-DQB1*03:02 e DRB1*14- DQA1*01:01-DQB1*05:03 conferiram risco à doença. DISCUSSÃO: Os alelos DRB1*04:02 e DQB1*05:03 estão associados com o Pênfigo Vulgar no presente estudo, bem como a diversas populações do mundo. A associação aqui estudada com o DRB1*08:04 foi confirmada por causa deste alelo específico e não do desequilíbrio de ligação a algum gene adjacente. A associação do alelo HLA-B*57 ao pênfigo vulgar é reportada pela primeira vez pelo presente estudo. CONCLUSÕES: Os alelos HLA-B*57, HLA-C*15, HLADRB1* 04:02, HLA-DRB1*08:04, HLA-DRB1*14:01, DQA1*03:01, DQB1*03:02 e DQB1*05:03 estão associados ao Pênfigo Vulgar em pacientes brasileiros / BACKGROUND: Pemphigus vulgaris is a mucocutaneous blistering autoimune disease that manifests as painful blisters or ulcerations on the skin and/or mucosal surfaces. The loss of cell-cell adhesion among the epithelial keratinocytes (acantholisis) leads to pemphigus vulgaris clinical findings. IgG autoantibodies target desmoglein - anti-Desmoglein 3 (Dsg3) and/or 1 (Dsg1) - play a major role in the disease pathogenesis. Genetic predisposal to pemphigus vulgaris, especially the HLA DR and DQ alleles, was revealed since the 80s and has been proven through genetic and serologic analysis repeatedly. The unique constitution of the Brazilian population favours genetics exploratory studies. PATIENTS AND METHODS: The study group included fifty-one patients with confirmed diagnosis of Pemphigus Vulgaris from a tertiary hospital in Sao Paulo\'s city and state, southeast Brazil. DNA extraction and HLA A, B, C, DR and DQ typing using Qiagen kits (QIAamp DNA Mini Kit®). The control group was composed by a database of 297 unrelated deceased donors from the city of São Paulo that were typed through the same method. This database is a part of the Transplants State System of the Government\'s Health Secretary from the State of Sao Paulo. The statistical significance level was adjusted by using the Bonferroni correction depending on the phenotypic frequencies evaluated to HLA A, HLA B, HLA C, HLA DRB1 e HLA DQB1. RESULTS: The alleles HLA-B*57, HLA-C*15, HLADRB1* 04:02, HLA-DRB1*08:04, HLA-DRB1*14:01, DQA1*03:01, DQB1*03:02 and DQB1*05:03 were associated with susceptibility. Both alleles HLA DRB1*04:02 and HLA-DRB1*14:01 and their respective haplotypes DRB1*04-DQA1*03:01-DQB1*03:02 and DRB1*14-DQA1*01:01-DQB1*05:03 conferred risk to the disease. DISCUSSION: The DRB1*04:02 and DQB1*05:03 alleles are associated with Pemphigus Vulgaris in our study, as well in various populations. The association in our study with HLA-DRB1*08:04 was confirmed to be specific to this allele and not to linkage disequilibrium to any adjacent gene. The association between HLA-B*57 and pemphigus vulgaris is being reported for the first time at the present study. CONCLUSIONS: The alleles HLA-B*57, HLA-C*15, HLA-DRB1*04:02, HLADRB1* 08:04, HLA-DRB1*14:01, DQA1*03:01, DQB1*03:02 and DQB1*05:03 were associated with Pemphigus Vulgaris in Brazilian patients
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