Dans les dernières années, une explosion de la recherche sur les ARN a eu lieue à cause de nombreuses découvertes démontrant l’importance de l’ARN dans plusieurs processus biologiques. Ainsi, de grandes quantités d’ARN sont devenues indispensables au bon déroulement de plusieurs études, notamment pour la biologie structurale et la caractérisation fonctionnelle. Cependant, il existe encore peu de méthodes de purification simples, efficaces, fiables et produisant un ARN sous forme native. Dans les dernières années, le laboratoire Legault a mis au point une méthode de purification par affinité utilisant une étiquette ARiBo pour la purification d’ARN transcrits in vitro par la polymérase à ARN du phage T7. Cette méthode de purification d’ARN a été spécifiquement développée pour maximiser la pureté et le rendement. De plus, elle est très rapide et fonctionne avec plusieurs types d’ARN. Cependant, comme plusieurs autres méthodes de purification, cette méthode produit des ARN avec des extrémités 5′ hétérogènes. Dans ce mémoire, des solutions sont proposées pour remédier au problème d’hétérogénéité en 5ʹ′ des ARN transcrits avec la polymérase à ARN du phage T7 et purifiés par la méthode ARiBo. La première solution consiste à choisir la séquence en 5′ parmi celles des 32 séquences testées qui ne présentent pas d’hétérogénéité en 5ʹ′. La seconde solution est d’utiliser une étiquette clivable en 5ʹ′ de l’ARN d’intérêt, tel que le ribozyme hammerhead, déjà utilisée pour ce genre d’application, ou le système CRISPR/Cse3 que nous proposons dans l’article présenté dans ce mémoire. De plus, nous avons adapté la méthode ARiBo pour rendre possible la purification d’un long ARN de 614 nt, le polycistron miR-106b-25. Nous avons également démontré la possibilité d’utiliser la méthode ARiBo pour l’isolation de protéines qui se lient à un ARN donné, le précurseur de miRNA pre-miR-153-2. En conclusion, ce mémoire démontre la possibilité d’adapter la méthode ARiBo à plusieurs applications. / In recent years, the field of RNA research has exploded due to several discoveries demonstrating the importance of RNA in many biological processes. Along with the increased interest in this field, large amounts of RNA have become essential to the success of several studies, in particular for structural biology and functional characterization. However, there are still very few native purification methods that are simple, efficient and reliable. In the past few years, the Legault laboratory has established an affinity purification method using an ARiBo tag to purify RNAs produced by in vitro transcription with the T7 RNA polymerase. This RNA purification method was specifically developed to maximise purity and yield. In addition, this method is fast and works with several types of RNAs. However, like several other purification methods, this method produces RNAs with 5' heterogeneity. This Master’s thesis propose solutions to overcome the problem of 5' heterogeneity for RNAs transcribed with the T7 RNA polymerase and purified with the ARiBo method. The first solution proposed is to choose a 5' sequence among those of the 32 sequences tested that do not present 5'- heterogeneity. The other possibility is the use of a cleavable tag at the 5'-end of the RNA of interest, such as the hammerhead ribozyme, already used for this purpose or the CRISPR/Cse3 system, which is presented here. Furthermore, we have adapted the ARiBo method to purify an RNA of 614 nt, the miRNAs cluster miR- 106b-25. We also demonstrate the possibility to use the ARiBo method to isolate proteins that bind a given RNA, the miRNA precursor pre-miR-153-2. In conclusion, this Master’s thesis demonstrates the possibility of adapting the ARiBo method for several applications.

Dans les maladies neurodégénératives comme la sclérose en plaques, la neuro-inflammation modifie l'activité de la barrière hémato-encéphalique (BHE) par des altérations cellulaires et moléculaires complexes. La caractérisation de tels changements moléculaires par une approche d'étiquetage in vivo justifie la recherche d’outils de ciblage fiables et de biomarqueurs. Les stratégies pour définir in vivo ces marqueurs sont cependant compliquées par la pléthore de molécules cibles accessibles, par l’intrication des régions atteintes au sein du tissu sain et par les altérations structurales potentielles des molécules cibles étudiées par histopathologie. Le but de ce travail est de rationaliser la découverte de biomarqueurs des altérations moléculaires dans les tissus par une stratégie de sélection in vivo de répertoires de phages présentant des peptides à leur surface (phage display), les ligands présents dans les deux répertoires (sain et pathologique) étant ensuite soustraits physiquement. Cette stratégie de soustraction (« PhiSSH ») permettant d’enrichir un répertoire en ligands spécifiques est d’un intérêt majeur dans le cas de répertoires complexes tels ceux obtenus dans des sélections in vivo.Nous présentons l'application de cette stratégie dans le modèle de rat de la sclérose en plaques, l’Encéphalomyélite Autoimmune Expérimentale (EAE), où les lésions disséminées dans le système nerveux central engendrent la sélection d’une grande quantité de clones s’associant au tissu sain, par comparaison avec les rats témoins en bonne santé. L'efficacité de la technique de soustraction a été contrôlée par séquençage massif des trois repertoires, «EAE», «SAIN», et «SOUSTRACTION». Plus de 95 % des clones communs aux répertoires EAE et contrôle sont absents du répertoire de la soustraction. Un ensemble de clones de phages et des peptides synthétisés chimiquement dessinés après l’analyse bioinformatique du répertoire de soustraction a été testé a) sur des tissus de rats EAE et sains et b) sur des cellules humaines en culture (HCMEC/D3) constituant un modèle de BHE, dans des conditions inflammatoires, (activation IL- 1ß) ou non activées. Un des clones et quatre peptide testés ont montré une association spécifique sur les cellules endothéliales de BHE dans des conditions inflammatoires. Pour identifier la cible d’un phage spécifique des lésions neuro-inflammatoires, nous avons mis en œuvre un procédé de création de liaison covalente entre ce phage et les protéines exprimées par des cellules de BHE cultivées en présence d’IL-1ß, puis effectué une analyse par spectométrie de masse. La galectine-1 est apparue comme une cible potential de ce phage. La découverte de biomarqueurs spécifiques de modifications moléculaires et cellulaires de régions inflammatoires disséminées dans les tissus sains, comme c’est le cas dans la plupart des pathologies présentant une activité neuro–inflammatoire, sera facilitée par l’utilisation de la stratégie de soustraction PhiSSH décrite dans ce document. / In neurodegenerative disorders like multiple sclerosis, neuroinflammation modifies the blood brain barrier (BBB) status by causing complex cellular and molecular alterations. Characterization of such molecular changes by an in vivo labeling approach is most challenging to generate reliable in vivo targeting tools and biomarkers. In vivo strategies to define such markers are, however, hampered by the plethora of the accessible target molecules, the vicinity of diseased target expression among healthy tissue and the potentially structural alterations of target molecules when studied by histopathology. The aim of this work is to streamline the biomarker discovery of pathological molecular tissue alterations by in vivo selection of phage displayed peptide repertoires that are further submitted to physical DNA subtraction (“PhiSSH”) of sequences encoding common peptides in both repertoires (HEALTHY and PATHOLOGY). The strategy of Subtraction allows thus the enrichment of clones specific for one repertoire and is of particular interest for complex repertoires produced by in vivo selection. We present the application of this strategy in the multiple sclerosis rat model, Experimental Autoimmune Encephalomyelitis (EAE) pathology, where target lesions are disseminated in the central nervous system (CNS) generating a large amount of clones binding to healthy tissue among the recovered repertoire clones binding to the lesions by comparison with healthy control rats. The efficiency of the subtraction was monitored by massive sequencing of the three repertoires, «EAE», «HEALTHY», and «SUBTRACTION». More than 95% of the clones common to EAE and Healthy repertoires were shown to be absent from the Subtraction repertoire. A set of randomly chosen clones and synthesized peptides from the EAE and subtraction repertoires were tested for differential labeling of a) diseased and healthy animal tissues and b) an in vitro BBB model, in IL-1ß challenged and resting control state culture human cells (hCMEC/D3). One of the phage clones and 4 chemically synthesized peptides showed specific binding to brain ECs in neuro-inflammatory conditions. Using a strategy of crosslinking of an EAE specific phage clone on protein targets expressed by IL-1ß activated ECs followed by mass spectrometry, we propose hypothetically Galectin-1 as a possible target of this phage. PhiSSH will be useful for in vivo screening of small peptide combinatorial libraries for the discovery of biomarkers specific of molecular and cellular alterations untangled with healthy tissues, as in most pathologies presenting neuroinflammatory activity.

O objetivo desse trabalho foi construir o fago recombinante D29::gfp e testar a sua utilização como um agente revelador da viabilidade bacilar na determinação da concentração inibitória mínima (GIM) aos principais fármacos administrados no tratamento da tuberculose. O fago recombinante contém o promotor hsp70 e o gene da proteína verde fluorescente (gfp) e foi construído através da restrição pela Spe I em uma região intergênica próxima a extremidade coesiva direita no genoma do fago D29. O promotor hsp70 e gfp clonados no pYL GFP foram amplificados pela PCR utilizando iniciadores com sítios para Spe I. O DNA do fago D29 digerido pela Spe I foi ligado com o fragmento hsp 70- gfp empregando a T 4 DNA ligase e os produtos da reação de ligação foram transformados de acordo com o protocolo de encapsulamento. A infecção do M.smegmatis com esse fago recombinante induziu a expressão da proteína verde fluorescente (GFP). Para avaliar o uso do fago recombinante em teste de sensibilidade aos fármacos anti-tuberculose, 100 isolados clínicos foram testados quanto ao perfil de sensibilidade a isoniazida (H), rifampicina (R), estreptomicina (S) e etambutol (E), utilizando o método das proporções em Lowenstein-Jensen (L-J), técnica em microplaca com a resazurina (REMA) e técnica em microplaca com D29::gfp. Os resultados do REMA demonstraram que 30 isolados clínicos foram sensíveis à H e 58 (66 %) isolados clínicos foram resistentes, dentre os quais a CIM foi 1 µg/mL ou maior para 41 (71 %). A CIM da R para 49 (56%) dos isolados clínicos resistentes foi de 0,5 µg/mL para 17 (35%). A CIM da S para 33 (37%) dos isolados clínicos resistentes foi de 2 µg/mL para 13 (40%) e CIM do E para 34 (39%) dos isolados clínicos resistentes foi de 16 µg/mL ou maior para 19 (56%). A caracterização molecular pela PCR IS6110 identificou 88 isolados clínicos como M.tuberculosis e pelo PRA hsp65, sete isolados clínicos foram M.kansasii, quatro foram M.abscessus e um M.szulgai. Após empregar o fago recombinante como um agente indicador da viabilidade bacilar para testar a atividade dos fármacos anti-tuberculose conclui-se que a expressão da proteína verde fluorescente foi inespecífica e não reprodutiva, não justificando o seu uso para determinar a CIM para os principais fármacos administrados no tratamento da tuberculose. / The objective of this work was to construct the recombinant phage D29::gfp and to use this phage as an indicator agent of cell viability in a minimal inhibitory concentration (MIC) assay for the mains drugs used for tuberculosis treatment. The recombinant phage contains the mycobacteria-specific hsp70 promoter controlling the green fluorescent protein gene (gfp) and was constructed by Spe I restriction in the intergenic region next to the right cohesive termini of the D29 phage genome. An hsp 70 promoter and gfp previously cloned in p YL GFP was amplified by PCR using primers with Spe I sites. The Spe I-restricted D29 phage DNA was ligated with the hsp 70-gfp fragment using T4 DNA ligase and ligated product was transformed using the packing protocol. Infection of M.smegmatis with this recombinant phage indicated the expression of green f1uorescent protein (GFP). To use the recombinant phage for assaying the activity of anti-TB drugs, 100 clinical isolates was tested for susceptibility to isoniazid (H), rifampicin (R), streptomycin (S), and ethambutol (E) using both the proportion method on Lowenstein-Jensen (L-J) medium, resazurin microtiter assay plate (REMA), as well as a microplate assay using D29::gfp. The REMA plate method showed that 30 clinical isolates were susceptible to H and 58 (66%) clinical isolates were resistant, where the MICs were 1 µg/mL or higher for 41 (71%). The R MICs for 49 (56%) resistant clinical isolates were 0,5 µg/mL for 17 (35%). The S MICs for 33 (37%) resistant clinical isolates were 2 µg/mL for 13 (40%) and E MICs for 34 (39%) resistant clinical isolates were 16 µg/mL or higher for 19 (56%). Molecular characterization by PCR IS6110 showed that 88 clinical isolates were M.tuberculosis and by PRA hsp65 were seven clinical isolates were M.kansasii and four was M.abscessus, and one M.zulgai. After using the recombinant phage as an indicator agent of cell viability for assaying the activitity of anti-TB drugs we can conclude that the expression of green fluorescent protein was non-specific and not reproducible, rendering it not useful for the determination of the MIC of the principal drugs used for the treatment of tb.

Les anticorps catalytiques (ou abzyme) ont fait l’objet de nombreuses recherches et ont été produits pour réaliser de nombreuses réactions. Ces protéines ont été ensuite découvertes dans le sérum d’individus sains ou atteints de pathologies, dont les pathologies autoimmunes. Les études suggèrent que ces abzymes peuvent avoir des effets bénéfiques ou délétères sur la santé des individus. L’origine des anticorps catalytiques et leur rôle restent ambigus et doivent être approfondis. Nous avons développé une nouvelle stratégie visant à étudier les abzymes, basée sur la technologie du phage display. Nous avons construit 4 banques de fragments d’anticorps, chacune présentant un répertoire immun différent (fond génétique et état d’immunitaire) : saine et naïve, saine et immunisée, autoimmune et naïve, et autoimmune et immunisée. Les stratégies d’amplification et de clonage des régions variables des immunoglobulines ont été conçues afin d’optimiser la taille et la diversité des banques. Nous avons rassemblé les 4 banques en une banque unique élargie contenant 2.7×109 séquences. L’analyse des séquences a mis en évidence des différences dans les profils d’expression des sous-groupes de gènes selon la banque. Nous avons ensuite procédé à la sélection d’abzymes à activité β-lactamase en utilisant deux cibles : un peptide cyclique, et un dérivé de sulfone pénam, inhibiteurs de l’enzyme. Nous avons sélectionné 5 abzymes. Chacun de ces immunoglobulines ont des séquences protéiques propres, incluant un potentiel site actif. Ces résultats montrent que différents motifs peuvent assurer la fonction catalytique de la β-lactamase, confirmant la flexibilité moléculaire de cette enzyme. / Catalytic antibodies (or abzymes) have been the focus numerous studies for some decades and have been produced with the ability to catalyze a wide range of reactions. They have also been discovered naturally in normal physiological and pathological conditions, notably on the background of autoimmune disease. Some have beneficial effects and others are detrimental to individual’s health. Hence, the origin of abzymes and their role in the immune response are ambiguous and must be enhanced. We have developed a novel strategy for the study of abzymes based on the phage display technology. We have constructed 4 libraries representing 4 murine immune repertoires with different genetic backgrounds and immunological states : healthy and naïve, healthy and immunized, autoimmune and naïve , and autoimmune and immunized. The strategies for the amplification and cloning of the immunoglobulin (lg) variable regions have been designed to optimize the size and diversity of the libraries. We have been able to pool the four libraries to create a large repertoire of size 2.7x109. After sequence analysis, we have found a number of statistically significant differences between the libraries. We have then used two strategically chosen targets to select for antibodies endowed with β lactamase activity : a cycle peptide and a penam sulfone, both inhibitors of the enzyme. We have selected for a total of 5 lgs endowed with β lactamase activity. The selected abzymes have different amino acid sequences. 3D modeling has provides insights on potential active sites demonstrating the ability of different structures to maintain the β lactamase activity and confirming the flexibility of the active site.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / CHAPTER I: Leprosy presents a clinical spectrum that spans from a strong cellular mediated immunity and bacili growth control of Mycobacterium leprae at the tuberculoid pole to a poor T cell immunity with extensive bacterial load at the lepromatous pole. The antigenic profile characterization in both clinical forms is a necessary step for discover and evaluation of recombinant peptides that are mimotopes of M. leprae antigens, which may present immunogenic potential, in order to obtain a beTer understanding of the disease evolution, and allowing the improvement of diagnosis, prognosis and therapeutics. Mimotopes of M. leprae antigens were selected from a random heptapeptide conformational library expressed in fusion with the pIII protein of the M13 phage, using as the ligand target the total purified IgM from leprosy patients of clinical forms, tuberculoid (TT) and lepromatous (LL), and a healthy control population. Recombinant peptides were selected by glycine elution (unspecific) and by mitsudin elution (specific). All clones, after bioinformatic analyses, were validated by immunoenzymatic and colony reduction assays. For the glycine selection, the TT pole presented 24 distinct fagotypes, while the LL pole presented only 14 fagotypes. For the mitsudin selection, only 4 fagotypes were obtained in the LL pole, and 8 fagotypes in the TT pole. The two most frequent mimotopes, in both TT and LL poles and in both elution protocols, were coincidents. The peptides LFPAMHQ and VERHPST were more frequent in the LL pole, and the peptides KNPTTGT and ETHPTTR were more frequent in the TT pole. The three cited first mimotopes had an accentuated plaque reduction with incubation of sera from LL patients; however, the mimotope ETHPTTR presented the highest reduction with sera from TT patients. The immunogenic potential of these mimotopes may be useful in the development of new diagnostic and therapeutic strategies for leprosy control in the future. CHAPTER II: The phenolic glycolipid 1 (PGL-1) is a membrane antigen highly specific of M. leprae, and it is not found in other mycobacteria. Serological tests with PGL-1 have been performed to detect circulating antibodies in multibacillary patients. Due to its importance in the clinical classification of leprosy patients, we have developed mimotopes of this non-proteic antigen through phage display in order to improve serological assays. In this investigation, a random heptapetide conformational library was selected to obtain specific ligands to the monoclonal antibody anti-PGL-1 CS-48. After three rounds of selection, 14 clones were sequenced and translated, generating six distinct peptides. The mimotope HWMLPED was the most frequent one (57%), suggesting an immunodominance. Serological tests with this mimotope were performed in comparison to the synthetic PGL-1 for 39 patients, classified according to their clinical form, together with their 44 household contacts, classified according to their index cases. Results were similar for T and LL patients. However, the intermediate forms were variable, differently from those results with PGL-1, which presented positivity only for multibacillary patients. The clinical form BT presented a seropositivity of 55.5% for the mimotope against 0% for the PGL-1, probably due the greater avidity of the mimotope to circulating antibodies, or due to the greater spepcificity of the peptide in detecting pure neural reaction, or yet a cross reaction with other human antibodies. The serological tests of household contacts for this same phage clone presented an average positivity of 20.5% versus an average of 7.5 for the PGL-1 antigen. It is probable that there was cross reaction of the mimotope with other antibodies; once it presented partial identity with other M. leprae proteins. The mimotopes must be further investigated, once they may be putative targets for the PGL-1 action in the immune humoral response, and also they could be useful in diagnostics and therapeutic strategies. / CAPITULO I: A hanseníase apresenta um espectro clínico que varia de uma forte resposta imune mediada por células e controle do crescimento do bacilo Mycobacterium leprae no pólo tuberculóide (T), a uma anergia em resposta celular, com alta carga bacteriana, no pólo virchoviano (V). A caracterização do perfil antigênico do bacilo nas formas clínicas se faz necessária para que novos peptídeos recombinantes, mimotopos de antígenos de M. leprae, sejam avaliados quanto ao seu potencial imunogênico, para que se tenha um melhor entendimento dos mecanismos de evolução da doença, e para permitir o aprimoramento do diagnóstico, prognóstico e terapêutica. Mimotopos de antígenos de M. leprae foram selecionados a partir de uma biblioteca conformacional de heptapeptídeos randômicos expressos em fusão com proteína pIII de fagos M13, utilizando como alvo ligante IgM total purificada de pacientes portadores de hanseníase de ambos os pólos, tuberculóide e virchoviano, e de contatos intradomiciliares sadios. Os peptídeos recombinantes foram selecionados por eluição em tampão glicina (inespecífico) e por eluição com mitsudina (específico). Todos os clones, após análises de bioinformática, foram validados por ensaios imunoenzimáticos e alguns por ensaios de redução de colônias. Na eluição com glicina, o pólo tuberculóide apresentou 24 fagótopos distintos, enquanto que o virchoviano apresentou 14. Já na eluição com mitsudina, foram obtidos apenas 4 fagótopos para pólo virchoviano e 8 para o pólo tuberculóide. Os dois mimotopos mais freqüentes, em ambas as formas clínicas e para as duas eluições foram coincidentes, sendo que os peptídeos LFPAMHQ e VERHPST foram os mais freqüentes no pólo virchoviano e os peptídeos KNPTTGT e ETHPTTR os mais freqüentes no pólo tuberculóide. Os três primeiros peptídeos, dos quatro acima citados, tiveram redução de colônias mais acentuada com soro de pacientes V, e o mimotopo ETHPTTR foi o que apresentou a maior redução com soro de pacientes T. O potencial imunogênico destes mimotopos pode ser útil no desenvolvimento de novas estratégias diagnósticas e terapêuticas para o controle da hanseníase. CAPITULO II: O Glicolipídeo Fenólico-1 (PGL-1) é um antígeno de membrana altamente específico de M. leprae, não sendo encontrado em outras micobactérias. Os testes sorológicos com o PGL-1 têm sido implementados para a detecção de anticorpos circulantes nas formas clínicas multibacilares. Por ser um alvo importante na classificação clínica dos pacientes, procurou-se desenvolver peptídicos miméticos deste antígeno não-protéico por phage display, como forma de aprimorar o teste sorológico. Neste estudo uma biblioteca conformacional de heptapeptídeos randômicos foi selecionada para obtenção de ligantes específicos ao anticorpo monoclonal anti-PGL-1 CS-48. Após 3 ciclos de seleção, 13 clones foram seqüenciados e traduzidos, gerando seis mimotopos distintos. O mimotopo HWMLPED foi o mais freqüente (61,5%), indicando ser imundominante entre os peptídeos. Testes sorológicos com este mimotopo foram realizados em comparação com o PGL-1 sintético para 37 pacientes, classificados conforme a forma clínica, juntamente com seus 44 contatos, classificados conforme seus casos índice. Os resultados obtidos com o mimotopo e PGL-1 foram similares nos pacientes com as formas clínicas polares T e V. Contudo, as formas intermediárias dimorfas foram altamente variáveis e significantes, diferentemente do PGL-1, que apresentou positividade somente para as formas multibacilares. A forma clínica DT, apresentou 55,5% de positividade com a utilização do fagótopo, contra 0% para o PGL-1, podendo ser uma maior avidez do fagótopo ao anticorpo circulante, ou maior especificidade do fagótopo para lesão neural pura, como também reação cruzada com outros anticorpos. O teste sorológico em contatos intradomiciliares para o fagótopo selecionado, apresentou uma média de 20,5% de positividade contra uma média de 7,5% no teste sorológico para o PGL-1. É provável que tenha ocorrido reação cruzada do mimotopo por este apresentar identidade parcial com proteínas do M. leprae. Os mimotopos devem ser analisados mais profundamente, pois podem indicar provável alvo de ação do PGL-1 na resposta imune humoral e ainda podem ser usados em estratégias diagnósticas e terapêuticas. / Doutor em Genética e Bioquímica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Prostate cancer is the second cause of death in men by tumor, surpassed only by lung cancer. Its occurrence is estimated to be 51 to 100,000 cases per year. The increasing incidence levels observed may be partially explained by the evolution of diagnostic methods, quality of information systems and longer life expectancy. The identification of new cancer specific antigens and genes may provide important biomarkers for diagnosis and instruments for the development of new treatment strategies. The Phage Display technology may be able to select peptides with different aims, such as the discovery of mimetic antigens that are recognized by specific antibodies. Selected peptides may become potential tumor biomarkers for prostate cancer diagnosis. It could be possible to use this technology to identify proteins that are able to detect cancer earlier than the conventional methods, to predict disease staging, and to develop new treatment strategies based on more efficient biological targets. The immunization of SPF (specific pathogen free) male chickens with total proteins of tissues of prostate cancer has generated polyclonal specific IgY sera, which were used in biopanning procedures against random peptide libraries. Selected phages were characterized by sequencing and bioinformatics, and subsequently by dot immunoblotting and ELISA to validate their specificity. Selected peptides were mimotopes of putative proteins involved in the carcinogenesis process. These peptides were further tested for their possible use in the immune response diagnostics associated with tumor processes. In this work, we have also successfully developed a general immunosensor for diagnostics, performed on an exclusion liquid chromatography system based on a micro column resin separation, using the selected bacteriophages as carriers of antigens and antibodies. These phage are coupled to colored latex beads, which are activated with different chemical groups. The presence of phage in the process is of fundamental importance, once they favor the formation of the antigen-antibody complex, peptide-protein or peptide-substrate, amplifying the optical detection during chromatographic separation or by micro-agglutination in slides for optical microscopy detection. The new technology is practical and simple, and may also be used for detection of other biomolecules or chemical substances associated with infectious and genetic diseases, with high precision, sensitivity, specificity, and rapidity, using low sample volumes and presenting a low cost. / O câncer de próstata é a segunda causa de óbitos por câncer em homens, sendo superado apenas pelo câncer de pulmão. A ocorrência estimada é de 51 casos novos para cada 100 mil homens por ano para este tipo de câncer. O aumento observado nas taxas de incidência pode ser parcialmente justificado pela evolução dos métodos diagnósticos, pela melhoria na qualidade dos sistemas de informação do país e pelo aumento na expectativa de vida do brasileiro. A identificação de novos antígenos ou genes específicos do câncer de próstata pode prover novos biomarcadores e também fornecer instrumentos para o desenvolvimento de novas modalidades de tratamento. A tecnologia de Phage Display é capaz de selecionar peptídeos com diversas finalidades, como mimetizar antígenos reconhecidos por anticorpos. Peptídeos selecionados por esta técnica são potenciais marcadores tumorais para o diagnóstico do câncer de próstata. Por meio desta metodologia pode ser possível identificar proteínas capazes de detectar a resposta imune contra o tumor mais precocemente do que os métodos tradicionais, predizer o estadio atual do tumor, além de permitir o desenvolvimento de tratamentos mais eficientes. Pela imunização de galos SPF (livre de patógenos específicos) com proteínas totais de tecidos tumorais da próstata, foram obtidas IgY policlonais específicas que foram utilizadas no biopanning contra uma biblioteca de peptídeos recombinantes randômicos. Os fagos selecionados foram caracterizados por seqüenciamento e subsequentemente testados por dot immunoblotting e ELISA para validar a especificidade dos mesmos. Selecionou-se peptídeos que mimetizam proteínas prostáticas, possivelmente proteínas envolvidas no processo de tumorigênese. Esses peptídeos foram testados quanto a sua possível utilização no diagnóstico da resposta imune associada a processos tumorais. Neste trabalho, também foi desenvolvido com sucesso um imunossensor para diagnóstico que tem como base de detecção um sistema de cromatografia líquida por exclusão em micro colunas cromatográficas com bacteriófagos filamentosos carreadores de antígeno(s) e/ou anticorpo(s), selecionados por phage display, acoplados microesferas de látex coloridas, ativadas com diferentes grupamentos químicos. A presença do fago é de grande importância no processo, pois favorece a formação dos complexos antígeno-anticorpo, peptídeo-proteína ou peptídeo-substrato, ampliando a detecção ótica durante a separação por cromatografia ou por microaglutinação em microscopia ótica. A nova tecnologia pode também ser usada para a detecção de biomoléculas ou substâncias químicas associados a doenças infecciosas, parasitárias e genéticas, com rapidez, precisão, sensibilidade e reprodutibilidade, utilizando-se pequenos volumes de amostras e reagentes, apresentando praticidade e baixos custos. / Doutor em Genética e Bioquímica

O objetivo desse trabalho foi construir o fago recombinante D29::gfp e testar a sua utilização como um agente revelador da viabilidade bacilar na determinação da concentração inibitória mínima (GIM) aos principais fármacos administrados no tratamento da tuberculose. O fago recombinante contém o promotor hsp70 e o gene da proteína verde fluorescente (gfp) e foi construído através da restrição pela Spe I em uma região intergênica próxima a extremidade coesiva direita no genoma do fago D29. O promotor hsp70 e gfp clonados no pYL GFP foram amplificados pela PCR utilizando iniciadores com sítios para Spe I. O DNA do fago D29 digerido pela Spe I foi ligado com o fragmento hsp 70- gfp empregando a T 4 DNA ligase e os produtos da reação de ligação foram transformados de acordo com o protocolo de encapsulamento. A infecção do M.smegmatis com esse fago recombinante induziu a expressão da proteína verde fluorescente (GFP). Para avaliar o uso do fago recombinante em teste de sensibilidade aos fármacos anti-tuberculose, 100 isolados clínicos foram testados quanto ao perfil de sensibilidade a isoniazida (H), rifampicina (R), estreptomicina (S) e etambutol (E), utilizando o método das proporções em Lowenstein-Jensen (L-J), técnica em microplaca com a resazurina (REMA) e técnica em microplaca com D29::gfp. Os resultados do REMA demonstraram que 30 isolados clínicos foram sensíveis à H e 58 (66 %) isolados clínicos foram resistentes, dentre os quais a CIM foi 1 µg/mL ou maior para 41 (71 %). A CIM da R para 49 (56%) dos isolados clínicos resistentes foi de 0,5 µg/mL para 17 (35%). A CIM da S para 33 (37%) dos isolados clínicos resistentes foi de 2 µg/mL para 13 (40%) e CIM do E para 34 (39%) dos isolados clínicos resistentes foi de 16 µg/mL ou maior para 19 (56%). A caracterização molecular pela PCR IS6110 identificou 88 isolados clínicos como M.tuberculosis e pelo PRA hsp65, sete isolados clínicos foram M.kansasii, quatro foram M.abscessus e um M.szulgai. Após empregar o fago recombinante como um agente indicador da viabilidade bacilar para testar a atividade dos fármacos anti-tuberculose conclui-se que a expressão da proteína verde fluorescente foi inespecífica e não reprodutiva, não justificando o seu uso para determinar a CIM para os principais fármacos administrados no tratamento da tuberculose. / The objective of this work was to construct the recombinant phage D29::gfp and to use this phage as an indicator agent of cell viability in a minimal inhibitory concentration (MIC) assay for the mains drugs used for tuberculosis treatment. The recombinant phage contains the mycobacteria-specific hsp70 promoter controlling the green fluorescent protein gene (gfp) and was constructed by Spe I restriction in the intergenic region next to the right cohesive termini of the D29 phage genome. An hsp 70 promoter and gfp previously cloned in p YL GFP was amplified by PCR using primers with Spe I sites. The Spe I-restricted D29 phage DNA was ligated with the hsp 70-gfp fragment using T4 DNA ligase and ligated product was transformed using the packing protocol. Infection of M.smegmatis with this recombinant phage indicated the expression of green f1uorescent protein (GFP). To use the recombinant phage for assaying the activity of anti-TB drugs, 100 clinical isolates was tested for susceptibility to isoniazid (H), rifampicin (R), streptomycin (S), and ethambutol (E) using both the proportion method on Lowenstein-Jensen (L-J) medium, resazurin microtiter assay plate (REMA), as well as a microplate assay using D29::gfp. The REMA plate method showed that 30 clinical isolates were susceptible to H and 58 (66%) clinical isolates were resistant, where the MICs were 1 µg/mL or higher for 41 (71%). The R MICs for 49 (56%) resistant clinical isolates were 0,5 µg/mL for 17 (35%). The S MICs for 33 (37%) resistant clinical isolates were 2 µg/mL for 13 (40%) and E MICs for 34 (39%) resistant clinical isolates were 16 µg/mL or higher for 19 (56%). Molecular characterization by PCR IS6110 showed that 88 clinical isolates were M.tuberculosis and by PRA hsp65 were seven clinical isolates were M.kansasii and four was M.abscessus, and one M.zulgai. After using the recombinant phage as an indicator agent of cell viability for assaying the activitity of anti-TB drugs we can conclude that the expression of green fluorescent protein was non-specific and not reproducible, rendering it not useful for the determination of the MIC of the principal drugs used for the treatment of tb.

Utilistions d'anticorps monoclonaux est une partie prometteuse de la thérapie du cancer. À ce jour, il existe plus de 30 anticorps monoclonaux approuvés pour la thérapie contre le cancer. Plus de 350 anticorps se situent également dans différentes phases du développement clinique. La mésothéline est l'une des cibles les plus prometteuses pour l'immunothérapie. La mésothéline est présente à des niveaux relativement faibles dans les cellules mésothéliales de la plèvre, du péritonéum et du péricarde normaux, mais est fortement exprimée dans un certain nombre de cancers différents, y compris les mésothéliomes, le cancer de l'estomac, les carcinomes à cellules squameuses, le cancer de la prostate, le cancer du pancréas, le cancer du poumon et le cancer de l'ovaire. La mésothéline est une glycoprotéine liée au glycosylphosphatidylinositol (GPI) synthétisée sous la forme d'un précurseur de 69 kDa et transformée de façon protéolytique en une forme sécrétée à 30 kDa (anciennement appelée Facteur de potentialisation des mégacaryocytes (MPF)) et une forme liée à la membrane de 40 kDa. Par ailleurs, il peut être clivé par une protéase et peut produire une forme de mésothéline soluble. Il a été déjà montré que cette forme soluble de mésothéline agit comme un ligand et neutralise les anticorps thérapeutiques ciblant la mésothéline. Par conséquent, les anticorps ne pouvaient pas atteindre les cellules cancéreuses et reste inefficaces. Dans notre travail, nous avons décidé de développer un anticorps discriminant spécifique à la forme associée à la membrane pour surmonter l'antagonisme produit par les formes solubles de mésothéline. Pour ce but, nous avons utilisé une nouvelle méthode d'immunisation de souris, que nous avons d'abord toléré la souris avec une mésothéline soluble et ensuite ré-immunisée avec des cellules exprimant la mésothéline. En utilisant la technologie de phage display, nous avons obtenu près de 150 clones de ciblant mésothéline dans 34 familles de VH-CDR3 parmi lesquelles nous avons identifié seulement 2 familles qui se lient à la mésothéline membranaire avec une affinité élevée et ne reconnaissent aucune autre forme soluble de mésothéline. Ici, nous proposons qu'ils puissent être des bons candidats pour être utilisés pour la thérapie contre le cancer de qui permet de passer à travers la barrière de mésothéline soluble. Pour démontrer leur efficacité pour une utilisation thérapeutique, nous avons construit une CAR avec le sc-Fv d'un anticorps discriminant de la forme membranaire. / Antibody based immune treatment is a promising component of cancer therapy. To date there are more than 30 approved monoclonal antibodies for cancer therapy. More than 350 antibodies are also in different phases of clinical development. Mesothelin is one of the most promising targets for immunotherapy. It is present at relatively low levels in mesothelial cells of the pleura, peritoneum and pericardium of healthy individuals, but is highly expressed in a number of different cancers, including mesotheliomas, stomach cancers, squamous cell carcinomas, as well as prostate, pancreatic, lung, and ovarian cancers. Mesothelin is a glycosylphosphatidylinositol (GPI)-linked glycoprotein synthesized as a 69 kDa precursor and proteolytically processed into a 30 kDa NH2-terminal secreted form (formerly referred to as Megakaryocyte Potentiating Factor (MPF)) and a 40 kDa membrane-bound form. Besides that it can be cleaved by a protease leading to the production of a soluble, shedded, form of mesothelin. It has already been shown that this soluble form of mesothelin acts as a ligand and neutralizes the mesothelin targeting therapeutic antibodies. Therefore antibodies could not reach cancer cells and remained inefficient. In our work we decided to develop discriminating antibodies specific to a membrane associated form so as to overcome the antagonism produced by soluble forms of mesothelin. To this aim we used a novel method of mouse immunization, in which we first tolerized the mouse with soluble mesothelin before immunization with mesothelin expressing cells. By using phage display technology we obtained nearly 150 mesothelin recognizing clones in 34 VH-CDR3 families, among which we identified only 2 families that bind membrane mesothelin with high affinity and do not recognize any other soluble form of mesothelin. Here we suggest that this Fab can be effective candidates to be used for mesothelin expressing cancer therapy being allowed to pass through the soluble mesothelin barrier. To show their efficacy for therapeutic use we constructed a CAR with the sc-Fv of a membrane-form discriminating antibody

The extracellular matrix (ECM) provides mechanical and biochemical support to tissues and cells. It is crucial for cell attachment, differentiation, and migration, as well as for ailment-associated processes such as angiogenesis, metastases and cancer development. An approach to study these phenomena is through emulation of the ECM by synthetic gels constructed of natural polymers, such as collagen and fibronectin, or simple but tunable materials such as poly(ethylene glycol) (PEG) crosslinked with short peptide sequences susceptible to digestion by metalloproteases and cell-binding domains. Our lab uses PEG gels to study cell behavior in three dimensions (3D). Although this system fosters cell attachment and crosslinking peptides mentioned, the regenerative process of the ECM has not been mimicked yet in 3D synthetic gels. In an attempt to build in this functionality to PEG-based gels, I performed phage display to identify short oligopeptides that bind either collagen or fibronectin to assess them as potential nucleation points for crosslinking elements in order to emulate the in vivo reconstitution process. A phage display is a library of random oligopeptides expressed on a M13 bacteriophage that allows identification of a phenotype and a genotype with a single screening step. This inexpensive strategy could yield a short oligopeptide with high specificity. I identified the conditions under which phage display is compatible with our targets, and I isolated and identified five peptide candidates for fibronectin binding and two for collagen. Future work includes assessing whether these candidates could facilitate the formation of cell-created crosslinking in 3D synthetic hydrogels.

A novel aryl hydrocarbon receptor nuclear translocator (ARNT)-interacting peptide (Ainpl) was characterized from human liver cDNA library using phage display. Ainpl suppresses hypoxia inducible factor-1a (HIF-1α) signaling pathway through an ARNTdependent manner. HIF-1α is known to be overexpressed in more than 90% of solid tumors, and the inhibition of HIF-1α is proved as an effective approach to suppress tumor growth. ARNT, as the obligatory heterodimeric partner of HIF-1α for downstream gene activation, was used as a bait to screen for Ainpl. Ainpl specifically interacts with the helix-loop-helix (HLH) subdomain of ARNT, but not with HIF-1α. GFP-Ainpl is localized in both cytoplasm and nucleus, and suppresses HIF-1α signaling by two mechanisms: (1) cytoplasmic GFP-Ainp 1 retains ARNT in the cell cytoplasm and (2) nuclear GFP-Ainpl inhibits HIF-1α/ARNT heterodimerization. The suppression of Ainpl on HIF-1α signaling was reversed by introducing ARNT into the cells using transient transfection. We further utilized HIV TAT protein transduction domain to deliver 6His-TAT-Ainpl into three different cancer cell lines (Hep3B, HeLa, MCF-7), and found that 6His-TAT-Ainpl co-localizes with ARNT in the cell nucleus. 6His-TATAinpl can be detected inside the cells after 30 min of transduction, and can reach the maximum level at 2 h. 6His-TAT-Ainp 1 remained detectable in the cells up to 96 h and had a half life of 24 h after transduction. In addition, 6His-TAT-Ainp 1 suppresses HIF-1α downstream genes at both message and protein levels in a dose-dependent manner. Taken together, molecules that target the HIF-1α and ARNT interface can be developed as viable drugs to suppress HIF-1α signaling.