Ce travail de thèse repose sur le développement de méthodes en spectrométrie de masse native et mobilité ionique pour la caractérisation structurale de protéines d’intérêt thérapeutique et de complexes multiprotéiques. L’optimisation fine et conséquente de la préparation d’échantillon et des conditions analytiques ont permis la caractérisation de protéines membranaires solubilisées en milieu détergent, protéines hydrophobes habituellement réfractaires à l’analyse par MS. D’autre part, une nouvelle approche de mobilité ionique appelée Collision Induced Unfolding a été évaluée et mise en place au laboratoire. Elle a permis une caractérisation conformationnelle approfondie et originale de plusieurs formats d’anticorps monoclonaux thérapeutiques. Enfin, les techniques de MS native et de mobilité ionique ont été utilisées pour caractériser des complexes multiprotéiques d’hétérogénéité variable mettant ainsi en lumière leurs avantages et les progrès réalisés dans le domaine de la MS structurale. / This PhD work focuses on developments in native mass spectrometry and ion mobility methods for the structural characterization of therapeutic proteins and multiprotein complexes. First, careful optimizations of sample preparation and analytical conditions allowed the characterization of membrane proteins, which are hydrophobic proteins difficult to analyze by MS approaches in detergent environment. Then, a new ion mobility-based activation approach called Collision Induced Unfolding has been set up and evaluated. CIU allowed extensive and original conformational characterization of several therapeutic monoclonal antibody formats. Finally, native MS and ion mobility techniques were used for the characterization of heterogeneous multiprotein complexes depicting their benefit when combined to other biophysical techniques for the structural characterization of multiprotein complexes.

Le cancer de l’ovaire est la première cause de décès par cancer gynécologique en France et il présente un fort taux de récidive justifiant la recherche de nouvelles thérapeutiques. Notre projet consiste à développer et à explorer sur des modèles expérimentaux précliniques de carcinose péritonéale de nouveaux agents thérapeutiques radiopharmaceutiques et des voies d’administration innovantes ciblant plus particulièrement la maladie résiduelle micro-métastatique présente après chirurgie de cytoréduction. Nous utilisons des anticorps monoclonaux internalisants spécifiques d’un récepteur membranaire surexprimé dans le cancer de l’ovaire et d’autres cancers gynécologiques, le récepteur de type 2 de l’hormone anti-müllerienne (AMHR2). Ces anticorps sont couplés à des radionucléides aux propriétés thérapeutiques : le Lutecium-177 (un émetteur de particules beta moins) et le Bismuth-213 (un émetteur de particules alpha) réalisant un traitement de radioimmunothérapie. Ils sont évalués après injection intrapéritonéale mais également en utilisant la technique RadioImmunoThérapie Intrapéritonéale Brève (BIP-RIT) consistant à instiller de fortes activités d’anticorps radiomarqués dans le péritoine avant d’en réaliser un rinçage abondant, à l’image de la chimiothérapie hyperthermique intrapéritonéale (CHIP). Sont étudiés sur différents modèles la biodistribution, la dosimétrie, la toxicité et l’efficacité thérapeutique des différentes combinaisons de radionucléides et de voies d’administration. La BIP-RIT présente un profil de biodistribution et de dosimétrie toujours favorable, quel que soit le radionucléide utilisé même si l’utilisation du Bismuth-213 apparait plus particulièrement adaptée à cette technique (bonne efficacité thérapeutique avec absence de toxicité). L’imagerie PET/CT de la biodistribution in-vivo de ces anticorps a été réalisée à l’aide de l’émetteur de positrons Zirconium-89 ouvrant la voie à une approche théragnostique du traitement des cancers gynécologiques AMHR2+ par (radio)immunothérapie. Les mécanismes d’action thérapeutique d’une version humanisée de l’anticorps anti-AMHR2 sont également étudiés. Ce travail ouvre des perspectives cliniques intéressantes dans la prise en charge du cancer de l’ovaire. / Ovarian cancer is the first cause of cancer death from gynaecologic malignancy in France and it has high rate of recurrence justifying the development of new therapeutic tools. Our project aims at developing new radiopharmaceuticals and innovative route of administration to target the small volume residual disease after complete cytoreductive surgery of peritoneal carcinomatosis on preclinical models. We use internalising monoclonal antibodies specific of the anti-müllerian hormone type 2 receptor (AMHR2), overexpressed in ovarian cancer and gynaecologic malignancies. Antibodies are radiolabelled with Lutecium-177, a beta minus emitter, and Bismuth-213, an alpha emitter, to perform radioimmunotherapy. Radiolabelled antibodies are injected intraperitoneally but also after Brief IntraPeritoneal RadioImmunoTherapy (BIP-RIT), a technique delivering high activities in the peritoneal cavity for a short time before washing, like Hyperthermic IntraPEritoneal Chemotherapy (HIPEC). We studied biodistribution, dosimetry, toxicity and therapeutic efficacy on various models and combinaison of radionuclides and route of administration. BIP-RIT appears to be always favourable in term of biodistribution and dosimetry (especially for the tumour-over-blood ratio) whatever the radionuclide used. Bismuth-213 is particularly adapted for radioimmunotherapy of small residual tumours, showing therapeutic efficacy with no toxicity. PET/CT imaging of radiolabelled antibodies with Zirconium-89 was performed and may be used as a theranostic tool for (radio)immunotherapy with anti-AMHR2 antibodies. The anti-tumour efficacy mechanisms of a humanized version of anti-AMHR2 antibody are also presented. This work may lead to realistic theranostic options in ovarian cancer in clinic.

La acetilcolinesterasa (AChE) hidroliza el neurotransmisor acetilcolina. La enzima se presenta en distintas formas moleculares. Tetrámeros hidrofílicos de AChE de suero fetal bovino se purificaron, sometieron a un tratamiento químico desnaturalizante o reductor, y estudiaron mediante análisis de sedimentación, cromatografía, fluorescencia intrínseca y unión de sondas hidrofóbicas. La transformación de los tetrámeros hidrofílicos en dímeros y monómeros anfifílicos demostró la alta flexibilidad conformacional de las subunidades de AChE, lo que podría ser crucial en la síntesis del conjunto completo de sus formas moleculares, y aportó una explicación de cómo algunas de sus formas interaccionan con las membranas. Para entender la heterogeneidad molecular de la AChE, también se empleó el anticuerpo AE-1, que interaccionó de forma desigual con oligómeros y monómeros de AChE de distintas fuentes. Experimentos de Western blot demostraron que el epítopo de AE-1 es de naturaleza confor macional. Finalmente, los datos experimentales descartaron la fosforilación de la AChE con proteína quinasa A. / Acetylcholinesterase (AChE) hydrolyzes the neurotransmitter acetylcholine. The enzyme exists in several molecular forms. AChE hydrophilic tetramers from fetal bovine serum were purified, chemically denatured or reduced, and studied by sedimentation analysis, hydrophobic chromatography, intrinsic fluorescence spectra and binding of amphiphilic probes. Conversion of the hydrophilic tetramers into amphiphilic dimers and monomers showed that AChE subunits possess a flexible conformation, which may be important for generating a full set of molecular forms, and gave an explanation of the interaction of certain AChE forms with membranes. Another approach to determine the molecular basis for the structural heterogeneity of AChE was to use the antibody AE-1, which distinctly reacted with AChE oligomers and monomers from different sources. The results of Western blot revealed that the determinant for AE-1 consisted of a conformational domain, not a primary sequence region. Finally, the experimental data rejected the phosphorylation of AChE at non-consensus protein kinase A sites.

No description available.

Hepatitis C virus (HCV) is a major cause of liver cirrhosis and hepatocellular carcinoma. In the first part of my PhD, we aimed to further characterize the role of scavenger receptor class B type I (SR-BI) in HCV infection. While the SR-BI determinants involved in HCV binding have been partially characterized, the post-binding function of SR-BI remains remained largely unknown. To further explore the role of HCV-SR-BI interaction during HCV infection, we generated a novel class of anti-SR-BI monoclonal antibodies inhibiting HCV infection. We demonstrated that human SR-BI plays a dual role in the HCV entry process during both binding and post-binding steps. Targeting the post-binding function of SR-BI thus represents an interesting antiviral strategy against HCV infection. In the second part of my PhD, we aimed to characterize the molecular mechanisms underlying HCV re-infection of the graft after liver transplantation (LT). We identified threeadaptive mutations in envelope glycoprotein E2 mediating enhanced entry and evasion of a highly infectious escape variant. These mutations markedly modulated CD81 receptor dependency resulting in enhanced viral entry. The identification of these mechanisms advances our understanding of the pathogenesis of HCV infection and paves the way for the development of novel antiviral strategies and vaccines.

Inhibitors of proteases in tick saliva play an important role during tick feeding. Tick saliva contains a wide range of bioactive components which are able to modulate host imunity. Therefore, ticks are able to feed for a long time and transfer tick-borne diseases pathogens. The risk of transfer can be significantly reduced by deactivation of theese protease inhibitors. In this study I made monoclonal antibodies for detection and quantification of two serine protease inhibitors in tick saliva and other tick-body parts.

Globalmente ocorrem cerca de 800.000 mortes de crianças menores de cinco anos associadas à diarreia, principalmente na África subsaariana, sul da Ásia e América Latina. Dentre os patógenos causadores de diarreia, Escherichia coli diarreiogênica (DEC) é o agente etiológico bacteriano mais comum, incluindo E. coli enteropatogênica (EPEC) e E. coli produtora da toxina de Shiga e seu subgrupo enterohemorrágica (STEC/EHEC). Os dados epidemiológicos indicam a importância do diagnóstico precoce e sua realização em locais com pouca infraestrutura. Desta forma o objetivo deste trabalho foi o desenvolvimento de um teste rápido, sensível e específico para o diagnóstico de EPEC e STEC/EHEC. Primeiramente, foram definidas diferentes condições do cultivo bacteriano: Dulbecco\'s modified Eagle\'s (DMEM), DMEM contendo 1% de triptona e DMEM pré-condicionado para o cultivo dos isolados de EPEC/EHEC e avaliação da produção/secreção das proteínas secretadas EspA e EspB, utilizando anticorpos monoclonais (MAb) e policlonais (PAb) anti-EspA ou anti-EspB por ELISA indireto. Para a avaliação da liberação das toxinas de Shiga para o sobrenadante do cultivo bacteriano de STEC/EHEC, foram testados diferentes condições de tratamento, o cultivo bacteriano foi tratado com Triton X-100 e o sedimento foi tratado com tampão de lise B-PER utilizando MAb e PAb anti-Stx1 ou anti-Stx2 por ELISA de captura. Subsequentemente, foi desenvolvido e avaliado o teste de aglutinação em látex para a detecção de EspB em isolados de EPEC/EHEC, e Stx1 e Stx2 em isolados de STEC/EHEC. EspB foi definida como biomarcador, o MAb anti-EspB como ferramenta para o diagnóstico de EPEC/EHEC, e a condição ideal para a produção/secreção de EspB foi o cultivo em DMEM. Para o diagnóstico de STEC/EHEC a condição ideal para liberação das toxinas Stx foi o tratamento do cultivo com Triton X-100. Tanto o ELISA, como a aglutinação em látex apresentaram sensibilidades e especificidades exigidas para testes diagnósticos de doenças negligenciadas em países em desenvolvimento e os testes de aglutinação em látex para a detecção destes patógenos foram precisos, rápidos e fáceis de executar, sendo portanto promissores para a utilização em laboratórios com mínima infraestrutura. / There are 800,000 deaths associated with diarrhea worldwide in children under five, and these are mainly in sub-Saharan Africa, Southeast Asia and Latin America. Among the causative pathogens of diarrhea, diarrheagenic Escherichia coli (DEC) is the most common bacterial etiological agent, including enteropathogenic E. coli (EPEC) and Shiga toxin-producing E. coli and its subgroup enterohemorrhagic E. coli (STEC/EHEC). Epidemiological data indicate the importance of early diagnosis and its realization in places with limited resources. Therefore, the objective of this work was to develop a rapid, sensitive and specific test for the diagnosis of EPEC and STEC/EHEC. First, different bacterial growth conditions were evaluated: Dulbecco\'s modified Eagle\'s medium (DMEM) or DMEM containing 1% tryptone, and DMEM pre-conditioned with EPEC/EHEC isolates. The production/secretion of the secreted proteins EspA and EspB was determined by indirect ELISA utilizing anti-EspA or anti-EspB monoclonal (MAb) and polyclonal (PAb) antibodies. Different treatments were tested for their effect on the release of Shiga toxins into the medium of STEC/EHEC bacterial cultures. The bacterial culture supernatant was treated with Triton X-100, and the sediment was treated with B-PER lysis buffer. The toxins release was determined by capture ELISA using anti-Stx1 or anti-Stx2 MAb and PAb. Subsequently, a latex agglutination test was developed and evaluated for the detection of EspB in EPEC/EHEC isolates and of Stx1 and Stx2 in STEC/EHEC isolates. EspB was defined as the biomarker and anti-EspB MAb as the tool for the diagnosis of EPEC/EHEC. The ideal conditions for the production/secretion of EspB were cultivation in DMEM. For the diagnosis of STEC/EHEC, the ideal conditions for the release of Stx were Triton X-100 treatment. ELISA as well as latex agglutination showed the sensitivities and specificities required for diagnostic tests of neglected diseases in developing countries. The latex agglutination test for the detection of these pathogens was precise, rapid and easy to perform, thereby being promising for their utilization in laboratories with limited resources.

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

Les anticorps monoclonaux (mAbs) sont des glycoprotéines complexes possédant de nombreuses micro-hétérogénéités qui peuvent influencer leur efficacité dans l’organisme. Il est par conséquent nécessaire de développer des méthodes analytiques robustes, sensibles et spécifiques pour les caractériser avec la plus grande précision. L’objectif de cette thèse a été de développer des méthodes analytiques permettant la caractérisation fine et à différents niveaux d’un anticorps monoclonal, le cetuximab, ainsi qu’un anticorps monoclonal conjugués à un principe actif, le brentuximab vedotin, sur des couplages direct ou indirect de l’électrophorèse capillaire et la spectrométrie de masse. Dans une première partie, une approche middle-up protéomique du cetuximab a été réalisé sur le couplage indirect CZE-UV/MALDI-MS afin de séparer et caractériser les variants de charges du fragment F/2 et F(ab)’2 ainsi que la caractérisation top-down des fragments Fc/2. Ensuite une nouvelle stratégie indirecte CZE-UV/nanoESI-MS a été développée pour permettre la caractérisation fine de ce mAbs partiellement digéré. Enfin un couplage direct par CESI-MS a été développé pour permettre l’analyse rapide et précise du cetuximab middle-up. Dans une deuxième partie, la combinaison d’analyse de mAbs d’intact, middle-up et bottom-up protéomique a été réalisée sur le couplage CZE-UV/nanoESI-MS et CESI-MS. Cela a permis la caractérisation à différent niveau du brentuximab vedotin. Cette méthodologie a permis l’analyse du DAR, l’identification de fragments conjugués, la caractérisation simultanée de la séquence complète de l’anticorps, d’un grand nombre de modifications post-traductionnelles, la caractérisation des peptides conjugués ainsi que l’identification d’ions diagnostiques du principe actif. / Monoclonal antibodies (mAbs) are highly complex glycoproteins having a lot of micro-heterogeneities which can influence their effectiveness. As a consequence, it is necessary to develop robust analytical methods, sensitive and specific to characterize them with high accuracy. The purpose of this thesis was to develop analytical methods allowing the multi-level characterization of monoclonal antibody (cetuximab), and antibody drug conjugates (brentuximab vedotin), using on-online or off-line capillary electrophoresis – mass spectrometry coupling. In the first section, a middle-up proteomic approach of cetuximab was carried out using Off-line CZE-UV/MALDI-MS coupling to separate and to characterize Fc/2 and F(ab)’2 charge variants. A top-down characterization of Fc/2 fragments was also employed. Then a new strategy off-line CZE-UV/nanoESI-MS was used to allow the characterization of this partially digest mAbs. Finally, an online coupling by CESI-MS was developed to allow the fast and accurate analysis of middle-up cetuximab. In a second part, the combination of intact, middle-up and bottom-up proteomic carried out on CZE-UV/nanoESI-MS and CESI coupling allowed the most exhaustive characterization of brentuximab vedotin. This methodology allowed the analyze of DAR, the identification of fragments drug conjugates, the simultaneous characterization of the complete structure of antibody, a significant number of post-translational modifications, all peptides drug conjugates and the identification of diagnostic ions.

High grade aggressive lymphomas have high mortality. By their nature, more than 40% of patients die from these diseases even with the improved treatment strategies currently available for oncology patients. The characteristic feature is that they are functionally heterogeneous and therefore have different biological and molecular signatures which make it difficult for all groups to respond to same line of treatment. Based on the above, I set out to look at the impact of viral and cellular gene products on these groups of diseases: In chapter 3 I developed monoclonal antibodies against HERV‐K10. I subsequently investigated their expressions in aggressive lymphomas including Diffuse Large B‐cell lymphoma, Hodgkin’s lymphoma and Primary CNS lymphomas. I showed HERV‐K10 is expressed in cell lines of aggressive lymphomas, but not in paraffin‐embedded tissues. In chapter 4 I showed that the expression of ATM using immune‐histochemistry techniques in aggressive lymphomas does offer a guide to prognosis and treatment. Nearly 30% of Diffuse Large B‐cell lymphomas express ATM, 55% of Hodgkin’s lymphomas and more than 80% of Primary CNS lymphomas. I also showed there is a correlation of ATM expression and EBV‐driven aggressive lymphomas and that this has a poor prognostic significance. Chapter 5 analysed the results obtained by generating, validating and evaluating data base of DLBCL and PCNSL from a retrospective cohort over a 17‐year period. The results confirmed that prognostic indicators including ATM, S1PR2, Autotaxin and EBV using immuno‐histochemistry techniques help with categorising aggressive lymphomas into different prognostic groups and does influence future management. In summary, my results showed there is a critical place for immuno‐histochemistry techniques in convincingly helping understand the expressions of viral and cellular gene products in aggressive lymphomas and in contributing positively to their management.