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Bladder cancer (BCa) is the fourth most commonly diagnosed cancers in men and the eighth most common in women. It is an abnormal growth of tissues which develops in the bladder lining. Histological analysis of bladder tissue facilities diagnosis as well as it serves as an important tool for research. To bet- ter understand the molecular profile of bladder cancer and to detect predictive and prognostic features, microscopy methods, such as immunofluorescence (IF), are used to investigate the characteristics of bladder cancer tissue. For this project, a new method is proposed to segment cancer epithelial us- ing nuclei morphology captured with IF staining. The method is implemented using deep learning algorithms and performance achieved is compared with the literature. The dataset is stained for nuclei (DAPI) and a marker for cancer epithelial (panEPI) which was used to create the ground truth. Three popu- lar Convolutional Neural Network (CNN) namely U-Net, Residual U-Net and VGG16 were implemented to perform the segmentation task on the tissue mi- croarray dataset. In addition, a transfer learning approach was tested with the VGG16 network that was pre-trained with ImageNet dataset. Further, the performance from the three networks were compared using 3fold cross-validation. The dice accuracies achieved were 83.32% for U-Net, 88.05% for Residual U-Net and 82.73% for VGG16. These findings suggest that segmentation of cancerous tissue regions, using only the nuclear morphol- ogy, is feasible with high accuracy. Computer vision methods better utilizing nuclear morphology captured by the nuclear stain, are promising approaches to digitally augment the conventional IF marker panels, and therefore offer im- proved resolution of the molecular characteristics for research settings.

Arsenic is a human carcinogen associated with urinary bladder transitional cell carcinoma and other cancers. Arsenic is also a strong comutagen and cocarcinogen. One possible mode of action for arsenic carcinogenesis/cocarcinogenesis is inhibition of DNA damage repair. In laboratory animals, urinary bladder transitional cell carcinoma has only been observed in dimethylarsinic acid [DMA(V)]-exposed F344 rats. The goal of the present studies was to investigate inhibition of DNA repair as a mode of action for arsenic carcinogenesis/ cocarcinogenesis in the urinary bladder. Methods were first developed to harvest only transitional cells, the target cell type of arsenic carcinogenesis, suitable for RNA extraction or for DNA damage detection by Comet assay. Morphological studies established that DMA(V) in drinking water at 40 ppm was cytotoxic to the urothelium of Sprague-Dawley and F344 rats, and mitochondria were targeted by DAM(V). To investigate whether DMA(V) decreases the expression of DNA repair genes, mRNA levels of DNA repair genes in transitional cells were next measured in F344 rats exposed to up to 100 ppm DMA(V) in drinking water for 4 weeks. The mRNA levels of Ataxia Telangectasia mutant (ATM), X-ray repair cross-complementing group 1 (XRCC1), excision repair cross-complementing group 3/Xeroderma Pigmentosum B (ERCC3/XPB), and DNA polymerase beta genes were not altered, as measured by real time RT PCR. These results suggested either that DMA(V) affects DNA repair without affecting the baseline expression of DNA repair genes or that DMA(V) does not affect DNA repair in the bladder. Arsenic effects on DNA repair were further investigated in F344 rats given 100 ppm DMA(V) or arsenate in drinking water for 1 week. DNA damage levels in transitional cells and micronuclei frequency (MN) in bone marrow were measured. Dimethylarsinic acid did not affect in vivo cyclophosphamide-induced DNA damage, and neither DMA(V) nor arsenate inhibited in vitro repair of hydrogen peroxide- or formaldehyde-induced DNA damage, as measured by Comet assay. Neither DMA(V) nor arsenate increased MN or elevated in vivo cyclophosphamide-increased MN. These results suggest inhibition of DNA repair by arsenic, in the transitional epithelium, may not be a major mechanism responsible for carcinogensis/cocarcinogenesis in the bladder. / Ph. D.

A central theme within the concept of enzyme-directed bioreductive drug development is the potential to predict tumour response based on the profiling of enzymes involved in the bioreductive activation process. Mitomycin C (MMC) is the prototypical bioreductive drug that is reduced to active intermediates by several reductases including NAD(P)H:quinone oxidoreductase (NQO1) and NADPH cytochrome P450 reductase (P450R). The purpose of our study was to determine whether NQO1 and P450R protein expression in a panel of low-grade, human superficial bladder tumours correlates with clinical response to MMC. A retrospective clinical study was conducted in which the response to MMC of 92 bladder cancer patients was compared to the immunohistochemical expression of NQO1 and P450R protein in archived paraffin-embedded bladder tumour specimens. A broad spectrum of NQO1 protein levels exists in bladder tumours between individual patients, ranging from intense to no immunohistochemical staining. In contrast, levels of P450R were similar with most tumours having moderate to high levels. All patients were chemotherapy naïve prior to receiving MMC and clinical response was defined as the time to first recurrence. A poor correlation exists between clinical response and NQO1, P450R or the expression patterns of various combinations of the 2 proteins. The results of our study demonstrate that the clinical response of superficial bladder cancers to MMC cannot be predicted on the basis of NQO1 and/or P450R protein expression and suggest that other factors (other reductases or post DNA damage events) have a significant bearing on tumour response.

Câncer de bexiga (CB) é a segunda doença mais prevalente do trato urinário. Atualmente as principais terapias para o CB apresentam baixa eficácia, altas taxas de recorrência e vários efeitos adversos. Assim, avalia-se o potencial de novas moléculas para a terapia do CB. Quercetina (QT) é um flavonóide com propriedades inibidora da proliferação celular e apoptótica que são interessantes para o tratamento do câncer, porém é um composto instável e fotossensível, o que inviabiliza sua administração na forma livre. Desta forma, o encapsulamento da QT em carreadores lipídicos nanoestruturados (CLN) funcionalizados com folato (CLN-F) pode ser um sistema efetivo de entrega de QT em células de CB que poderá superar os desafios da terapia intravesical do CB. O encapsulamento da QT pode aumentar a estabilidade da QT, sua permeação pelo urotélio, internalização em células tumorais, seu tempo de residência na bexiga e sua eficácia farmacológica. Os objetivos deste trabalho foram preparar, caracterizar e avaliar a citotoxicidade de QT livre e encapsulada em CLN e CLN-F em células de CB. O CLN e CLN-F foram preparados pelo método de emulsão e sonicação. A funcionalização do CLN foi realizada pela reação do estabilizante Pluronic F68 com folato (PF68F). Esta funcionalização foi avaliada por espectroscopia de ressonância magnética Nuclear (RMN) unidimensional de 1H. Os CLNs foram caracterizados quanto ao diâmetro, índice de polidispersão (PdI), potencial zeta (PZ), cristalinidade, eficiência de encapsulamento (EE) e morfologia. Além disso, foi avaliado o perfil de liberação da QT, a atividade antioxidante e a citotoxicidade da QT livre e encapsulada. A funcionalização foi confirmada pelos espectros de RMN que apresentaram sinais atribuídos ao PF68 e ao folato. O diâmetro, PdI e o PZ dos CLN foram 176,5 nm, 0,124 e -11,4 mV, respectivamente. O CLN-F apresentou 197,9 nm de diâmetro, 0,160 de PdI e -17,5mV de PZ. O encapsulamento da QT não alterou significativamente estes parâmetros para ambas as partículas. Obteve-se uma alta eficiência de encapsulamento da QT, para os dois carreadores (~98%), devido, provavelmente, ao baixo valor de índice de recristalização (~28) dos CLNs. Os CLN apresentam forma esférica, estabilidade por 330 dias e um perfil de liberação sustentada da QT. O IC50 do CLN-F-QT (83,4 ?g/mL) foi menor que o IC50 do CLN-QT (94,9 ?g/mL) provavelmente devido ao aumento da internalização causada pela funcionalização das partículas com folato. Os CLN-QT e CLN-F-QT apresentaram alta atividade antioxidante. Os resultados obtidos sugerem que o CLN-F-Q é um sistema com potencial para a futura terapia do CB, pois apresenta tamanho menor que 200 nm, baixo PdI, alta estabilidade, EE e atividade antioxidante, liberação sustentada além de ser citotóxico para as células RT4. / Bladder cancer (BC) is the second most prevalent tumor of urinary tract. Currently the main BC therapies have low effectiveness, high recurrence rate and several adverse effects. Thus, new molecule have been investigate to CB therapy. Quercetin (QT) is a flavonoid with interesting properties for cancer therapy such as inhibition of cancer cell proliferation and apoptosis. However, QT is an unstable and photosensitive compound. Therefore, QT encapsulated in nanostructure lipid carriers (NLC) functionalized with folate (F-NLC) might be an alternative targeting system of QT for tumor cell and can be strategy to overcome intravesical CB therapy challenges. The QT encapsulation can improve QT stability, increase its permeation in the urothelium and uptake in tumor cells, increase retention time in the bladder and enhancing its pharmacological efficacy. Aims of this study were preparation, characterization of NLC-QT and F-NLC-QT and cytotoxic evaluation of these particles in BC cells. NLC and F-NLC were prepared by ultrasonication method. NLC were funcionalized by conjugated between surfactant Pluronic and folate (PL68F). This conjugation was characterized by proton nuclear magnetic resonance spectroscopy (NMR). The particles were characterized regarding to size, polydispersity index (PdI), zeta potential (ZP), crystallinity, encapsulation efficiency (EE) and morphology. Furthermore, stability, release profile, cytotoxicity and antioxidant activity of QT encapsulated or not in NLC, were evaluated. RMN spectrums confirmed the PF68 functionalization, exhibiting peaks attributed to PF68 and folate. Size, PdI and ZP of NCL were respectively 176.5 nm, 0.124 and -11.4, whereas F-NLC showed 197.9 nm of size, 0.160 of PdI and ZP of -17.5mV. The QT encapsulation did not affect these physical parameters. Low values of crystalization index (~28) might promote high EE of quercetin (~98%). NLC shows spherical shape, sustained release profile of QT and were stable for 330 days. IC50 of NLC-QT (87.4 ?g/mL) was smaller thanthe IC50 of F-NLC-QT (94.9 ?g/mL). This difference might be explained by the increase of NLC uptake by endocytosis mediated by folate receptor. NLC-QT and F-NLC-QT showed high antioxidant activity. Therefore, our results suggest that QT-F-NLC is a carry system with potential for future BC therapy that show size smaller than 200 nm, low PdI, high long-term stability, high EE and antioxidant activity, sustained release and cytotoxic to CB cells (RT4).

L'analyse de données d'expression montre qu'il est avantageux d'analyser les processus biologiques en termes de modules plutôt que simplement considérer les gènes un par un. Dans ce projet nous avons conduit une analyse non supervisée des données d'expression de gènes de plusieurs cohortes de tumeurs urothéliales en appliquant la méthode d'Analyse en Composantes Indépendantes. Plusieurs études ont démontré les meilleures performances de l'ACI par rapport à l'ACP et les méthodes de clustering, pour obtenir une décomposition plus réaliste des données d'expression en patterns d'expression pertinents et associés avec le phénotype d'intérêt.Les tumeurs urothéliales apparaissent et évoluent selon deux voies distinctes dont la probabilité de progression en cancer musculo-invasif diffère radicalement. Excepté la mutation de FGFR3 dans le groupe le moins agressif, les processus moléculaires sous-jacents n'ont pas été complètement identifiés. Le principal objectif de cette thèse était dédié aux interprétations biologiques des différentes composantes indépendantes pour aider à confirmer et étendre la liste des processus biologiques connus pour être impliqués dans le cancer de vessie.Chaque composante indépendante est caractérisée par une liste de projections de gènes et de contributions pondérées d'échantillons tumoraux . En combinant expertise biologique et comparaison des listes de gènes à des voies existantes et en étudiant conjointement l'association des composantes aux annotations cliniques et moléculaires, nous avons pu différencier les CIscausées par des facteurs techniques, tels que le prélèvement chirurgical de celles ayant des interprétations biologiques pertinentes. De plus, parmi les signaux pertinents biologiquement, cette analyse nous a permis de différencier les signaux provenant du stroma, comme la réponse immunitaire médiée par les lymphocytesB&T, de ceux produits par les tumeurs elles-mêmes, comme les signaux reliés à la prolifération ou à la différenciation. La classification des tumeurs selon leurs contributions à certaines CIs a pu être étroitement associée à des annotations anatomo-cliniques, et a mis en évidence de nouveaux sous-types de tumeur spotentiels, qui suggèrent l'existence de voies de progression supplémentaires dans le cancer de vessie. De façon similaire, l'étude des contributions de groupes de tumeurs basés sur des annotations cliniques ou moléculaires a montré différents niveaux de contamination par le stroma entre les tumeurs mutées et nonmutées pour FGFR3. La reproductibilité des composantes a été étudiée en utilisant des graphes de corrélation. La majeure partie des CIs interprétées a été validée sur trois jeux de données indépendants, et plusieurs d'entre elles ont aussi détectées dans un jeu de données de lignées cellulaires.Une deuxième étude sur le rétinoblastome a montré que nous pouvions tirer partie de l'ACI dans des contextes variés. Le rétinoblastome est initié par la perte des deux alléles du gène suppresseur de tumeur RB1. D'autres évènements génomiques non identifiés sont nécessaires à la progression de la maladie. Nous avons observé une association entre âge des patients et altérations génomiques. Les patients jeunes présentant moins d'altérations que les patients âgés, ces derniers présentant des gains du 1q et des pertes du 16q. Cette séparation des tumeurs selon l'âge est également observée sur les données d'expression, notamment en appliquant l'ACI dont l'une des composantes discrimine les patients selon leur âge. Ces résultats suggèrent l'existence de deux voies de progression dans le rétinoblastome. L'analyse des données à haut débit fournit de nombreuses listes de gènes. Afin de les interpréter, une possibilité est d'extraire les dernières publications groupées par sujets prédéfinis (fonction, localisation,...). / Practice of gene expression data analysis shows that it is advantageous to analyze biologicalprocesses in terms of modules rather than simply consider gene one by one. In this project, we conducted anunsupervised analysis of the gene expression data of several cohorts of urothelial tumors, applying theIndependent Component Analysis method. Several studies demonstrated the outperformance of ICA overPCA and clustering-based methods in obtaining a more realistic decomposition of the expression data intoconsistent patterns of coexpressed genes associated with the studied phenotypes[1, 2, 3, 4].Urothelial tumors arise and evolve through two distinct pathways which radically differ on their probabilityof progression to muscle invasion. Except the mutation of FGFR3 in the less aggressive group, theunderlying molecular processes have not been completely identified. The first and main objective of the PhDthesis was dedicated to the biological interpretation of the different independent components to help toconfirm and extend the list of biological processes known to be involved in bladder cancer.Each independent component (IC) is characterized by a list of gene projections on the one hand and weightedcontributions of tumor samples on the other hand. By combining biological expertise and comparison of theassociated list of genes to known pathways, and jointly studying the association of the components tomolecular and clinical annotations, we have been able to differentiate components that were caused bytechnical factors, such as surgical sampling, from those having consistent biological interpretationin terms of tumor biology. Moreover, among the biologically meaningful signals, this analysis allowed us todifferentiate the signals from stroma of the tumor, like immune response mediated by B- and T-lymphocytes,from the signals produced by the tumors themselves, like signals related to proliferation, or differentiation.The clustering of the tumor samples according to their contributions on some ICs can be closely associated toanatomo-clinical annotations, and highlighted new potential subtypes of tumors which suggest existence ofadditional pathways of bladder cancer progression. Similarly, the study of the contributions of preestablishedgroups of tumors based on clinical or molecular criteria showed different levels of stromacontamination between FGFR3 non-mutated and mutated tumors. The reproducibility of the components wasinvestigated using correlation graphs. The major part of the interpreted ICs was validated on threeindependent bladder cancer datasets, and several of them were also identified in an urothelial cancer celllines data set.A second study about retinoblastoma gave us the occasion to show that we can take advantage ofICA in various contexts. Retinoblastoma is initiated by the loss of both alleles of the RB1 tumor suppressorgene. Although necessary for initiation, other genomic events, that remain to be identified, are needed for theprogression of the disease [5]. We observed, as it was previously described [6], an association between age ofthe patients and levels of genomic aberrations, the younger patients having fewer alterations than the olderpatients, which generally present gain of 1q and loss of 16q. We showed that this tendency of the tumors tobe clustered into two groups of age can also be observed on the expression data by applying ICA whose oneof the component was highly correlated to the age of the patients. These results suggest the existence of twopathways of progression in retinoblastoma.The analysis of high throughput data provides many lists of genes. To interpret them, a possibility isto study the latest related publications grouped by pre-defined group of topics (function, cellular location...).To that aim, in a third study, we introduced a web-based Java application tool named GeneValorization whichgives a clear and handful overview of the bibliography corresponding to one particular gene list [7].

Les tumeurs de vessie suivent deux voies de progression tumorale. La voie des carcinomes in situ (CIS) qui progressent pour envahir la membrane basale puis le muscle, et la voie des tumeurs papillaires de bas grade qui progressent peu mais qui récidivent fréquemment. Environ 65% des tumeurs papillaires de bas grade présentent une mutation du gène FGFR3 et récemment des protéines de fusion FGFR3-TACC3 ont été observées dans les tumeurs de vessie (dans 10% des tumeurs invasives). Le rôle oncogénique du récepteur FGFR3 muté et de FGFR3-TACC3 a été démontré in vivo et in vitro. Cependant, les voies de signalisation du récepteur FGFR3 muté ou de FGFR3-TACC3 sont à l’heure actuelle très peu caractérisées. Dans ce contexte, deux approches ont été mises en place pour caractériser ces voies de signalisation. La première s’appuie sur l’étude de la phosphorylation des protéines p38, AKT et ERK1/2 par le récepteur FGFR3 muté (S249C) ou sauvage dans la lignée cellulaire fibroblastique NIH3T3, et a permis d’identifier les protéines p38 et AKT comme activées par le récepteur FGFR3 muté et nécessaire pour induire la transformation cellulaire. L’étude de l’activation de ces deux voies de signalisation a été réalisée dans des lignées cellulaires dérivées de tumeurs de vessie exprimant le récepteur FGFR3 muté ou FGFR3-TACC3 de manière endogène et a montré que leur activation était dépendante de celle du récepteur FGFR3. De plus nous avons montré que les protéines p38 et AKT sont impliquées dans le maintien d’une boucle de rétro-contrôle positive entre FGFR3 et MYC : l’activation de FGFR3 induit une surexpression de MYC qui en retour promeut l’expression de FGFR3. La seconde approche est basée sur une étude visant à identifier les partenaires protéiques de FGFR3 par spectrométrie de masse après immunoprécipitation de celui-ci qui avait été réalisée précédemment au laboratoire. L’analyse des données a permis l’obtention d’une liste de 60 protéines identifiées comme partenaires protéiques de FGFR3 avec une grande confiance. La construction d’un réseau à partir de cette liste n’a pas été possible (trop peu d’interactions existant entre ces protéines), nous avons donc développé un algorithme (PEPPER) en collaboration avec un étudiant en bio-informatique au laboratoire, Rémy Nicolle, pour proposer un réseau de signalisation de FGFR3.Les deux approches mises en place au cours de cette thèse nous ont permis de mieux caractériser les voies de signalisation du récepteur FGFR3. L’identification d’une boucle de rétrocontrôle entre FGFR3 et MYC a permis de mieux comprendre pourquoi le récepteur FGFR3 possède des propriétés oncogéniques, et de proposer les protéines p38 et AKT comme cibles thérapeutiques potentielles pour traiter les tumeurs de vessie exprimant le récepteur FGFR3 altéré. La construction du réseau de signalisation de FGFR3 via PEPPER donne une vue d’ensemble des voies de signalisation de FGFR3 et ouvre de nouvelles pistes à étudier. / Bladder cancer progression can be divided in two main pathways. The pathway of In Situ Carcinoma (CIS) which progress through an invasion of the basement membrane and then the muscle and the pathway of Ta papillary tumors which change little but recur frequently after tumor resection. Approximately 65% of Ta papillary tumors harboring a FGFR3 mutation and recently FGFR3-TACC3 fusion proteins have been observed in bladder tumors (about 10% of bladder tumors). The oncogenic role of the mutated FGFR3 receptor and of the FGFR3-TACC3 fusion protein has been demonstrated in vivo and in vitro. However signaling pathways activated by the mutated FGFR3 receptor or by the FGFR3-TACC3 fusion protein are currently poorly characterized.In this context, two approaches have been developed to characterize these signaling pathways. The first is based on the study of p38, AKT and ERK1/2 phosphorylation by the mutated receptor (S249C) or the wild type receptor in the NIH3T3 fibroblastic cell line. This study allowed identifying p38 and AKT as activated by the mutated FGFR3 receptor. Moreover, activation of p38 and AKT by the mutated receptor is critical for cell transformation. Study of the activation of these two signaling has been realized in human bladder cancer cell lines endogenously expressing the mutated FGFR3 receptor or the FGFR3-TACC3 fusion protein. Moreover, we showed that p38 and AKT are involved in the maintenance of a FGFR3/MYC feedback positive loop: FGFR3 activation induce MYC over expression which in turns promotes FGFR3 expression. The second approach is based on a study whose aim was to identify FGFR3 proteins partners by mass spectrometry after a FGFR3 immunoprecipitation, which has been previously realized in the lab. Data analyze led to the obtaining of a list of 60 proteins identified has FGFR3 protein partners with a high confidence. Construction of a FGFR3 network with this list was not possible (too little interactions existing between these proteins), so we developed an algorithm (PEPPER) in collaboration with a student in bioinformatics in the lab, Remy Nicolle, to propose a FGFR3 signaling network.The two approaches developed during this thesis allowed us to better characterize the FGFR3 signaling pathways. Identification of a FGFR3/MYC feedback loop allowed us to better understand why the altered FGFR3 has oncogenic properties and to propose p38 and AKT as news promising therapeutic targets, to treat human bladder tumors harboring the altered FGFR3 receptor. Construction of the FGFR3 signaling network with the algorithme PEPPER give an overview of the FGFR3 signaling pathways and open new tracks to explore.