abstract: Early detection and treatment of disease is paramount for improving human health and wellness. Micro-scale devices promote new opportunities for the rapid, cost-effective, and accurate identification of altered biological states indicative of disease early-onset; these devices function at a scale more sensitive to numerous biological processes. The application of Micro-Electro-Mechanical Systems (MEMS) in biomedical settings has recently emerged and flourished over course of the last two decades, requiring a deep understanding of material biocompatibility, biosensing sensitively/selectively, biological constraints for artificial tissue/organ replacement, and the regulations in place to ensure device safety. Capitalizing on the inherent physical differences between cancerous and healthy cells, our ultra-thin silicone membrane enables earlier identification of bladder cancer—with a 70% recurrence rate. Building on this breakthrough, we have devised an array to multiplex this sample-analysis in real-time as well as expanding beyond bladder cancer. The introduction of new materials—with novel properties—to augment current and create innovative medical implants requires the careful analysis of material impact on cellular toxicity, mutagenicity, reactivity, and stability. Finally, the achievement of replacing defective biological systems with implanted artificial equivalents that must function within the same biological constraints, have consistent reliability, and ultimately show the promise of improving human health as demonstrated by our hydrogel check valve. The ongoing proliferation, expanding prevalence, and persistent improvement in MEMS devices through greater sensitivity, specificity, and integration with biological processes will undoubtedly bolster medical science with novel MEMS-based diagnostics and therapeutics. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2018

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).

Le potentiel invasif et métastatique d'une tumeur est contrôlé par l'angiogenèse via le VEGF (Vascular Endothelial Growth Factor) et les altérations des systèmes impliqués dans l'adhérence cellulaire via les cadhérines. Dans ce travail, nous montrons que le L-165041, agoniste du récepteur nucléaire PPARβ (Peroxisome Proliferator-Activated Receptor) régule l'expression du VEGF dans des cellules dérivées de cancer du col de l'utérus dont le facteur étiologique est un papillomavirus (HPV). Cependant, cet effet est observé uniquement dans des cellules HPV18 indépendamment de l'oncoprotéïne virale E6 et de sa cible p53. De façon intéressante, à la diflérence de ce que nous observons dans des cellules de cancer vésical, le L- 165041 ne contrôle pas la transcription mais stabilise les messagers des isoformes du VEGF (VEGF121, VEGF165, VEGF189) indépendamment du récepteur PPARβ. La stabilisation des ARNm VEGF nécessite la phosphorylation de la p38 MAPK qui conduit, seule ou suite à une cascade de phosphorylations, au déplacement de la protéine HuR du noyau vers le cytoplasme et in fine à la stabilisation des ARNm VEGF. D'autre part, l'agoniste du PPARβ interviendrait dans la« transition épithélio-mésenchymateuse » de cellules urothéliales malignes, puisqu'une augmentation de l'expression de la cadhérine E (marqueur épithélial) et une diminution de l'expression de la cadhérine N (marqueur mésenchymateux) sont observées selon le phénotype cellulaire. Elucider le mécanisme moléculaire d'action des agonistes de PPARβ est d'un intérêt crucial puisque certains ligands sont en cours d'évaluation clinique pour le traitement de maladies métaboliques (dyslipidémies diabète de tvpe II). / Tumor invasive and metastatic potential is controlled by angiogenesis through VEGF (Vascular Endothelial Growth Factor) up-regulation and altered cadherin-mediated cellular adhesion as well. In this work, we show that the L-165041 nuclear receptor PPARβ (Peroxisome Proliferator-Activated Receptor) agonist regulates VEGF expression in cervical cancer derived cells harboring a Human Papilloma Virus (HPV). However, this effect is only observed in HPVl8 positive cells through E6 viral oncoprotein and p53 independent mechanisms. Interestingly, unlike our data obtained in bladder cancer cells, L-165041 does not control VEGF transcription but stabilizes VEGF isoforms mRNA (VEGF121, VEGFl65, VEGFl89) and acts through PPARβ-independent mechanisms. This mRNA stabilization requires p38 MAPK phosphorylation leading to the nuclear/cytoplasmic shuttling ofHuR protein and consequently to the VEGF mRNA stabilization. Furthennore, the PPARβ agonist would be involved in epithelial to mesenchymal transition since it increases E-cadherin expression and decreases N-cadherin one according to the cellular phenotype. To elucidate the molecular mechanism of PPARβ agonists action is crucial because some of ligands are currently in clinical trials for the treatment of metabolic diseases (dyslipidemia, type II diabetes).

Les tumeurs de la vessie sont le quatrième cancer en terme de fréquence chez l’homme dans les pays industrialisés. Elles peuvent schématiquement être séparées en deux sous-groupes principaux : les tumeurs basales, peu différenciées, et les tumeurs luminales, différenciées. PPARγ est un récepteur nucléaire fortement exprimé dans ce second groupe, qui agit en hétérodimère avec un co-récepteur partenaire, RXRα, et possède un rôle essentiel dans la différenciation des cellules de l’urothélium normal. Récemment, un rôle protumorigénique de PPARγ a été mis en évidence dans les tumeurs luminales de vessie, où son activité est augmentée par le biais d’amplifications de PPARγ, ainsi que des mutations activatrices de son partenaire, RXRα. Le premier axe de mon projet a consisté à mieux caractériser ce rôle protumorigénique de PPARγ. J’ai d’abord participé à la mise en évidence de mutations récurrentes activatrices de PPARγ dans les tumeurs luminales de la vessie renforçant le rôle protumorigénique du récepteur dans ces tumeurs. J’ai ensuite cherché à identifier les gènes cibles de l’hétérodimère PPARγ/RXRα pouvant médier cet effet protumorigénique. Grâce à des analyses transcriptomiques après extinction de l’expression PPARγ ou de RXRα et des expériences de ChIP-sequencing de PPARγ et RXRα, j’ai pu identifier 30 gènes candidats. L’étude de l’implication de ces gènes dans la progression tumorale des tumeurs luminales présentant des altérations de la voie PPARγ/RXRα est actuellement en cours. Parallèlement à ce rôle protumorigénique dans les tumeurs luminales, des résultats suggéraient que ce gène pourrait posséder un rôle suppresseur de tumeurs dans le sous-groupe basal. La deuxième partie de mon projet a consisté à explorer cette hypothèse. J’ai pu montrer que des délétions hétérozygotes de PPARγ sont associées à ce sous-groupe de tumeurs basales, qui présente également une diminution globale de l’expression de PPARγ. De plus, parmi les mutations non-récurrentes de PPARγ identifiées dans ces tumeurs, certaines sont des mutations inactivatrices, capables d’inhiber l’activité transcriptomique de l’hétérodimère PPARγ/RXRα en favorisant la fixation de co-répresseurs de l’hétérodimère. J’ai également pu montrer un rôle anti-tumoral de PPARG dans les tumeurs basales puisque l’expression de PPARγ dans des lignées cellulaires basales à la suite de leur transfection avec un plasmide codant pour PPARγ est capable d’inhiber leur viabilité. Ce projet a ainsi permis de mettre en évidence un rôle dual de PPARγ dans les tumeurs de vessie, avec un rôle protumorigénique dans les tumeurs luminales, où il est suractivé par des amplifications et des mutations activatrices, et un rôle suppresseur de tumeurs dans les tumeurs basales, où il est réprimé par des délétions et de mutations inactivatrices. / Bladder tumors are the fourth cancer in terms of frequency in men, in industrialized countries. Bladder cancers can be divided into two main subgroups: undifferentiated basal tumors and differentiated luminal tumors. The nuclear receptor PPARγ, which is highly expressed in the second subgroup, forms a heterodimer with its partner, the nuclear receptor RXRα, and plays a key role in normal urothelial differentiation. A protumorigenic role of PPARγ has been established in luminal bladder cancer, with an increased activity through PPARγ genomic amplification or activating mutations of its partner, RXRα. The first part of my project aimed to better characterize this protumorigenic effect. I first participated in the identification of recurrent activating mutations of PPARγ in the luminal subgroup, enhancing its protumorigenic role in those tumors. Then, I tried to identify the PPARγ/RXRα heterodimer target genes that drive its protumorigenic role. By analyzing transcriptomic data following down regulation of PPARγ and RXRα, as well as ChIP-sequencing data for each of them, I identified 30 candidate target genes. The implication of the candidate genes in tumor progression of luminal cancer carrying PPARγ/RXRα pathway alteration is in progress. As opposed to its protumorigenic role in luminal tumors, some results suggested that PPARγ could play a tumor suppressor role in the basal subgroup. The second part of my project explored this hypothesis. I characterized PPARγ deletions associated with the basal subgroup, which presents a global PPARγ downregulation. Moreover, some of the non-recurrent mutations identified in this subgroup are inactivating mutations, able to inhibit the transcriptomic activity of the PPARγ/RXRα heterodimer, by an enhanced affinity of the heterodimer for co-repressors. I also showed an antitumor effect of PPARγ in basal tumors: its expression in basal bladder cell lines after transfection with a plasmid coding for PPARγ was able to inhibit cell viability. This project highlighted the dual role of PPARγ in bladder tumors, with a protumorigenic effect in luminal tumors through amplifications and activating mutations, and a tumor suppressor effect in basal tumors through deletions and inactivating mutations.

No description available.

Objectives Previous studies have demonstrated that intravesical administration of apaziquone (EOquin) has ablative activity against superficial bladder cancer marker lesions with 8 out of 12 complete responses recorded. We present a comparison between the rates of tumor recurrence before and after treatment with apaziquone. Methods The rate of tumor recurrence after treatment with apaziquone was compared with each patient's historical record of recurrences obtained from a retrospective analysis of the patients' case notes. The time to each recurrence event before apaziquone treatment and the time to the first recurrence after apaziquone treatment were recorded, and the data were analyzed using a population-averaged linear regression model using Stata Release, version 9.2, software. Results Of the eight complete responses obtained in the Phase I study, tumor recurrence occurred in 4 patients and the remaining 4 patients remained disease free after a median follow-up of 31 months. The time to the first recurrence after apaziquone treatment was significantly longer (P <0.001) compared with the historical pattern and recurrence interval before apaziquone. Before apaziquone instillation, the mean ± SE recurrence rate and tumor rate per year was 1.5 ± 0.2 and 4.8 ± 1.2, respectively, and these decreased to 0.6 ± 0.25 and 1.5 ± 0.8, respectively, after apaziquone treatment (P <0.05). Conclusions The results of this study indicate that early recurrences after treatment with apaziquone are infrequent and the interval to recurrence is significantly greater compared with the historical recurrence times for these patients. Larger prospective randomised trials are warranted to confirm these results. Aapaziquone (EOquin, USAN, E09, 3-hydroxy-5-aziridinyl-1-methyl-2[indole-4,7-dione]¿prop-¿-en-¿-ol) belongs to a class of anticancer agents known as bioreductive drugs that require metabolism by cellular reductases to generate a cytotoxic species.1 Although it is chemically related to mitomycin C, apaziquone has a distinctly different mechanism of action and preclinical activity profile.1 and 2 The initial optimism generated by its preclinical activity profile rapidly evaporated after the demonstration that intravenously administered apaziquone was clinically inactive against a range of solid tumors in Phase II clinical trials.3 and 4 Several possible explanations were considered for its lack of efficacy, but poor drug delivery to the tumor because of the rapid pharmacokinetic elimination of apaziquone in conjunction with relatively poor penetration through avascular tissue was considered to be the principal reason.5 On the basis of the rationale that intravesical administration would circumvent the problem of drug delivery and any apaziquone absorbed into the blood stream would be rapidly cleared,6 a Phase I-II clinical pilot study of intravesical administration of apaziquone to superficial bladder tumors was established.7 The results of that trial demonstrated that intravesically administered apaziquone has ablative activity against superficial bladder transitional cell carcinoma (TCC) marker lesions.7 These results were confirmed and extended in a Phase II clinical trial of 47 patients with superficial bladder TCC, in which complete responses were obtained in 67% of patients.8 Because all the enrolled patients in the original trial7 had had multiple recurrences after previous intravesical chemotherapy and/or immunotherapy, the purpose of the present study was, first, to report the recurrences that occurred after apaziquone treatment and, second, to study the effect of apaziquone instillation on the recurrence rate by statistically comparing these results with the historical pattern of recurrences for each patient before treatment with apaziquone.

Background: A hallmark of Notch signaling is its variable role in tumor biology, ranging from tumor-suppressive to oncogenic effects. Until now, the mechanisms and functions of Notch pathways in bladder cancer (BCa) are still unclear. Methods: We used publicly available data from the GTEx and TCGA-BLCA databases to explore the role of the canonical Notch pathways in BCa on the basis of the RNA expression levels of Notch receptors, ligands, and downstream genes. For statistical analyses of cancer and non-cancerous samples, we used R software packages and public databases/webservers. Results: We found differential expression between control and BCa samples for all Notch receptors (NOTCH1, 2, 3, 4), the delta-like Notch ligands (DLL1, 3, 4), and the typical downstream gene hairy and enhancer of split 1 (HES1). NOTCH2/3 and DLL4 can significantly differentiate non-cancerous samples from cancers and were broadly altered in subgroups. High expression levels of NOTCH2/3 receptors correlated with worse overall survival (OS) and shorter disease-free survival (DFS). However, at long-term (>8 years) follow-up, NOTCH2 expression was associated with a better OS and DFS. Furthermore, the cases with the high levels of DLL4 were associated with worse OS but improved DFS. Pathway network analysis revealed that NOTCH2/3 in particular correlated with cell cycle, epithelial–mesenchymal transition (EMT), numbers of lymphocyte subtypes, and modulation of the immune system. Conclusions: NOTCH2/3 and DLL4 are potential drivers of Notch signaling in BCa, indicating that Notch and associated pathways play an essential role in the progression and prognosis of BCa through directly modulating immune cells or through interaction with cell cycle and EMT.

Bladder cancer (BCa) is one of the most common malignancies and has a relatively poor outcome worldwide. However, the molecular mechanisms and processes of BCa development and progression remain poorly understood. Therefore, the present study aimed to identify candidate genes in the carcinogenesis and progression of BCa. Five GEO datasets and TCGA-BLCA datasets were analyzed by statistical software R, FUNRICH, Cytoscape, and online instruments to identify differentially expressed genes (DEGs), to construct protein‒protein interaction networks (PPIs) and perform functional enrichment analysis and survival analyses. In total, we found 418 DEGs. We found 14 hub genes, and gene ontology (GO) analysis revealed DEG enrichment in networks and pathways related to cell cycle and proliferation, but also in cell movement, receptor signaling, and viral carcinogenesis. Compared with noncancerous tissues, TPM1, CRYAB, and CASQ2 were significantly downregulated in BCa, and the other hub genes were significant upregulated. Furthermore, MAD2L1 and CASQ2 potentially play a pivotal role in lymph nodal metastasis. CRYAB and CASQ2 were both significantly correlated with overall survival (OS) and disease-free survival (DFS). The present study highlights an up to now unrecognized possible role of CASQ2 in cancer (BCa). Furthermore, CRYAB has never been described in BCa, but our study suggests that it may also be a candidate biomarker in BCa.

No description available.

During the past few decades, the landscape of available therapeutic interventions for cancer treatment has widely expanded, boosted mainly by immunotherapy progress and the precision oncology paradigm. The extensive use of pre-clinical models in cancer research has led to the discovery of new effective treatment options for patients. Despite the notable advancements, some cancer types have found minor benefits from the use of precision-oncology interventions. Characterized by a heterogeneous molecular landscape, bladder cancer is one of the most frequent cancer types in which standard-of- care treatments involve surgical operations accompanied by broad-spectrum chemotherapy. My research stems from the need for precision oncology interventions in bladder cancer and specifically focuses on the development of computational frameworks to guide the discovery of new therapeutic opportunities. This work first introduces the exploration of possible therapeutic interventions in 9p21.3 depleted bladder tumors through the analysis of an in-house large High-Content Drug Screening that tested 2,349 compounds. By combining cell count changes and morphological quantitative features extracted from fluorescence images, we nominate cytarabine as a putative candidate eliciting specific cytotoxic effects in an engineered 9p21.3 depleted bladder cancer model compared to an isogenic wild-type clone. Focusing on the development of computational methodologies to nominate robust context-specific vulnerabilities, I further describe PRODE (PROtein interactions informed Differential Essentiality), an analytical workflow that integrates protein-protein interaction data and Loss of Function screening data. I extensively tested PRODE against the most commonly used and alternative methodologies and demonstrated its superior performance when classifying reference essential and context-essential genes collected from experimental and literature sources. Furthermore, we applied PRODE to a real case scenario, seeking essential genes selectively in the context of HER2+ Breast Cancer tumors. Finally, I report the computational analyses performed on Patient-Derived Organoids (PDOs) established from a bladder cancer cohort. PDOs are demonstrated as informative models when assessing the therapeutic sensitivity of patients to drugs. Overall, this research highlights novel precision-oncology applications by ad-hoc computational analyses that address key open technical and biological challenges in the field of bladder cancer and beyond.