abstract: Signal transduction networks comprising protein-protein interactions (PPIs) mediate homeostatic, diseased, and therapeutic cellular responses. Mapping these networks has primarily focused on identifying interactors, but less is known about the interaction affinity, rates of interaction or their regulation. To better understand the extent of the annotated human interactome, I first examined > 2500 protein interactions within the B cell receptor (BCR) signaling pathway using a current, cutting-edge bioluminescence-based platform called “NanoBRET” that is capable of analyzing transient and stable interactions in high throughput. Eighty-three percent (83%) of the detected interactions have not been previously reported, indicating that much of the BCR pathway is still unexplored. Unfortunately, NanoBRET, as with all other high throughput methods, cannot determine binding kinetics or affinities. To address this shortcoming, I developed a hybrid platform that characterizes > 400 PPIs quantitatively and simultaneously in < 1 hour by combining the high throughput and flexible nature of nucleic programmable protein arrays (NAPPA) with the quantitative abilities of surface plasmon resonance imaging (SPRi). NAPPA-SPRi was then used to study the kinetics and affinities of > 12,000 PPIs in the BCR signaling pathway, revealing unique kinetic mechanisms that are employed by proteins, phosphorylation and activation states to regulate PPIs. In one example, activation of the GTPase RAC1 with nonhydrolyzable GTP-γS minimally affected its binding affinities with phosphorylated proteins but increased, on average, its on- and off-rates by 4 orders of magnitude for one-third of its interactions. In contrast, this phenomenon occurred with virtually all unphosphorylated proteins. The majority of the interactions (85%) were novel, sharing 40% of the same interactions as NanoBRET as well as detecting 55% more interactions than NanoBRET. In addition, I further validated four novel interactions identified by NAPPA-SPRi using SDS-PAGE migration and Western blot analyses. In one case, we have the first evidence of a direct enzyme-substrate interaction between two well-known proto-oncogenes that are abnormally regulated in > 30% of cancers, PI3K and MYC. Herein, PI3K is demonstrated to phosphorylate MYC at serine 62, a phosphosite that increases the stability of MYC. This study provides valuable insight into how PPIs, phosphorylation, and GTPase activation regulate the BCR signal transduction pathway. In addition, these methods could be applied toward understanding other signaling pathways, pathogen-host interactions, and the effect of protein mutations on protein interactions. / Dissertation/Thesis / Doctoral Dissertation Biological Design 2018

Background: The biological mechanisms underlying early-and advanced-stage epithelial ovarian cancers (EOCs) are still poorly understood. This study explored kinase-driven metabolic signalling in early and advanced EOCs, and its role in tumour progression and response to carboplatin-paclitaxel treatment. Methods: Tumour epithelia were isolated from two independent sets of primary EOC (n-72 and 30 for the discovery and the validation sets, respectively) via laser capture microdissection. Reverse phase protein microarrays were used to broadly profile the kinase-driven metabolic signalling of EOC with particular emphasis on the LBK1-AMPK and AKT-mTOR axes. Signalling activation was compared between early and advanced lesions, and carboplatin-paclitaxel-sensitive and -resistant tumours. Results: Advanced EOCs were characterised by a heterogeneous kinase-driven metabolic signature and decreased phosphorylation of the AMPK-AKT-mTOR axis compared to early EOC (P<0.05 for AMPK alpha T172, AMPK alpha 1 S485, AMPK beta 1 S108, AKT S473 and T308, mTOR S2448, p70S6 S371, 4EBP1 S65, GSK-3 alpha/beta S21/9, FOXO1 T24/FOXO3 T32, and FOXO1 S256). Advanced tumours with low relative activation of the metabolic signature and increased FOXO1 T24/FOXO3 T32 phosphorylation (P=0.041) were associated with carboplatin-paclitaxel resistance. Conclusions: If validated in a larger cohort of patients, the decreased AMPK-AKT-mTOR activation and phosphorylation of FOXO1 T24/FOXO3 T32 may help identify carboplatin-paclitaxel-resistant EOC patients.

No description available.

Epigenetic regulatory mechanisms play important roles in the control of lineage-specific differentiation during development. However, mechanisms that regulate higher-order chromatin remodelling and transcription of keratinocyte-specific genes that are clustered in the genome into three distinct loci (Keratin type I/II loci and Epidermal Differentiation Complex (EDC)) during differentiation of the epidermis are poorly understood. By using 3D-Fluorescent In Situ Hybridization (FISH), we determined that in the epidermal keratinocytes, the KtyII and EDC loci are located closely to each other in the nuclear compartment enriched by the nuclear speckles. However, in KtyII locus knockout mice, EDC locus moved away from the KtyII locus flanking regions and nuclear speckles towards the nuclear periphery, which is associated with marked changes in gene expression described previously. Chromatin architectural protein Ctcf has previously been implicated in the control of long-range enhancer-promoter contacts and inter-chromosomal interactions. Ctcf is broadly expressed in the skin including epidermal keratinocytes and hair follicles. Conditional Keratin 14-driven Ctcf ablation in mice results in the increase of the epidermal thickness, proliferation, alterations of the epidermal barrier and the development of epidermal pro-inflammatory response. Epidermal barrier defects in Krt14CreER/Ctcf fl/fl mice are associated with marked changes in gene expression in the EDC and KtyII loci, which become topologically segregated in the nucleus upon Ctcf ablation. Therefore, these data suggest that Ctcf serves as critical determinant regulating higher-order chromatin organization in lineage-specific gene loci in epidermal keratinocytes, which is required for the proper control of gene expression, maintenance of the epidermal barrier and its function.

Protein microarrays are becoming powerful tools to screen and identify tumor markers for cancer diagnosis, because of the multiplex detection and minute volume of sample requirement. Due to the diversity and variation in different cancers, no single tumor marker is sensitive and specific enough to meet strict diagnostic criteria. Therefore, a combination of tumor markers is required to increase sensitivity and to establish distinct patterns to increase specificity. To obtain reliable tests, the development of reproducible surface chemistry and immobilization procedure are crucial steps in the elaboration of efficient protein microarrays. In this thesis, 3D micro-structured glass slides were functionalized with various surface chemistries like silane monolayer (amino, epoxy and carboxy), and polymer layers of Jeff amine, chitosan, carboxymethyl dextran (CMD), maleic anhydride-alt-methyl vinyl ether copolymer (MAMVE) for physical adsorption or covalent binding with proteins. Surface characterizations, such as X-ray photoelectron spectroscopy (XPS) and Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), confirmed the monolayer/polymer grafting on the glass slides. Colorimetric assay for determining amine density of three aminated surfaces demonstrated that APDMES had more grafting density than Jeffamine and chitosan. Contact angle measurements show that polymer surfaces were more hydrophilic than monolayer surfaces due to the increasing dosages of polar functional groups. Moreover, the parameters such as additives and pH of spotting buffer, probe concentration, blocking procedures etc, were optimized for tumor marker detection. Under the optimized conditions, antibody microarrays were validated with purified tumor antigens. The best analytical performances obtained for each tumor antigen tested were strongly dependent on functionalized surfaces, e.g. MAMVE exhibited best analytical performances for CEA andHsp60 while NHS leads to best results for PDI and CA19-9. Besides, the implemented antibody microarrays were applied to tumor marker detection from colorectal cancer sera. This evaluation shows the interest to combine several tumor markers on the same surface and the combination of tumor markers on their specific surface lead to remarkably increase the positive responses of tested cancer sera (even up to 100 %). A second type of microarrays (tumor-associated antigens - TAA microarrays) was designed to discriminate breast cancer patients from healthy donors through the detection of tumor autoantibodies. This study included a cohort of 29 breast cancer patients' and 28 healthy donors' sera. A panel of fiveTAAs (Hsp60, p53, Her2, NY-ESO-1 and Hsp70) immobilized on their respective optimized surface chemistry allowed to specifically detect over 82% of breast cancer patients.

Le cancer du sein demeure un problème de santé publique majeure dans le monde. Afin d'améliorer les chances de survie et la qualité de vie des femmes, il est nécessaire d’effectuer le diagnostic à un stade précoce et d’appliquer le traitement. Dans ce contexte, un des objectifs de cette thèse est de développer des puces à protéines pour le diagnostic et le pronostic du cancer du sein. Parmi les nombreux marqueurs biologiques potentiels, des recherches récentes ont montré que des anticorps anti-heat shock proteins (anti-HSPs) sont associés à la genèse tumorale. Ces anticorps seraient donc de bons biomarqueurs diagnostiques et pronostiques pour le cancer du sein. Par conséquent, nous avons élaboré une puce à antigènes afin de détecter les anticorps anti-HSP dans le sérum de 50 patients atteints de cancer du sein et de 26 témoins sains. Nos résultats indiquent clairement que la la détection multiplex d’une combinaison d'anticorps anti-HSP permet de discriminer les patients atteints de cancer du sein des témoins sains avec une sensibilité de 86% et une spécificité de 100%. Ensuite, nous avons élaboré une puce à anticorps pour doser la concentration de l'activateur du plasminogène de type urokinase (uPA) et de son inhibiteur principal (PAI-1) dans 16 extraits cytosoliques de tissus tumoraux. uPA et PAI-1 sont décrits comme étant de bons biomarqueurs pronostiques et prédictifs du cancer du sein. De faibles taux de uPA (≤3 ng / mg de protéine) et PAI-1 (≤14 ng / mg de protéine) sont associés à un faible risque de récidive et pas de bénéfice d’une chimiothérapie pour les patients atteints de cancer du sein. Les résultats obtenus à partir de puces à anticorps étaient surface dépendante par rapport aux résultats obtenus sous forme ELISA. En outre, l'utilisation de nos puces à anticorps nécessite 25 fois moins de volume d'échantillon par rapport à un dosage ELISA, résolvant ainsi les principales limites de la méthode ELISA. Enfin, nous avons déterminé et optimisé les paramètres influençant les performances des puces à protéines, comme par exemple la chimie de surface, la durée expérimentale, la concentration des solutions, etc. Nous avons également étudié les conditions de stockage à la fois pour des surfaces chimiquement fonctionnalisées et pour les puces à protéines. Les résultats ont montré que les puces à protéines conservent leur activité biologique jusqu’à trois mois de stockage. / Breast cancer becomes the most common cancer among women. In order to improve women's chances of survival and life quality, to be diagnosed at an early stage and to receive correct treatment are the most promising ways. In this context, we aim at developing an antigen microarray for screening serological biomarkers to diagnose breast cancer patients as early as possible. Among numerous potential biomarkers, recent researches showed that antibodies against heat shock proteins (HSPs) are associated with tumor genesis and would be good diagnostic and prognostic biomarkers for breast cancer. Therefore, we used customized antigen microarray to screen anti-HSP antibodies in 50 breast cancer patients and 26 healthy controls. Our results indicated clearly that combining multiplex detection of anti-HSPs antibodies could discriminate breast cancer patients from healthy controls with sensitivity 86% and specificity 100%. Then, we elaborated an antibody microarray to detect the concentration of urokinase type plasminogen activator (uPA) in 16 cytosolic extracts of breast tummor tissue. uPA is good prognostic and predictive biomarker for breast cancer, low levels of uPA (≤3 ng/mg of protein) is associated with low risk of recurrence and no benefit of chemotherapy for breast cancer patients, and vice versa. Our results showed that the results obtained from our antibody microarray were surface dependent compared with the results obtained from ELISA. Furthermore, the use of our antibody microarray requires 25 times less sample volume compared with ELISA kit, thus solving the main limitations of ELISA. Finally, we determined and optimized the parameters which affected the performances of protein microarray, e.g. microarray surface chemistry, experimental duration, the concentration of solutions, etc. Furthermore, we studied the storage conditions for both chemically functionalized microarray surface as well as printed protein microarray. Results showed that our protein microarrays retain efficient biological activity for at least 3 month of storage.

Epigenetic regulatory mechanisms play important roles in the control of lineage-specific differentiation during development. However, mechanisms that regulate higher-order chromatin remodelling and transcription of keratinocyte-specific genes that are clustered in the genome into three distinct loci (Keratin type I/II loci and Epidermal Differentiation Complex (EDC) during differentiation of the epidermis are poorly understood. By using 3D-Fluorescent In Situ Hybridization (FISH), we determined that in the epidermal keratinocytes, the KtyII and EDC loci are located closely to each other in the nuclear compartment enriched by the nuclear speckles. However, in KtyII locus knockout mice, EDC locus moved away from the KtyII locus flanking regions and nuclear speckles towards the nuclear periphery, which is associated with marked changes in gene expression described previously. Chromatin architectural protein Ctcf has previously been implicated in the control of long-range enhancer-promoter contacts and inter-chromosomal interactions. Ctcf is broadly expressed in the skin including epidermal keratinocytes and hair follicles. Conditional Keratin 14-driven Ctcf ablation in mice results in the increase of the epidermal thickness, proliferation, alterations of the epidermal barrier and the development of epidermal pro-inflammatory response. Epidermal barrier defects in Krt14CreER/Ctcf fl/fl mice are associated with marked changes in gene expression in the EDC and KtyII loci, which become topologically segregated in the nucleus upon Ctcf ablation. Therefore, these data suggest that Ctcf serves as critical determinant regulating higher-order chromatin organization in lineage-specific gene loci in epidermal keratinocytes, which is required for the proper control of gene expression, maintenance of the epidermal barrier and its function.

Les travaux présentés dans cette thèse concernent le développement d'un outil d'analyse multiparamétrique pour la quantification de biomarqueurs urinaires du cancer de la vessie.La première partie des travaux de recherche a pour objectif la sélection de marqueurs pour le diagnostic et la récidive des tumeurs urothéliales. Une première étude a permis l'évaluation de la sélectivité de marqueurs candidats dans des échantillons urinaires de patients atteints de cancer de la vessie. Cinq des vingt marqueurs initiaux ont été sélectionnés pour leur performance diagnostique, définissant le Panel 1 : VEGF, MMP9, IL8, PTGS2 et EN2. Une seconde étude a été réalisée afin d'évaluer le potentiel de marqueurs et de paramètres cliniques pour le diagnostic de la récidive des tumeurs urothéliales. Les échantillons urinaires évalués provenaient donc de patients présentant une récidive du cancer de la vessie et de patients ne présentant pas de récidive. Le Panel 2 a ainsi été défini, basé sur le modèle de régression multiple le plus performant. Il comprend les paramètres cliniques et moléculaires suivants : nombre de récidives antérieures, nombre de thérapies par BCG, stade de la tumeur au moment du diagnostic, CDH1, IL8, ErbB2, IL6, EN2 et VEGF.La seconde partie concerne le développement d'un test multiparamétrique pour la quantification des marqueurs sélectionnés. Il s'agit d'une plateforme automatisée, à haut-débit et sous un format de plaque de microtitration 96-puits. La méthode de quantification choisie est un immunoessai de type sandwich sous la forme de puce à protéines. Le développement de la plateforme a débuté avec le Panel 1 dont trois des cinq marqueurs (VEGF, MMP9 et IL8) ont été intégrés avec succès. Suite à la seconde étude de sélection de marqueurs, le développement de l'immunoessai multiparamétrique a été orienté vers le Panel 2. À l'exception du marqueur EN2, nécessitant une configuration d'immunoessai différente, tous les marqueurs du Panel 2 ont pu être intégrés à la plateforme / The work reported in this thesis focuses on the development of a multiplex analytical tool for the quantification of selected bladder cancer urinary biomarkers.The aim of the first part of this work is the selection of urinary biomarkers for the diagnosis and recurrence of urothelial tumors. A first study evaluated the selectivity of candidate markers in urine samples of bladder cancer patients. Five of the twenty initial markers were selected for their diagnostic performance. They define Panel 1: VEGF, MMP9, IL8, PTGS2 and EN2. A second study was then conducted to assess the potential of urinary markers and clinical parameters for the diagnosis of bladder cancer recurrence. Two types of urine samples were thus evaluated: samples from recurrent bladder cancer patients and samples from bladder cancer patients without recurrence. Panel 2 was then defined based on the best performing multivariate regression model. It includes the following clinical and molecular parameters: number of past recurrences, number of BCG therapies, tumor stage at diagnosis, CDH1, IL8, ErbB2, IL6, EN2 and VEGF.The second part involves the development of a multiplex test for the quantification of the selected markers. It is a high-throughput automated platform in a 96-well microtiter plate format. It was designed as a multiplex sandwich immunoassay based on a protein microarray. The platform development began with Panel 1 for which three of the five markers (VEGF, MMP9 and IL8) were successful integrated into a multiplex immunoassay. The end of the second marker selection study marked the development transition from Panel 1 to Panel 2. With the exception of EN2, requiring a different immunoassay configuration, all the Panel 2 markers were integrated into the platform