Prostate cancer is the most common noncutaneous cancer among men, yet current diagnostic methods are insufficient and more reliable diagnostic markers need to be developed. The answer that can bridge this gap and enable more efficient diagnoses may lie in microRNAs. These small, single stranded RNA molecules impact protein expression at the translational level and regulate important cellular pathways. Dysregulation of these small RNA molecules can have tumorigenic effects on cells and lead to many types of cancers. Currently the Prostate-Stimulating Antigen (PSA) is used as a diagnostic marker for prostate cancer. However, many factors can elevate PSA levels such as infections and certain medications, consequently leading to false positive diagnoses and unnecessary concern and over treatment with dire outcomes for the patient. Even worse, are the chances of false negative diagnoses, which result in prostate cancer not being diagnosed until its later stages. Therefore, although the use of the PSA level has had its uses in the clinic, it has failed to sufficiently bridge the gap or to distinguish indolent from aggressive disease. It has long been suggested in the literature that microRNAs are drastically altered throughout the course of cancer progression. Here, RNA sequencing was used to identify changes in miR expression profiles diagnostic for prostate cancer patients compared to non-patient controls. The RNA sequencing results were also used to identify normalization miRs to be used as endogenous controls. Confirmatory qRT-PCR was then used to corroborate these results for the top seven dysregulated miRs found from the RNA sequencing data. Data analysis of the Area Under the Curve (AUC) of the Receiver Operating Curves (ROC) of the selected miRs exhibited a better correlation with prostate cancer (AUC Range= 0.819- 0.950) than PSA (AUC of PSA=0.667). In summary, a panel of seven miRs are proposed, many of which have prostate specific targets, which would represent a significant improvement over current testing methods.

Les vésicules extracellulaires telles que les microvésicules et les exosomes sont libérées lors de l’apoptose ou de l’activation cellulaire. Ce sont des médiateurs importants dans la communication intercellulaire, suggérant que ces vésicules pourraient jouer un rôle physiopathologique, en particulier dans les maladies cardiovasculaires. L'athérosclérose est une maladie inflammatoire chronique de la paroi artérielle qui résulte de l’interaction entre les lipoprotéines, les cellules inflammatoires, et les cellules vasculaires. L'infarctus du myocarde est une complication aiguë et grave de l'athérosclérose. La réaction inflammatoire post-infarctus joue un rôle central dans la formation de néovaisseaux sanguins et la cicatrisation. Cependant, les mécanismes de l’inflammation sont encore mal connus dans ces pathologies. Mon travail de thèse a porté sur les effets des vésicules extracellulaires isolées de tissus pathologiques sur les cellules inflammatoires. Nous avons montré dans un premier travail que les microvésicules s’accumulant dans les lésions d’athérosclérose humaines contribuent à la surcharge en cholestérol et en triglycérides des macrophages et facilitent la formation de cellules spumeuses. L’accumulation des lipides intracellulaires induite par ces microvésicules est contrebalancée par une augmentation de l’efflux du cholestérol associée à une activation d’ABCA1. Dans un deuxième travail, nous avons examiné les effets des vésicules produites dans le cœur post-infarctus sur la réponse inflammatoire. Nos résultats montrent : 1- une augmentation de la libération in situ des microvésicules majoritairement d’origine cardiomyocytaire et des exosomes 15 heures après infarctus ; 2- la stimulation de la production de VEGF monocytaire par les vésicules extracellulaires ; 3- l’incapacité en ce qui concerne les vésicules isolées de cœur diabétique infarci à reproduire cet effet sur les monocytes des souris contrôles. Afin de clarifier les déterminants de l’angiogenèse post-ischémique, nous avons également étudié les profils de miARNs des vésicules contrôles et diabétiques. Après infarctus du myocarde, l’expression de miR-126-3p et de miR-92a-3p est significativement diminuée dans les vésicules diabétiques en comparaison avec les vésicules contrôles. Par ailleurs, nous avons observé une augmentation de miR-126-3p et de miR-92a-3p respectivement dans les microvésicules et les exosomes chez les souris contrôles post-infarctus. En conclusion, ce travail apporte des éléments nouveaux sur les fonctions des vésicules extracellulaires générées localement dans les tissus inflammatoires, en particulier leur capacité à promouvoir la transformation des macrophages en cellules spumeuses dans la plaque. Par ailleurs, les vésicules isolées du cœur ischémique pourraient favoriser l’angiogenèse post-infarctus en stimulant la production de VEGF monocytaire. La disparition de cet effet bénéfique dans le diabète pourrait être associée à des modifications d’adressage des miARNs dans les vésicules extracellulaires au cours de cette pathologie. / Extracellular vesicles, such as microvesicles and exosomes, are released during cell apoptosis or activation. They are important mediators of intercellular communication, suggesting that these vesicles could play a pathophysiological role, especially in cardiovascular diseases. Atherosclerosis is a chronic inflammatory disease of the arterial wall which results from the interaction between lipoproteins, inflammatory cells, and vascular cells. Myocardial infarction is an acute and severe complication of atherosclerosis. The postinfarction inflammatory response plays a central role in the formation of new blood vessels and scarring. However, the mechanisms of inflammation are still poorly known in these pathologies. My thesis concerned the effects of extracellular vesicles isolated from pathological tissues on inflammatory cells. We showed in the first work that microvesicles accumulating in human atherosclerotic lesions contribute to cholesterol and triglyceride overload in macrophages and facilitate foam cell formation. The accumulation of the intracellular lipids induced by those microvesicles is offset by an increase in cholesterol efflux associated with activation of ABCA1. In the second study, we examined the effect of vesicles produced in the infarcted heart on the inflammatory response. Our results showed : 1- an increased release in situ of microvesicles mostly of cardiomyocyte origin and exosomes 15 hours after infarction ; 2- the stimulation of monocyte VEGF production by extracellular vesicles ; 3- the incapacity of diabetic vesicles isolated from infarcted heart to reproduce that effect on control mice monocytes. In order to clarify the determinants of postischemic angiogenesis, we also studied miRNA profiles of control and diabetic vesicles. After myocardial infarction, the expression level of miR-126-3p and miR-92a-3p was significantly decreased in diabetic vesicles compared to control vesicles. Furthermore, we observed an increased expression of miR-126-3p and miR-92a-3p respectively in the microvesicles and the exosomes isolated from control mice heart after myocardial infarction. In conclusion, this work provides new information on the functions of extracellular vesicles locally generated in inflamed tissues, particularly in promoting macrophage transformation into foam cells in the atherosclerotic plaque. Furthermore, vesicles isolated from ischemic heart could enhance postinfarction angiogenesis by stimulating monocyte VEGF production. The loss of this beneficial effect in diabetes may be associated with changes of miRNA cargo in extracellular vesicles in this pathology.

Les microARN jouent un grand rôle dans la régulation de l'expression des gènes bien que leur mécanisme d'action soit encore sujet à débat. Des premières études chez le vers C. elegans aux différents systèmes in vitro qui ont ensuite été développés, plusieurs modèles ont été proposés, comme l'inhibition de la traduction au niveau de l'initiation ou de l'élongation, et la déstabilisation du transcrit par déadénylation. Cependant, à la lumière des découvertes récentes, un consensus semble apparaître et indique que les miARN inhiberaient d'abord la traduction avant d'induire la déadénylation du transcrit, provoquant ainsi sa dégradation prématurée. D'autre part, le blocage traductionnel semble impliquer à la fois la coiffe en 5' et la queue poly(A) en 3' de l'ARNm ainsi que les facteurs qui s'y lient, c'est à dire le facteur d'initiation de la traduction eIF4F et la Poly(A) Binding Protein (PABP). Ces résultats ont conduit au modèle selon lequel, les miARN seraient capables d'empêcher la liaison entre ces deux facteurs et donc la circularisation du transcrit qui est essentielle à la fois au recrutement de la machinerie traductionnelle et à la stabilité de l'ARNm. Afin de mieux comprendre ce mécanisme, notre laboratoire a développé un système in vitro basé sur l'utilisation du lysat de réticulocytes de lapin qui permet d'étudier l'effet traductionnel des miARN en s'affranchissant de dégradation du transcrit. L'étude de l'effet de drogues et d'enzymes virales, capables de bloquer spécifiquement la fonction de chaque facteur d'initiation dans ce système, a permis de déterminer le rôle clé de eIF4G et PABP dans l'inhibition traductionnelle par les miARN. Cependant, leur interaction n'est pas requise et le blocage s'effectue plutôt au cours de l'étape de balayage de la région 5' non codante par la petite sous-unité ribosomique. En parallèle de cette étude in vitro, un travail sur des lignées cellulaires a permis de déterminer l'influence de la queue poly(A) sur l'effet miARN. De façon très surprenante, l'expression des transcrits non polyadénylés n'est plus inhibée et est même stimulée par les miARN. Cet effet est dépendant de l'association du domaine MIF4G du facteur eIF4G avec le facteur eIF3, ce qui suggère qu'en l'absence de queue poly(A), les miARN seraient capables de stimuler le recrutement de la petite sous-unité ribosomique sur l'ARNm. L'ensemble de ces résultats révèle la complexité de l'effet miARN sur la traduction et ouvre de nouvelles voies / The mechanism by which microRNAs (miRNAs) can control gene expression has been a great matter of debate. From the first studies in worm to the in vitro systems that are used today, many models have been proposed that include regulation at the level of translation or at the level of mRNA stability by controlling 3' deadenylation and decay. Recent studies provided a consensus model of all these discrepancies and suggested that translation inhibition occured first and is followed by deadenylation and further degradation of the target transcript. Moreover, translation silencing seems to occur at the initiation level, and requires eIF4F and PABP initiation factors. This led to the hypothesis that miRNAs could interfere with the interaction between these two factors thus affecting the circularisation of the mRNA, which is essential for translation efficiency. In order to gain insight into this mechanism, we have used an in vitro system based on the rabbit reticulocyte lysate that fully recapitulates miRNA effects on translation with virtually no effect on deadenylation and decay. Using this system and a wide spectrum of translational inhibitors, we have narrowed down the step of initiation at which repression is exerted and we found that miRNAs affect mainly ribosomal scanning. This effect requires the presence of both eIF4G and PABP but does not rely on their physical interaction. Further analysis of miRNA repression in cells revealed that the poly(A) tail was an absolute requirement for miRNA action. To most of our surprise, we observed that removal of the poly(A) resulted in a shift from repression to stimulation of mRNA expression. This effect seems to require the middle domain of eIF4G and the presence of the Ago proteins. Altogether, these results reveal the complexity of miRNA effect and open new prospects on translation regulation

L'aquaculture a connu un développement considérable au cours des dernières décennies. De par leurs disponibilités limitées, la farine de poisson et l'huile de poisson, considérées comme des ingrédients traditionnels de l'alimentation des poissons d’élevage, ont été largement remplacées par des matières premières végétales afin de soutenir le développement durable de l'aquaculture. Cette évolution de la composition des aliments aquacoles a entraîné une réduction importante de la teneur en cholestérol des aliments aquacoles. Dans ce contexte, l'objectif de la thèse était d’analyser les modifications du métabolisme du cholestérol chez la truite arc-en-ciel en réponse à une alimentation strictement végétale. Nous avons porté une attention particulière aux mécanismes sous-jacents à la régulation du métabolisme du cholestérol, en nous concentrant sur les facteurs de transcription et les microARNs. Enfin, nous avons évalué la possibilité d'utiliser les microARNs comme biomarqueurs non invasifs. Nos études ont montré qu’une alimentation végétale induit chez la truite une hypocholestérolémie associée à une modification de l’expression des gènes impliqués dans la synthèse et dans l'efflux du cholestérol mais aussi des facteurs de transcription SREBP-2 et LXRα. Nous avons également observé une diminution de l’expression du miR-223 dans le foie des truites nourries avec un régime à base de plantes ce qui suggère l'implication de mécanismes post-transcriptionnels dans la régulation de la synthèse du cholestérol chez la truite arc-en-ciel. Nous avons ensuite effectué une étude de la régulation du métabolisme du cholestérol chez une lignée de truite arc-en-ciel sélectionnée pour sa meilleure capacité de croissance sur aliment végétal. Nous avons observé une augmentation de l'expression du miR-33a chez les truites nourries avec un régime à base de plantes et une expression plus importante des miR-122 et 128 chez les truites de la lignée sélectionnée, quel que soit le régime. En analysant l’expression de gènes cibles potentiels des miR-33a, 122 et 128, nous avons pu mettre en évidence une régulation cohérente entre les miR-33a et 128 et leurs cibles potentielles que sont respectivement la caspase 6 apoptosis-related cysteine peptidase like 2 (casp6l2) et la phosphodiesterase 4B cAMP-specific a (pde4ba). Ces résultats mettent en évidence deux nouvelles voies moléculaires affectées par l’alimentation végétale chez la truite. Grâce à la combinaison d’approches in vivo et in vitro, nous avons constaté que l'expression des gènes impliqués dans la synthèse de cholestérol et celle du facteur de transcription SREBP-2 et du miR-33a augmentent chez les truites nourris avec l’aliment végétal et inversement diminuent en culture primaire d’hépatocytes de truite stimulés par du 25-hydroxycholestérol. Il semble donc SREBP-2 et miR-33a agissent en synergie pour réguler la synthèse du cholestérol. Enfin, nous avons détecté avec succès miR-1, miR-33a, miR-122, miR-128 et miR-223 dans le plasma de truite. Nous avons observé que les taux plasmatiques de miR-128 et de miR-223 sont soumis à des variations postprandiales similaires à celles observées pour leurs homologues hépatiques. Des corrélations significatives ont été observées entre les taux hépatiques et plasmatiques des miR-128 et miR-223. D’autres corrélations apparaissent entre les miR-122, 128 et 223 et l'expression de gènes liés à la synthèse et à l'efflux du cholestérol. Ces résultats indiquent que les micrARNs plasmatiques 122, 128 et 223 constituent de potentiels biomarqueurs non invasifs du métabolisme du cholestérol chez la truite arc-en-ciel. / Aquaculture has been subjected to a huge development during the last decades. Due to limiting availabilities, fishmeal and fish oil, the traditional ingredients of fish feed, have been widely replaced with vegetable ingredients in order to support the sustainable development of aquaculture. This evolution of aquafeeds has resulted in a reduction of the cholesterol content of the diets. In this context, the major objective of the thesis was to decipher the physiological changes related to cholesterol metabolism occurring in fish fed the plant-based diet. We furthermore analyzed the mechanisms underlying the regulation of cholesterol metabolism, focusing on transcription factors and microRNAs. Additionally, the possibility of utilizing miRNA as potential noninvasive biomarker was also investigated in the thesis. Our studies have shown that utilization of plant-based diet resulted in hypocholesterolemia and modified the expression of genes involved in cholesterol synthesis and efflux as well as that of their corresponding transcriptional factors SREBP-2 and LXRα. We also observed a lower expression of miR-223 in the liver of trout fed the plant-based diet suggesting the involvement of posttranscriptional mechanisms in the regulation of cholesterol synthesis. We then carried out another experiment using a line of rainbow trout selected for better growth performance on plant-based diet. We found that the hepatic expression of miR-33a increased in trout fed the plant-based diet, while the expression of miR-122 and miR-128 was much higher in the selected line regardless of the diet. By analyzing the expression of putative target genes of miR-33a, 122 and 128, we noticed consistent regulations between miR-33a and 128 and their respective putative targets, which were caspase 6 apoptosis-related cysteine peptidase like 2 (casp612) and cAMP-specific phosphodiesterase 4B a (pde4ba). These results highlighted two new molecular pathways affected by the plant-based diet. Through the combination in vivo and in vitro approaches, we demonstrated that the expression of the genes involved in cholesterol synthesis and that of the transcription factor SREBP-2 and the miR-33a increased in trout fed plant-based diet devoid of cholesterol while conversely decreased in rainbow trout primary cell culture of hepatocytes stimulated by 25-hydroxycholesterol. These data indicate that SREBP-2 and miR-33a act synergistically to control cholesterol synthesis. Finally, we successfully detected miR-1, miR-33a, miR-122, miR-128 and miR-223 in trout plasma. We observed similar postprandial changes between plasma levels of miR-128 and miR-223 and their hepatic counterparts. Significant correlations were observed between hepatic and plasma levels of miR-128 and miR-223. Other correlations appeared between miR-122, 128 and 223 and the expression of genes related to synthesis and efflux of cholesterol. Altogether, these results indicate that plasma microRNAs 122, 128 and 223 are potential non-invasive biomarkers of cholesterol metabolism in rainbow trout.

O timo é um orgão linfóide primário, no qual ocorre a indução da tolerância imunológica central aos antígenos do próprio que são expressos pelos tecidos periféricos (PTAs). A medula tímica é formada por células tímicas medulares epiteliais (mTECs) que expressam centenas desses PTAs que representam virtualmente todos os órgãos e tecidos do corpo. Esse fenômeno foi denominado de expressão gênica promíscua (PGE) a qual é parcialmente regulada pelo modulador da transcrição Autoimmune regulator (Aire). Os precursores de células T oriundos da medula óssea migram para o timo (agora são denominados de timócitos) e na medula desse órgão, passam pela seleção negativa mediada pelas mTECs. As células sobreviventes evoluem para células T maduras e funcionais que migram para a periferia com capacidade de reconhecimento das moléculas de MHC e tolerantes aos PTAs. Além de controlar a transcrição de genes PTAs, Aire também controla a expressão de microRNAs (miRNAs), relacionados com a integridade e funcionalidade do microambiente tímico. A seleção negativa no timo é um processo essencial para a manutenção da autotolerância imunológica e o desbalanço desse processo está associado com o desenvolvimento de doenças autoimunes como, por exemplo, o diabetes mellitus do tipo 1 (DM1).Tendo em vista essas premissas, nosso trabalho se fundamentou em duas hipóteses: 1) Variações na expressão do gene Aire podem perturbar a expressão de genes PTAs e miRNAs no timo, causando alterações na PGE, 2) A expressão balanceada de genes como Aire e/ou PTAs nas mTECs, é fundamental para a integridade da tolerância central. O desbalanço na expressão desses genes, está associado com a emergência do diabetes mellitus tipo 1 no camundongo. Para testar nossa primeira hipótese efetuamos o silenciamento de Aire (Aire knockdown) por meio de eletrotransfeção de RNA interferente (siRNA) anti-Aire in vivo no timo de camundongos BALB/c. Análises do transcriptoma (mRNAs) e miRNoma (miRNAs) das mTECs, revelaram que silenciamento parcial e transitório de Aire foi suficiente para afetar a expressão de PTAs Aire dependentes bem como a de miRNAs. Redes de interação miRNA-mRNA, revelaram que o controle pós-transcricional da PGE também é afetado pelo silenciamento de Aire. Os resultados encontrados revelam que Aire e miRNAs podem formar uma via essencial durante a indução da tolerância central. Para testar nossa segunda hipótese comparamos o transcriptoma de mTECs de camundongos BALB/c (linhagem não-autoimune) com mTECs de camundongos non-obese diabetic NOD (modelo animal utilizado nos estudos de DM1 autoimune). Nossos resultados revelaram que a expressão transcricional de autoantígenos relacionados ao DM1 está desbalanceada em camundongos NOD já numa fase precoce, quando esses animais ainda não apresentavam a doença clínica (fase pré-diabética). Inesperadamente, os níveis transcrionais de Aire apresentaram-se equivalentes no timo dessas duas linhagens, porém os níveis da proteína AIRE estavam reduzidos no timo da linhagem NOD. Esses resultados sugerem a participação de algum mecanismo de atenuação póstrascricional de Aire nessa linhagem provavelmente envolvendo atuação de miRNAs. Isso poderia explicar o desbalanço de PTAs Aire-dependentes e a repressão autoantígenos relacionados ao DM1. Concluímos que nossos resultados, além de abrir novas perspectivas para pesquisas nesta área, contribuem com melhor compreensão dos mecanismos moleculares desencadeados por Aire e por miRNAs no controle da expressão de autoantígenos no timo o que é importante para a tolerância imunológica central. / The thymus is a primary lymphoid organ, in which occurs in the induction of central immune tolerance to self peripheral tissue antigens (PTAs). The thymic medulla is formed by medullary thymic epithelial cells (mTECs) expressing hundreds of such PTAs representing virtually all organs and tissues of the body. This phenomenon has been termed promiscuous gene expression (PGE), which is partially regulated by the Autoimmune regulator (Aire) gene. The T cell precursors derived from the bone marrow migrate to the thymus (now termed thymocytes). A part of these thymocytes are eliminated by negative selection mediated mTEC cells. The surviving cells to evolve and functional mature T cells that migrate to the periphery and are capable of recognizing MHC molecules and are tolerant to PTAs. In addition to controlling the transcription of PTA genes, Aire also controls the expression of microRNAs (miRNAs). The negative selection in the thymus is a process essential to the maintenance of immunologic self-tolerance and imbalance of this process is associated with the development of autoimmune diseases such as type 1 diabetes mellitus (DM1) . Given these assumptions, our work was based on two hypothesis: 1) Changes in the expression of the Aire gene can disrupt the expression of PTA genes and miRNAs in the thymus, causing changes in PGE, 2) The balanced expression of Aire / or PTA genes in mTECs is fundamental for central tolerance. The imbalance in the expression of these genes is associated with the emergence of type 1 diabetes in mice. To test our first hypothesis we made Aire silencing (Aire knockdown) through electrotransfection of anti - Aire interfering RNA (siRNA) in vivo in the thymus of BALB/c mice. Analysis of the transcriptome (mRNAs) and miRNome (miRNAs) of mTECs revealed that partial and transient silencing of Aire was enough to affect the expression of Aire - dependent PTAs as well as miRNAs. miRNA -mRNA interaction networks revealed that the posttranscriptional control of PGE is also affected by the silencing of Aire. The results show that Aire and can form an miRNA pathway essential for the induction of central tolerance. To test our second hypothesis we compared the transcriptome of mTECs of BALB/c mice (non-autoimmune strain) with mTECs from non - obese diabetic NOD (animal model used in studies of autoimmune DM1) . Our results indicate that the transcriptional expression of DM1-related autoantigens are unbalanced in NOD mice in an very early stage, when these animals have not had clinical disease (pre-diabetic period). Unexpectedly, the transcriptional levels of Aire in the thymus was equivalent in these two strains, but the AIRE protein levels were reduced in thymus of NOD strain. These results suggest that some mechanism of post-transcriptional attenuation of Aire is acting in this lineage probably involving action of miRNAs . This could explain the imbalance of Aire - dependent PTAs and repression autoantigens related to DM1. Our results open perspectives for research in this area, contributing to better understanding the molecular mechanisms triggered by Aire and miRNAs in control of the expression of autoantigens in the thymus, which is important for the central immune tolerance.

L’infarctus du myocarde (IDM), responsable du remodelage ventriculaire, peut conduire, s’il est délétère, à l’insuffisance cardiaque (IC), principale cause de mortalité à travers le monde. Les récentes découvertes ont montré l’implication des ARNs non codants, microARNs (miARNs) et les longs ARNs non codants (lncARNs), dans les processus physiologiques et pathologiques et notamment dans les maladies cardiovasculaires. L’objectif de ce travail a été d’étudier le potentiel des miARNs et des lncARNs en tant que biomarqueurs pronostiques et diagnostiques ainsi qu’en tant que cibles thérapeutiques dans l’IDM et le remodelage ventriculaire. Dans un premier temps, nous avons évalué le pouvoir diagnostique des miARNs sur une cohorte de patients présentant des douleurs thoraciques. Le miR-208b et le miR-499 ont montré une bonne capacité diagnostique de l’IDM, ne dépassant toutefois pas celle des troponines. Nous avons ensuite observé que le miR-150 présente une plus faible concentration dans le sang de patients avec un remodelage ventriculaire post-IDM par rapport aux patients sans remodelage, le positionnant comme un biomarqueur intéressant dans le pronostic de l’IC. Enfin, nous avons montré une régulation importante de plusieurs lncARNs dans le cœur de souris, 24 heures après IDM et 2 lncARNs, MIRT1 et MIRT2, ont été mis en avant pour leur association avec le remodelage. En conclusion, nos études ont montré l’utilité des ARNs non codants pour améliorer l’identification des patients à risque de développer une IC après IDM et ont permis également de mettre en évidence de nouvelles cibles thérapeutiques qui pourraient prévenir le remodelage ventriculaire post-IDM / Myocardial infarction (MI responsible for left ventricular remodeling which can be deleterious and the development of heart failure (HF). HF is one of the leading causes of mortality worldwide and despite many improvements, it remains a major challenge in clinical practice. Recent discoveries in genomics have showed the involvement of non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), in physiological and pathological processes and notably linked to cardiovascular diseases. The goal of this work was to study the potential of miRNAs and lncRNAs as prognostic and diagnostic biomarkers and as therapeutic targets in MI and left ventricular remodeling leading to HF. First, we evaluated the diagnostic value of miRNAs in patients with chest pain. MiRNA-208b and miR-499 have shown a good diagnostic capacity for MI. However, these miARNs failed to improve the diagnosis of MI by troponins. MiRNA-208b could also predict patient mortality after MI but this capacity was modest. Then, we observed that miR-150 was present at a low level in the blood of patients with left ventricular remodeling post-MI compared to patients without remodeling. Therefore, miRNA-150 is an interesting prognostic biomarker. Finally, we have shown a significant regulation of several lncRNAs in mouse heart, 24 hours after MI, and 2 lncRNAs, MIRT1 and MIRT2, have been demonstrated for their association with left ventricular remodeling. In conclusion, our studies have shown the utility of non-coding RNAs to improve the identification of patients at risk of developing HF after MI and also allowed to identify potential therapeutic targets to prevent left ventricular remodeling

Les vésicules extracellulaires telles que les microvésicules et les exosomes sont libérées lors de l’apoptose ou de l’activation cellulaire. Ce sont des médiateurs importants dans la communication intercellulaire, suggérant que ces vésicules pourraient jouer un rôle physiopathologique, en particulier dans les maladies cardiovasculaires. L'athérosclérose est une maladie inflammatoire chronique de la paroi artérielle qui résulte de l’interaction entre les lipoprotéines, les cellules inflammatoires, et les cellules vasculaires. L'infarctus du myocarde est une complication aiguë et grave de l'athérosclérose. La réaction inflammatoire post-infarctus joue un rôle central dans la formation de néovaisseaux sanguins et la cicatrisation. Cependant, les mécanismes de l’inflammation sont encore mal connus dans ces pathologies. Mon travail de thèse a porté sur les effets des vésicules extracellulaires isolées de tissus pathologiques sur les cellules inflammatoires. Nous avons montré dans un premier travail que les microvésicules s’accumulant dans les lésions d’athérosclérose humaines contribuent à la surcharge en cholestérol et en triglycérides des macrophages et facilitent la formation de cellules spumeuses. L’accumulation des lipides intracellulaires induite par ces microvésicules est contrebalancée par une augmentation de l’efflux du cholestérol associée à une activation d’ABCA1. Dans un deuxième travail, nous avons examiné les effets des vésicules produites dans le cœur post-infarctus sur la réponse inflammatoire. Nos résultats montrent : 1- une augmentation de la libération in situ des microvésicules majoritairement d’origine cardiomyocytaire et des exosomes 15 heures après infarctus ; 2- la stimulation de la production de VEGF monocytaire par les vésicules extracellulaires ; 3- l’incapacité en ce qui concerne les vésicules isolées de cœur diabétique infarci à reproduire cet effet sur les monocytes des souris contrôles. Afin de clarifier les déterminants de l’angiogenèse post-ischémique, nous avons également étudié les profils de miARNs des vésicules contrôles et diabétiques. Après infarctus du myocarde, l’expression de miR-126-3p et de miR-92a-3p est significativement diminuée dans les vésicules diabétiques en comparaison avec les vésicules contrôles. Par ailleurs, nous avons observé une augmentation de miR-126-3p et de miR-92a-3p respectivement dans les microvésicules et les exosomes chez les souris contrôles post-infarctus. En conclusion, ce travail apporte des éléments nouveaux sur les fonctions des vésicules extracellulaires générées localement dans les tissus inflammatoires, en particulier leur capacité à promouvoir la transformation des macrophages en cellules spumeuses dans la plaque. Par ailleurs, les vésicules isolées du cœur ischémique pourraient favoriser l’angiogenèse post-infarctus en stimulant la production de VEGF monocytaire. La disparition de cet effet bénéfique dans le diabète pourrait être associée à des modifications d’adressage des miARNs dans les vésicules extracellulaires au cours de cette pathologie. / Extracellular vesicles, such as microvesicles and exosomes, are released during cell apoptosis or activation. They are important mediators of intercellular communication, suggesting that these vesicles could play a pathophysiological role, especially in cardiovascular diseases. Atherosclerosis is a chronic inflammatory disease of the arterial wall which results from the interaction between lipoproteins, inflammatory cells, and vascular cells. Myocardial infarction is an acute and severe complication of atherosclerosis. The postinfarction inflammatory response plays a central role in the formation of new blood vessels and scarring. However, the mechanisms of inflammation are still poorly known in these pathologies. My thesis concerned the effects of extracellular vesicles isolated from pathological tissues on inflammatory cells. We showed in the first work that microvesicles accumulating in human atherosclerotic lesions contribute to cholesterol and triglyceride overload in macrophages and facilitate foam cell formation. The accumulation of the intracellular lipids induced by those microvesicles is offset by an increase in cholesterol efflux associated with activation of ABCA1. In the second study, we examined the effect of vesicles produced in the infarcted heart on the inflammatory response. Our results showed : 1- an increased release in situ of microvesicles mostly of cardiomyocyte origin and exosomes 15 hours after infarction ; 2- the stimulation of monocyte VEGF production by extracellular vesicles ; 3- the incapacity of diabetic vesicles isolated from infarcted heart to reproduce that effect on control mice monocytes. In order to clarify the determinants of postischemic angiogenesis, we also studied miRNA profiles of control and diabetic vesicles. After myocardial infarction, the expression level of miR-126-3p and miR-92a-3p was significantly decreased in diabetic vesicles compared to control vesicles. Furthermore, we observed an increased expression of miR-126-3p and miR-92a-3p respectively in the microvesicles and the exosomes isolated from control mice heart after myocardial infarction. In conclusion, this work provides new information on the functions of extracellular vesicles locally generated in inflamed tissues, particularly in promoting macrophage transformation into foam cells in the atherosclerotic plaque. Furthermore, vesicles isolated from ischemic heart could enhance postinfarction angiogenesis by stimulating monocyte VEGF production. The loss of this beneficial effect in diabetes may be associated with changes of miRNA cargo in extracellular vesicles in this pathology.

L'oncogène ALK (Anaplastic Lymphoma Kinase) est une tyrosine kinase constitutivement active, impliquée dans divers cancers, tels que les lymphomes anaplasiques à grandes cellules (LAGC), ou certains carcinomes bronchiques. Ces tumeurs sont traitées par chimiothérapie, ce qui n'est pas un traitement optimal (30% de rechutes, abaissement de la qualité de vie). Dans ce contexte, de nombreux inhibiteurs spécifiques de la tyrosine kinase ALK tels que le Crizotinib ont été développés et ont prouvé leur efficacité à la fois dans des modèles in vitro, in vivo ainsi que chez les patients. Néanmoins, le succès de cette thérapie ciblée est limité par l'apparition de résistances. Il est donc essentiel de mettre au jour de nouvelles stratégies thérapeutiques permettant de contrecarrer ces résistances. Récemment, l'autophagie, un processus catabolique intracellulaire de dégradation lysosomale, a été proposée comme nouvelle cible thérapeutique dans le traitement des cancers résistants aux inhibiteurs de tyrosine kinase. Le premier objectif de mon projet de thèse a été de caractériser ce processus autophagique dans les LAGC ALK+, en réponse à différents traitements. Nous avons montré que (1) l'autophagie était activée dans des lignées de LAGC en réponse à l'inhibition de ALK, (2) que cette autophagie jouait un rôle cytoprotecteur dans ce modèle et (3) que les traitements par chimiothérapies de ces cellules n'induisaient pas de réponse autophagique. Dans un deuxième temps, nous nous sommes intéressés à la régulation potentielle de l'autophagie par les microARNs. Nous avons montré que plusieurs microARNs, dont le miR-7, étaient sous-exprimés en réponse au traitement par le Crizotinib et que la réexpression ectopique de ce miR-7 permettait une potentialisation de l'effet du Crizotinib, par l'induction d'autophagie cytotoxique dans notre modèle. Nous avançons également l'hypothèse que le " switch " autophagique de la cytoprotection à la cytotoxicité, que nous observons pourrait s'expliquer par la régulation de l'expression de plusieurs protéines cibles de miR-7 telles que Bcl-2 ou c-Raf. Ainsi, l'ensemble de nos résultats nous permettent de mieux comprendre le rôle et la régulation de l'autophagie induite en réponse à l'inhibition de ALK dans les LAGC ALK+, et pourrait à terme contribuer à l'amélioration des thérapies actuelles de divers cancers dépendants de l'oncogène ALK. / The ALK oncogene (Anaplastic Lymphoma Kinase) is a constitutively activated tyrosine kinase implied in various cancers including Anaplastic Large Cell Lymphomas (ALCL), or some lung adenocarcinomas. The current operative treatment is standard chemotherapy, which is not optimal (30% of relapses, low quality of life). In this context, new specific ALK inhibitors such as Crizotinib have been developed, and have showed their efficiency in vitro, in vivo and in patients. However, the emergence of resistant mutations has been described. Thus, the identification of alternative therapies targeting new pathways appears as mandatory to counteract those resistances. In this context, autophagy, an intracellular catabolic lysosomal process, has been described as a new therapeutic target in the treatment of cancers resistant to tyrosine kinase inhibitors. The first aim of my project was to characterize the autophagic process in ALK+ ALCL, upon different treatments. We showed that (1) autophagy was activated in ALK+ ALCL cell lines in response to ALK inhibition (2) that this autophagy played a cytoprotective role in our model and (3) that treatment with chemotherapies did not trigger an autophagic response. In a second part of the project, we focused on the potential regulation of autophagy by microRNAs. We showed that several microRNAs including miR-7 were down-regulated upon Crizotinib treatment and that ectopic re-expression of this miR-7 potentiates the effects of Crizotinib by induction of cytotoxic autophagy in our model. We hypothesized that this switch in the role of autophagy from cytoprotection to cytotoxicity observed in our model, could be explained by the regulation of several protein targets of miR-7 such as Bcl-2 or c-Raf. Altogether, these results enable a better understanding of the role and regulation of autophagy induced upon ALK inhibition in ALCL, and could in the longer term, contribute to improvement of current therapies of cancers involving the ALK oncogene.

Submitted by JACIARA CRISTINA ALMEIDA DO AMARAL (jaciaramaral@ufpa.br) on 2018-10-31T18:09:43Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) FINAL_Dissertação_Emily_-merged.pdf: 1720360 bytes, checksum: 3ac1b4f683fc14f20cfd1e063914a0da (MD5) / Approved for entry into archive by JACIARA CRISTINA ALMEIDA DO AMARAL (jaciaramaral@ufpa.br) on 2018-10-31T18:10:07Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) FINAL_Dissertação_Emily_-merged.pdf: 1720360 bytes, checksum: 3ac1b4f683fc14f20cfd1e063914a0da (MD5) / Made available in DSpace on 2018-10-31T18:10:07Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) FINAL_Dissertação_Emily_-merged.pdf: 1720360 bytes, checksum: 3ac1b4f683fc14f20cfd1e063914a0da (MD5) Previous issue date: 2018-09-13 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O câncer, de acordo com a Globocan, 2018, foi responsável por uma taxa de 8,2 milhões de mortes e 14,1 milhões de casos novos. No que diz respeito especificamente à incidência de câncer gástrico (CG), para o estado do Pará, estima-se no ano de2018 um número de homens afetados de 23,30 e 11,45 de mulheres. No desenvolvimento do adenocarcinoma gástrico foram identificadas alterações moleculares significativamente aumentadas em vias metabólicas. Um desses elementos são os miRNAS, pequenos RNAs não codificantes que atuam na regulação da expressão gênica e podem agir como oncogenes ou supressores tumorais. O objetivo deste estudo foi investigar a possibilidade de genes das amostras tumorais depositadas no banco de dados Atlas Genômico do Câncer (TCGA) de serem modificados por miRNAs diferencialmente expressos. A análise foi realizada por plataforma de sequenciamento, RNA-Seq, e utilizou o software R-peridot na análise de expressão diferencial de microRNAs, o resultado identificou seis miRNAs alterados significativamente. Em seguida a plataforma miRTargetLink Human foi empregada e identificou oito genes alvos desses miRNAs entre amostras tumorais e seus correspondentes tecidos adjacentes no CG. As análises funcionais mostraram genes que participam de três vias metabólicas importantes associadas ao câncer: adesão focal, via de sinalização RAP1 e pela via de sinalização de cálcio. Por fim, a utilização do cálculo Z-Score confirmou os achados significantes. / The cancer, according to Globocan, in 2018, was responsible for a rate of 8.2 million deaths and about 14.1 million new cases. Regarding the analysis of gastric cancer (GC), in the state of Pará, it was estimated that for the year 2018 the number of affected men would be 23.30 and 11.45 for women. In the development of gastric adenocarcinoma, several significantly increased molecular alterations were identified when compared to non-cancerous tissues. One of these elements are miRNAS, small non-coding RNAs that act on the regulation of gene expression and can act as oncogenes or tumor suppressors. The objective of this study was to investigate the possibility of genes from tumor samples (deposited in The Cancer Genome Atlas - TCGA database) to be modified by differentially expressed miRNAs. The analysis was performed by sequencing platform, RNA-Seq, and used the software R-peridot in differential expression analysis, whose result identified six miRNAs. Next, the miRTargetLink Human platform identified eight miRNA target genes between tumor samples and their corresponding adjacent CG tissues. Functional analyzes identified important genes that can be enriched by three pathways associated with cancer: focal adhesion, RAP1 signaling pathway and calcium signaling pathway. Finally, the use of the Z-Score calculation confirmed significant findings.

O câncer de próstata é a segunda causa de morte entre homens no Brasil. É tipo um câncer de crescimento lento, podendo levar anos para o tumor atingir 1 cm3, porém, em alguns casos ele pode se espalhar pelo corpo, sendo o osso o principal sítio de metástase. No estágio de desenvolvimento do câncer conhecido como metástase, o principal tratamento consiste em terapia de restrição andrógena, levando as células prostáticas a pararem de proliferar, uma vez que elas crescem em resposta a presença de hormônios andrógenos, como a diidrotestosterona e testosterona. Porém, em alguns casos, as células proliferam mesmo na ausência de andrógenos e isto se deve a diversos fatores que, em geral, estão associados a mutações no receptor andrógeno e/ou alterações no metabolismo andrógeno. Quando isto acontece, os tratamentos disponíveis são menos efetivos e costumam falhar. Porém, estudos sugerem que o γ-orizanol, um fitoesterol extraído do óleo do farelo do arroz; e extratos amplamente utilizados na medicina popular, como o extrato hidroalcólico de Thuya occidentalis, poderiam atuar inibindo o desenvolvimento e progressão do câncer de próstata. Neste estudo, com o uso de abordagens bioquímicas e de biologia molecular, foi demonstrado que o tratamento com γ-orizanol diminui a viabilidade e biomassa celular em cultura, associado ao aumento da morte celular por apoptose e/ou necrose, em linhagens celulares responsivas (LNCaP) e não-responsivas a andrógenos (PC3 e DU145), além de aumentar a pERK1/2 em células LNCaP e DU145. O γ-orizanol também foi capaz de bloquear o ciclo celular em G2/M nas células PC3 e LNCaP e em G0/G1 nas células DU145. Estes efeitos foram ainda acompanhados por uma redução da expressão do gene e proteína caveolina-1- uma importante molécula envolvida no aumento da agressividade do câncer de próstata, e também, na progressão da doença para o fenótipo andrógeno resistente - nas células não-responsivas a andrógenos, e do gene PCGEM1 - gene específico da próstata regulado por andrógeno - nas células LNCaP e DU145. Ainda, γ-orizanol também mostrou capacidade de regular vários miRNAs - pequenas moléculas de RNA não codificantes de proteínas - envolvidos no controle de funções associadas ao desenvolvimento, progressão e invasão no câncer de próstata, como o miR16-1, miR19b-2, miR24b-1, miR24b-2, miR99a, miR133a-5p, miR182-5p, miR198 e miR222. O extrato hidroalcólico de Thuya occidentalis reduziu a viabilidade e biomassa celular nas linhagens responsiva (LNCaP) e não-responsivas (DU145 e PC3) a andrógenos, além de induzir parada do ciclo celular na fase G0/G1 nas células DU145 e aumentar a morte celular por apoptose e/ou necrose em todas as linhagens. Da mesma forma que o γ-orizanol, este extrato reduziu a expressão da caveolina-1 nas linhagens não-responsivas a andrógenos. Trabalhos anteriores mostram que o monoterpeno α-tujona é o principal composto ativo do extrato de Thuya occidentalis. Por cromatografia gasosa acoplada a detector de massas foi mostrada a existência de 0,0016 μg de α-tujona na dose de extrato usada neste estudo. No entanto, o tratamento com 0,0016μg de α-tujona foi efetivo somente sobre linhagem LNCaP, não tendo efeito sobre as outras linhagens estudadas, reforçando a hipótese da diferença de sensibilidade entre as linhagens responsivas e não responsivas a andrógeno e mostrando a contribuição de outros componentes do extrato nos efeitos observados neste estudo. Concluindo, estes resultados demonstram que tanto γ-orizanol como o extrato de Thuya occidentalis podem vir a ser agentes terapêuticos promissores no tratamento de câncer de próstata, não só por inibirem o crescimento celular, mas também e principalmente pela possibilidade de induzirem a recuperação da sensibilidade a andrógenos, aumentando as possibilidades de tratamento da doença. / Prostate cancer is the second cause of death among men in Brazil. It is a slowgrowing cancer and it may take years for tumor to reach 1 cm3, but in some cases it can spread throughout the body and the bone is the main site of metastasis. At this cancer stage known as metastasis, the principal treatment involves antiandrogen therapy, leading to prostate cells stop proliferating, because they grow in response to presence of androgens such as testosterone and dihydrotestosterone. However, in some cases, the cells can proliferate even in the absence of androgens and this fact occurs due to many factors and they are generally associated with mutations in the androgen receptor and/or alterations in androgen metabolism. In this stage, the treatments available are less effective and usually fail. However, studies suggest that γ-oryzanol, a phytosterol extracted of rice bran oil; and extracts widely used in folk medicine, as Thuya occidentalis hidroalcolic extract, could act inhibiting the development and progression of prostate cancer. In this study, using molecular biology and biochemical approaches we showed that γ- oryzanol treatment was able to decrease cell viability and biomass in culture, and this fact was linked to increased cell death by apoptosis and/or necrosis in androgen responsive (LNCaP) and unresponsive (DU145 and PC3) prostate cancer cell lines, besides increasing pERK1/2 in LNCaP and DU145 cells. γ- oryzanol was also able to cause cell cycle arrest at G2/M phase in LNCaP and PC3 cells and at G0/G1 phase in DU145 cells. These effects were also accompanied by a reduction in caveolin-1 gene and protein expression - an important molecule related to high aggressiveness in prostate cancer and also in the progression of the disease to androgen resistant phenotype - in androgen unresponsive cells, and also PCGEM1 gene - a prostate specific gene regulated by androgens - in LNCaP and DU145 cells. γ-oryzanol also showed ability to regulate several miRNAs - small non-coding RNA molecules - involved in the control of many functions associated with the development, progression and invasion of prostate cancer, such as miR16-1, miR19b-2, miR24b-1, miR24b-2, miR99a, miR133a-5p, miR182-5p, miR198 and miR222. Thuya occidentalis hidroalcolic extract also reduce cell viability and biomass in androgen responsive (LNCaP) and unresponsive (DU145 and PC3) cells, in addition to inducing cell cycle arrest at G0/G1 phase in DU145 cells and to increase apoptosis and/or necrosis cell death in all cell lines. The same way that γ-oryzanol, this extract reduced the caveolin-1 expression in androgen unresponsive prostate cancer cells. Prior studies showed that the monoterpene α-thujone is the main active compound in the T. occidentalis extract. By gas chromatography coupled to mass detector it was showed the existence of 0.0016 μg of α-thujone in extract dose used in this study. However, the treatment with 0.0016 μg of α-thujone was effective only on LNCaP cell line, having no effect on the other studied lines, supporting the hypothesis of difference in sensitivity between responsive and unresponsive cell lines and showing the contribution of other components in the effects caused by the extract, observed it this study. In conclusion, these results demonstrate that both γ-oryzanol as T. occidentalis extract may become promising therapeutic agents in treatment of prostate cancer, not only inhibit cell growth but also and manly by the possibility of inducing the recovery of androgen sensitivity, increasing the treatment chances of treatment this disease.