Eukaryotic cells tightly regulate metabolism in order to sustain normal processes. Dysregulation of cellular metabolism is associated with multiple diseases including cancer. Polyamine metabolism is a tightly regulated process that is co-opted by multiple cancers for selective growth advantages. Polyamines are small organic molecules with two or more amino groups attached, whose biosynthesis is initiated by ornithine decarboxylase (ODC). Although much is known regarding the effects of polyamine metabolism and ODC on cellular processes, little is known regarding the intracellular signaling events that are regulated by polyamines. Clinical studies demonstrated that the ODC inhibitor difluromethylornithine (DFMO) was an effective chemopreventative strategy causing a reduction of colon adenomas in patients with prior colon polyps. However, the molecular mechanisms leading to this reduction are unknown. This dissertation provides mechanistic insight into the biological roles of the polyamines and show that these amines are regulators of multiple non-coding RNAs involved in cellular responses including effects on the let-7 microRNA family. Moreover, the polyamine modified translation factor eIF5A is demonstrated to regulate the oncofetal factor LIN28. This work also indicates that polyamines regulate the mTOR pathway and suggests alternative signaling nodes for polyamine-mediated regulation of cellular processes. Overall, these findings support the notion that polyamines are oncometabolites that are targetable and serve as a promising approach to manipulate oncogenic signaling for cancer therapy.

CNS-PNETs are rare, aggressive, paediatric embryonal brain tumours that are poorly studied. We recently identified an aggressive sub-group of CNS-PNETs characterized by the amplification of the C19MC microRNA cluster, however, little is known regarding the features of other CNS-PNET tumours. This study was designed to define additional molecular sub-groups of CNS-PNET by interrogating a large cohort of CNS-PNETs. To elucidate the features of CNS-PNET, we examined transcriptional and copy number profiles from primary hemispheric CNS-PNETs. We then validated and examined the clinical significance of novel sub-group markers in 123 primary CNS-PNETs. This thesis demonstrates that CNS-PNET can be categorized into three molecular sub-groups that are distinguished by distinct primitive neural, oligo-neural and mesenchymal lineage gene expression signatures and also correlated with distinct clinical features. Data from my thesis has generated a substantial body of knowledge to fuel both biological and clinical investigations of childhood CNS-PNETs.

CNS-PNETs are rare, aggressive, paediatric embryonal brain tumours that are poorly studied. We recently identified an aggressive sub-group of CNS-PNETs characterized by the amplification of the C19MC microRNA cluster, however, little is known regarding the features of other CNS-PNET tumours. This study was designed to define additional molecular sub-groups of CNS-PNET by interrogating a large cohort of CNS-PNETs. To elucidate the features of CNS-PNET, we examined transcriptional and copy number profiles from primary hemispheric CNS-PNETs. We then validated and examined the clinical significance of novel sub-group markers in 123 primary CNS-PNETs. This thesis demonstrates that CNS-PNET can be categorized into three molecular sub-groups that are distinguished by distinct primitive neural, oligo-neural and mesenchymal lineage gene expression signatures and also correlated with distinct clinical features. Data from my thesis has generated a substantial body of knowledge to fuel both biological and clinical investigations of childhood CNS-PNETs.

No carcinoma papilífero de tiroide (CPT) ocorrem alterações na via MAPK (do inglês Mitogen-Activated Protein Kinase), sendo a mais frequente mutação a BRAFT1799A. A via MAPK é modulada pelo miRNA, como o let-7 que estão pouco expresso no CPT. A biogênese de let-7 é controlada por proteínas ligantes de RNA LIN28 que inibem o processamento das formas primária e precursora de let-7 (pri-let-7 e pre-let-7). Avaliamos a expressão gênica de LIN28, pri-let-7f, pre-let-7f e let-7f por rtPCR em tempo real, utilizando RNA total das linhagens TPC-1 e BCPAP de PTC e amostras tumorais de pacientes com CPT. A linhagem não tumoral Nthyori 3-1 foi utilizada para induzir LIN28. Observa-se redução de let-7f em 4 dos 5 pacientes analisados enquanto que LIN28A está aumentado em 2 pacientes com BRAFT1799A. Nota-se maior expressão de pri-let-7f em TPC-1 e menor expressão de pre-let-7f e let-7f. Observa-se maior expressão de LIN28A em TPC-1, enquanto que LIN28B está mais expresso em BCPAP com BRAFT1799A. A inibição de BRAFV600E em BCPAP diminui LIN28B e aumenta let-7f, enquanto que a indução de LIN28B reduz a expressão de let-7f. Concluímos que há relação inversa entre LIN28 e let-7f no CPT e LIN28 influencia a diminuição de let-7f podendo assim contribuir com tumorigênese tireoidiana. / In papillary thyroid cancer (PTC) changes in MAPK (Mitogen-Activated Protein Kinase) pathway are common being BRAFT1799A mutation the most frequent alteration. MAPK pathway is modulated by miRNA such as let-7, an under-expressed miRNA in PTC. The RNA binding protein LIN28 controls let-7 biogenesis, blocking primary and precursor let-7 (pri-let-7 e pre-let-7) processing. We evaluated LIN28, pri-let-7f, pre-let-7f and let-7f gene expression by real time RTPCR using total RNA of human PTC sample and PTC cell lines TPC-1 and BCPAP. Non-tumoral cell line Nthyori 3-1 was used to evaluate LIN28B influence in let-7f. We observed decreased let-7f expression in 4 out of 5 PTC patients, and increased LIN28A in 2 patients with BRAFT1799A mutation. TPC-1 cells express higher levels of pri-let-7f while pre-let-7f and let-7f are less expressed. We noted that LIN28A is more expressed in TPC-1, while LIN28B is more expressed in BCPAP cells with BRAFT1799A. The inhibition of BRAFV600E in BCPAP decreases LIN28B and increases let-7f, while the induction of LIN28B in Nthyori 3-1 reduces let-7f expression. We conclude there is an inverse association between LIN28 and let-7f in PTC, and that LIN28 influences let-7f reduction which could contribute to thyroid tumorigenesis.

Somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by over expression of the transcription factors OCT4, SOX2, KLF4 and c-MYC. Using serial live cell immunofluorescence imaging of human fibroblasts undergoing reprogramming, we traced the emergence of nascent iPS cell colonies among heterogeneous cell populations and defined the kinetics of marker expression. We identified distinct colony types that morphologically resemble embryonic stem (ES) cells yet differ in molecular phenotype and differentiation potential. By analyzing expression of pluripotency markers, methylation at the OCT4 and NANOG promoters, and differentiation into teratomas, we determined that only one colony type represented bona fide iPS cells, whereas the others represented reprogramming intermediates. Proviral silencing and expression of TRA-1-60, DNMT3B, and REX1 distinguished the fully reprogrammed state, whereas Alkaline Phosphatase, SSEA-4, GDF3, hTERT and NANOG proved insufficient as markers. Reprogramming in chemically defined medium favored formation of bona fide iPS cell colonies relative to partially reprogrammed colonies. These data highlight the need for rigorous characterization and standardization of putative iPS cells.

La régulation de l’expression des gènes est ce qui permet à nos cellules de s’adapter à leur environnement, de combattre les infections ou, plus généralement, de produire la quantité exacte de protéine nécessaire pour répondre à un besoin spécifique. Parmi les joueurs les plus importants dans cette régulation de l’expression des gènes on retrouve les microARN (miARN). Ces petits ARN de 22 nucléotides sont présents chez la majorité des espèces multicellulaires et sont responsables du contrôle direct de plus de 30% des gènes exprimant des protéines chez les vertébrés. La famille de miARN lethal-7 (let-7) est composée de miARN parmi les plus connus et ayant des fonctions cruciales pour la cellule. La régulation du niveau des miARN let-7 est essentielle au bon développement cellulaire. La biogenèse de ces miARN, du transcrit primaire jusqu’à leur forme mature, est régulée principalement par Lin28, une protéine pluripotente très conservée. Cette protéine est composée d’un domaine cold shock (CSD) et de deux domaines de liaison au zinc. C’est grâce à ces domaines de liaison à l’ARN que Lin28 peut lier et inhiber la maturation des miARN let-7. L’objectif de cette thèse est de caractériser l’interaction entre Lin28 et le microARN précurseur let-7g afin de mieux comprendre le rôle de cette protéine dans l’inhibition de la biogenèse du miARN. À l’aide de techniques biochimiques et biophysiques, nous avons d’abord défini les principaux déterminants de l’interaction entre Lin28 et la boucle terminale du miARN précurseur let-7g (TL-let-7g). Nous avons conclu que le domaine C-terminal de Lin28, composé d’un motif riche en lysines et arginines ainsi que de deux motifs de liaison au zinc, permet à la protéine de lier spécifiquement et avec haute affinité un renflement riche en guanine conservé chez les précurseurs de la famille let-7. Aussi, parce que la séquence et la spécificité de liaison à l’ARN de ce domaine C-terminal sont semblables à celles de la protéine NCp7 du VIH, nous avons défini ce dernier comme le domaine NCp7-like de Lin28. Par la suite, nous avons caractérisé la multimérisation de trois protéines Lin28 sur la boucle terminale de pre-let-7g. Ceci a permis de réconcilier d’apparentes contradictions retrouvées dans la littérature actuelle concernant les sites de liaison de Lin28 lors de sa liaison aux miARN précurseurs. Nous avons identifié trois sites de liaison à haute affinité sur TL-let-7g qui sont liés dans un ordre précis par trois protéines Lin28. Lors de la formation du complexe multimérique, le CSD permet une déstabilisation de l’ARN, ce qui rend accessible plusieurs sites de liaison. Le domaine NCp7-like permet plutôt un assemblage ordonné de la protéine et facilite la liaison initiale de cette dernière. Ces nouveaux résultats rendent possible la mise au point d’un nouveau modèle de l’interaction entre Lin28 et le miARN précurseur let-7g. En conclusion, les études réalisées dans cette thèse apportent une meilleure compréhension des mécanismes moléculaires impliqués dans la régulation post-transcriptionnelle d’une importante famille de miARN et permettront de guider les futures études dans le domaine de recherche en pleine effervescence qu’est celui de la biogenèse des miARN. / The regulation of gene expression is what allows our cells to adapt to their environment, to fight infections or, more generally, to express the appropriate level of proteins to meet a specific need. The microRNAs (miRNAs) are among the most important players in the regulation of gene expression. These small RNAs of 22 nucleotides are present in most multicellular species and are responsible for the direct control of more than 30% of protein-expressing genes in vertebrates. The miRNA lethal-7 (let-7) family consist of some of the most studied miRNAs and plays crucial roles in the cell. The appropriate regulation of the let-7 miRNAs level is essential for proper cellular development. The biogenesis of these miRNAs, from the primary transcript to their mature form is mainly regulated by Lin28, a highly-conserved pluripotent protein. This protein is composed of a cold shock domain (CSD) and two zinc-binding domains. These RNA-binding domains allow Lin28 to bind and inhibit the maturation of the let-7 miRNA. The objective of this thesis is to characterize the interaction between the Lin28 protein and the let-7g miRNA precursor to better understand the role of this protein in the inhibition of miARN biogenesis. Using biochemical and biophysical techniques, we first identified the main determinants of the interaction between Lin28 and the terminal loop of the precursor miRNA let-7g (TL-let-7g). We concluded that the C-terminal domain of Lin28, composed of a lysine-rich and arginine-rich motif in addition to two zinc-binding motifs, is sufficient to bind with high affinity a conserved guanine-rich bulge located on the TL-let-7g. In addition, because the sequence and RNA-binding specificity of this C-terminal domain are similar to those of the HIV protein NCp7, we defined this region as the NCp7-like domain of Lin28. Subsequently, we characterized the multimerization of three Lin28 proteins on the terminal loop of pre-let-7g. This study helped to reconcile apparent contradictions found in the current literature regarding the Lin28-binding sites on miRNA precursors. We identified three high-affinity binding sites on TL-let-7g that are bound in a stepwise manner by the three Lin28 proteins. As part of the formation of the multimeric complex, both RNA-binding domains of Lin28 play an important role. The CSD destabilizes the RNA and this exposes several binding sites, whereas the NCp7-like domain allows an orderly protein assembly and facilitates the initial binding of the protein. These results lead us to propose a new model for the interaction between Lin28 and pre-let-7g. In conclusion, these studies provide a better understanding of the molecular mechanisms involved in the post-transcriptional regulation of an important family of miRNAs and will help guide future projects in the expanding research area of miRNA biogenesis.