The misregulation of post-transcriptional mechanisms has been linked to the development and progression of numerous human diseases, in particular neurological disorders and cancer. Investigating these misregulated RNA pathways is essential to fully understand the disease mechanisms, identify novel biomarkers, and to develop effective therapies. In this thesis, I present three manuscripts that investigate the mechanisms behind the post-transcriptional misregulation of RNA in human disease, with a focus on pre-mRNA splicing. In the first manuscript (Bondy-Chorney et al., 2016a), we investigated the role of Staufen1 (Stau1) in splicing regulation in the neuromuscular disorder Myotonic Dystrophy Type 1 (DM1). Here we report the first insights into the mechanism that Stau1 uses to regulate the alternative splicing of INSR exon 11 through an interaction with Alu elements located in intron 10. Moreover, using a high-throughput RT-PCR screen, we uncovered a number of additional Stau1-regulated alternative splicing events in both wild-type and DM1 myoblast cell lines. As Stau1 is known to be aberrantly upregulated in DM1 skeletal muscle, our findings suggest that Stau1 acts as a disease modifier in this disorder. The second manuscript (Sanchez, Bondy-Chorney et al., 2015), describes a novel role of the protein methyltransferase Coactivator-Associated Methyltransferase-1 (CARM1), a protein found to be overexpressed in Spinal Muscular Atrophy (SMA). We found that CARM1 can act as a mediator in the nonsense-mediated decay pathway (NMD) and associated UPF1 to promoted its occupancy on PTC-containing transcripts. We identified a subset of natural non-PTC containing NMD targets that were dependent on CARM1, a number of which were misregulated in SMA. This work uncovered a novel role for CARM1 in the NMD pathway and revealed that defective targeting of PTC-containing mRNAs should be included in the complex array of molecular defects associated with SMA. Finally, the third manuscript (Bondy-Chorney et al., – in prep) examines the alternative iv splicing regulation of the Protein Arginine Methyltransferase PRMT1 exon 2, an event shown to alter the growth, survival, and invasion of breast cancer cells. Here, we used an RNA interference (RNAi) RT-PCR screen to uncover several splicing proteins that regulate the inclusion of exon 2, several of which we found to be misregulated in a panel of breast cancer cell lines and patient tumours. These findings confirmed that the inclusion of PRMT1 exon 2 was regulated by alternative splicing via splicing factors that are altered in breast cancer. Moreover, depletion of one of these splicing factors, RALY, resulted in a decrease in the motility and invasive potential of an aggressive breast cancer cell line. These three manuscripts represent a collection of work focused on elucidating the mechanisms involved in post-transcriptional misregulation of RNA in three diverse human diseases. Taken together, the data presented here highlight the broad impact that proteins, such as Stau1 and CARM1, can have in neuromuscular disorders. Moreover, we also uncovered novel misregulation of splicing proteins that alter alternative splicing patterns in breast cancer. Elucidating these mechanisms is of the highest importance in order to identify potential new and effective treatment avenues.

In oncology, there is a need to optimize drug treatment for efficient eradication of tumors, minimization of adverse effects (AEs), and prolonging patient survival. Pharmacometric models can be developed to streamline information between drug development phases, describe and quantify response to treatment, and determine dose regimens that balance toxicity and efficacy. In this thesis, data from trastuzumab emtansine (T-DM1) and taxane drug treatment were used to develop pharmacometric models of pharmacokinetics (PK), AEs, anti-tumor response, and survival, supporting drug development. T-DM1 is an antibody-drug conjugate (ADC) for treatment of human epidermal growth factor receptor 2 (HER2)–positive breast cancer. ADCs are a relatively new class of oncologic agents, and contain multiple drug-to-antibody ratio (DAR) moieties in their dose product. The complex distribution of T-DM1 was elucidated through PK models developed using in vitro and in vivo rat and cynomolgus monkey DAR data. Mechanism–based PK/pharmacodynamic (PKPD) models were also developed for T-DM1 that described the AEs thrombocytopenia (TCP) and hepatotoxicity in patients receiving T-DM1. Variable patterns of platelet and transaminase (ALT and AST) response were quantified, including an effect of Asian ethnicity that was related to higher incidences of TCP.  Model simulations, comparing dose intensities (DI) and Grade 3/4 incidences between the approved T-DM1 dose (3.6 mg/kg every three weeks) and weekly regimens, determined that 2.4 mg/kg weekly provided the highest DI. Docetaxel and paclitaxel are taxane treatment options for HER2–negative breast cancer. Tumor response data from these treatments were used to develop a mechanism–based model of tumor quiescence and drug–resistance. Subsequently, a parametric survival analysis found that tumor baseline and the model–predicted time to tumor growth (TTG) were predictors of overall survival (OS). This tumor and OS modeling approach can be applied to other anticancer treatments with similar patterns of drug–resistance. Overall, the pharmacometric models developed within this thesis present new modeling approaches and provide understanding on ADC PK and PKPD (TCP and hepatotoxicity), as well as drug–resistance tumor response. These models can inform simulation strategies and clinical study design, and be applied towards dose finding for anticancer drugs in development, especially ADCs.

Die Arbeit befasst sich mit Abschätzung der Häufigkeit der proximalen myotonen Myopahtie (PROMM/DM2) in der deutschen Bevölkerung. Zugrunde liegend sind Daten aus dem Institut für Humangenetik der Universität Würzburg von 1993 bis 2006, sowie Daten der deutschlandweiten Diagnostik anbietenden Zentren aus den Jahren 2005 und 2006. Die Auswertung der Daten der Humangenetik in Würzburg bestätigte die Vermutung, dass die myotone Dystrophie (DM1) und die proximale myotone Myopathie (PROMM/DM2) gleich häufig sind. Aus dem Wissen heraus, dass frühere Angaben für die Häufigkeit der DM1 nicht nur diese Erkrankung erfasst haben, sondern auch Fälle mit PROMM/DM2, kann man davon ausgehen, dass damalige Häufigkeitsangaben anteilig beide Erkrankungen gemeinsam erfasssen. Das Ergebniss spricht für eine Inzidenz von 2,75/100.000 Einwohnern in Deutschland. / The central question of this work was, to asses the frequency of proximal myotonic dystrophy (PROMM/DM2) in germanys population. Based on data of the years 1993 to 2006 from institute for human genetics at the university of wuerzburg and data from laboratories all over germany offering genetic testing for proximal myotonic myopathy, the assumption of having both, proximal myotonic myopathy and myotonic dytsrophy, the same frequency has been confirmed. We know that data refering to the frequency of myotonic dystrophy must also have includet cases of proximal myotonic dytsrophy. Proceeding that previous data includes both malaties and that they are both, same often, we can say that the incidence of proximal myotonic dystrophy must be 2,75/100.000 inhabitans.

Les amplifications de répétitions de triplets CTG dans le gène DMPK humain sont à l'origine de la dystrophie myotonique de type 1 ou DM1. Les répétitions CUG présentes dans les ARNm DMPK séquestrent le facteur d'épissage MBNL1 au sein de foci nucléaires et dérégulent l'épissage des pré-ARNm cibles de MBNL1. Par ailleurs, 9 isoformes de MBNL1, produites par épissage alternative, coexistent dans les cellules. Dans un premier temps nous avons recherché quels exons constitutifs ou alternatifs étaient requis pour la reconnaissance des ARN, la régulation de l'épissage et la localisation cellulaire de MBNL1. Nous avons ensuite entrepris de rechercher par l'approche SELEX les séquences de haute affinité pour MBNL1. Nous avons ainsi identifié une séquence conservée de 12 nucléotides de long, contenant un seul motif de fixation pour MBNL1 et adoptant une structuration tige-boucle particulière. L'importance de cette structuration a été confirmée par l'existence de mutants compensatoires au sein des ARN sélectionnés. Finalement nous avons étudié les mécanismes de régulation de l'inclusion de l'exon 5 du pré-ARNm de la troponine T cardiaque humaine (hcTNT). Une approche in cellulo nous a permis d'identifier les séquences minimales requises pour la régulation de l'épissage en conditions normales et en présence des répétitions CUG. Au sein de ces séquences nous avons identifié 6 nouveaux sites MBNL1 dont nous avons montré l'importance fonctionnelle in cellulo et in vitro. Nous avons également mis en évidence l'implication d'autres séquences régulatrices dans la régulation de l'inclusion de l'exon 5 du pré-ARNm hcTNT et un rôle de la protéine hnRNP H dans ces régulations. L'ensemble de ces données apportent de nouveaux éléments d'information importants pour la compréhension de la DM1 / Amplifications of CTG motifs in the human DMPK gene are responsible for Myotonic Dystrophy of type 1. The resulting CUG repeats in pre-mRNAs capture the MBNL1 splicing factor, leading to mis-regulation of MBNL1 pre-mRNA targets. Due to the recent discovery of MBNL1 and its numerous isoforms (9) resulting from alternative splicing, little is known on how MBNL1 regulates splicing and how a decreased level of available MBNL1 generates splicing miss-regulations. First, we defined which of the MBNL1 alternative and constitutive exons are required for: i) RNA binding, ii) splicing activity and, iii) MBNL1 sub-cellular localization. Second, for a more precise definition of the MBNL1 RNA binding properties, we performed SELEX experiments using a library of RNA stem-loop structures containing a 18-nt long randomized sequence. Its leads to the identification of 12-nt long sequence adopting a peculiar stem-loop structure, whose importance for MBNL1 binding was revealed by its preservation by compensatory base-pair mutations. Finally, based on the above data, we studied the mechanisms involved in regulation of hcTNT exon 5 splicing. By in cellulo assays, we defined the hcTNT pre-mRNA region required for both normal inclusion and for the trans-dominant effect of CUG repeats. Within this region, we identified six new potential MBNL1 sites and demonstrated their functional role by in vitro and in cellulo assays. We also identified several additional splicing regulatory elements involved in normal and CUG-deregulated exon 5 inclusion and already showed a role of hnRNP H in splicing regulation. Altogether, our data bring new information important for understanding the pathology

Les ARN hélicases DDX5 et DDX17 sont des protéines « multi-tâches », elles sont impliquées dans de nombreuses étapes de la régulation du métabolisme des ARNs dont la transcription, l’épissage et la dégradation des ARNs. Lors de processus biologiques complexes tels que la myogénèse, les programmes d’expression génique sont profondément modifiés. Durant mon travail de thèse, j’ai contribué à montrer que DDX5 et DDX17 sont des protéines orchestratrices de la différenciation en coordonnant de manière directe et dynamique plusieurs niveaux de régulation génique. DDX5 et DDX17 contrôlent l’activité du facteur de transcription MyoD, régulateur majeur de la myogénèse ainsi que des microARNs spécifiques du muscle miR-1 et miR-206. Ceux-ci ciblent et régulent en retour l’expression de DDX5 et DDX17 mettant en place une boucle de rétro-contrôle négative induisant la diminution d’expression de ces deux protéines au cours de la différenciation. Enfin, cette diminution d’expression permet la mise en place d’un programme d’épissage participant à l’acquisition de phénotypes morphologiques des cellules différenciées. D’un point de vue mécanistique, il apparaît qu’un sous-groupe des événements d’épissage régulés durant la différenciation est contrôlé par la coopération de DDX5 et DDX17 avec le facteur d’épissage hnRNP H/F. D’autre part, DDX5 a aussi été impliqué dans un contexte pathologique du muscle. Cette hélicase interagit avec la mutation responsable de la Dystrophie Myotonique de type 1 (DM1). Durant ma thèse, j’ai produit des résultats préliminaires suggérant un rôle de DDX5 dans la mise en place des défauts d’épissage observés dans cette pathologie / RNA helicases DDX5 and DDX17 are “multi-tasks” proteins involved in nearly all aspects of RNA metabolism such as transcription, splicing and RNA degradation. During complex biological processes like myogenesis, gene expression programs are deeply modified. During my PhD, I contributed to show that DDX5 and DDX17 are orchestrators of differentiation by dynamically and directly orchestrating several layers of gene expression. DDX5 and DDX17 control the activity of the transcription factor MyoD, master regulator of myogenesis, as well as the expression of miR1/206, muscle-specific micro-RNAs. During myogenesis, these miRNAs downregulate the protein expression of DDX5 and DDX17 in a negative feedback loop, contributing to the switch of splicing programs observed in differenciated cells. Mechanistically, this splicing subprogram appear to be in part regulated by DDX5 and DDX17 in cooperation with hnRNP H/F splicing factors. Moreover DDX5 has been involved in a pathological muscular pathology : Myotonic Dystrophy type 1 (DM1). This helicase interact with the DM1 pathological mutation. During my PhD, I produced preliminary results suggesting a role for DDX5 in the establishment of the splicing defects observed in DM1

Le T-DM1 est un immunoconjugué composé de l'anticorps trastuzumab qui cible HER2 lié au DM1, un agent anti-tubuline dérivé de la maytansine. Malgré son efficacité, la résistance acquise au T-DM1 a été démontré lors des tests précliniques et chez certains patients. Nous avons développé des lignées résistantes à partir de la lignée de cancer du sein MDA-MB-361 et de la lignée de cancer de l'œsophage OE-19, que nous avons exposées au T-DM1 à doses croissantes pendant une longue durée en absence ou en présence de ciclosporine A (CsA). A partir de ces conditions nous avons obtenus les lignées “TR” qui ont été exposées uniquement au T-DM1 et “TCR” qui ont été exposées au T-DM1 et CsA. Nous avons observé une augmentation de la vitesse de migration et une diminution de la force d'adhésion chez OE-19 TCR associées à une sensibilité accrue à un inhibiteur de RHOA. Aussi, la voie des prostaglandines était dérégulée chez OE-19 TR et TCR, avec une forte augmentation de l'expression de COX-2 et de prostaglandine E2 dans la lignée OE-19 TR. La sensibilité à l'aspirine, un inhibiteur des cyclooxygenases 1-2, était accrue chez les deux lignées OE-19 résistantes par rapport à la lignée parentale. En conclusion nous avons démontré que différentes voies de signalisation peuvent être impliquées dans la résistance au T-DM1. Nos résultats restent à être validés chez les patients. Nous suggérons que cibler la voie de régulation de la composition du cytosquelette ou la voie des prostaglandines pourrait permettre d'obtenir un effet thérapeutique dans le cas de cancers résistants au T-DM1 / T-DM1 is an antibody-drug conjugate composed of the monoclonal antibody trastuzumab linked to DM1, a potent tubulin binding agent. Despite its efficacy in the treatment of HER2-positive breast cancer patients, acquired resistance to T-DM1 was observed during clinical trials. In order to study resistance mechanisms to T-DM1, we developed resistance models using OE-19 (esophageal) and MDA-MB-361 (breast) cancer cell lines in the absence or presence of ciclosporin A (CsA), an inhibitor of MDR1 mediated efflux. Resistant cells selected with T-DM1 alone are named “TR” and cells selected in the presence of T-DM1 and CsA are called “TCR”. OE-19 TCR cells showed modifications in adhesion gene expression, migration and adhesion strength, combined with an increased sensitivity to a RHOA inhibitor. Also, OE-19 TR cells presented an overexpression of COX-2 associated with an increased amount of PGE2 in the supernatant. A deregulation of the genes involved in the prostaglandin pathways was found in OE-19 TR and TCR cells, associated with increased sensitivity to aspirin. In conclusion, we found two signaling pathways deregulated in cell lines resistant to T-DM1. These results need to be validated using samples from patients resistant to T-DM1. Targeting the adhesion or the prostaglandin pathway could be of benefit for patients with T-DM1 resistant cancers

Dystrophia myotonica (DM1), one of the most common forms of muscular dystrophy, is caused by a repeated trinucleotide expansion in the DMPK gene. This mutation results in the accumulation of toxic cellular RNA transcripts. Spliceosome-mediated RNA trans-splicing (SMaRT) technology is a form of gene therapy that possesses the potential to correct these toxic RNA transcripts and thus cure the disease. Despite its promise, prior research applications of SMaRT technology to DM1 have been hampered by poor efficiency and have not been validated in a relevant model of the disease. In order to improve the efficiency of trans-splicing, this study examined the use of novel SMaRT molecules containing altered binding domains. These SMaRT molecules were tested in a clinically relevant cell model of DM1 and their corrective ability compared with that of a standard SMaRT molecule. The results were quantified by RT-PCR. The outcome of this study indicated the need to utilize more specific methods for measuring efficiency and for understanding the specific interactions of SMaRT molecules with target transcripts.

L’imagerie en oncologie a fait des progrès considérables ces dernières années avec l’introduction du CT scan spiralé, de la résonance magnétique, de la mammographie digitalisée et du PET scan. Des combinaisons de différentes techniques ont vu le jour, telles que le PET/CT, et améliorent encore les possibilités de stadification de la maladie cancéreuse ainsi que le monitoring de son évolution dans le temps, et notamment sous traitement.Parallèlement, de grands progrès thérapeutiques ont étés réalisés en oncologie, en particulier le développement de médicaments « ciblés » dont l’efficacité dépend de l’expression par la cellule tumorale d’une molécule cible jouant un rôle important dans sa survie et/ou sa prolifération. L’expression de la molécule cible est une condition nécessaire mais pas suffisante pour observer une réponse au traitement ciblé :l’échec de ce dernier peut aussi s’expliquer par des altérations moléculaires en amont ou en aval de la « cible ».Le cancer du sein dit « HER2 positif » représente 20 à 25% des cancers du sein. Celui-ci est caractérisé par l’expression membranaire, en quantités importantes, d’une protéine, appelée HER2, qui lui confère une biologie agressive et un mauvais pronostic. L’expression de HER2 au niveau de la tumeur, déterminée en routine clinique par immunohistochimie et/ou par hybridation in situ en fluorescence, est le seul biomarqueur validé aujourd’hui dans le cancer du sein HER2 positif pour prédire l’efficacité des traitements ciblés anti-HER2. Cette prédiction est toutefois peu satisfaisante en termes de valeur prédictive positive (50% environ). Après une revue de la litérature sur les études d’imagerie fonctionnelle, peu nombreuses, réalisées dans le cancer du sein HER2 positif, nous avons décidé d’explorer le rôle de l’imagerie moléculaire avec la technologie PET/CT dans l’individualisation de la prise en charge du cancer du sein HER2 positif avec deux radio traceurs (FDG et zirconium89-trastuzumab), et ce, dans deux contextes cliniques distincts :dans la maladie précoce soumise à un traitement neoadjuvant et dans le contexte métastatique, en cas de traitement par le T-DM1. / Doctorat en Sciences médicales (Médecine) / info:eu-repo/semantics/nonPublished

Myotonic dystrophy type 1 (DM1) is an autosomal dominant and progressive neuromuscular disorder caused by the CTG trinucleotide repeat expansion in the 3’ untranslated region of the DMPK gene. Clinical manifestations include extensive atrophy of skeletal muscle (SkM) concomitant with muscle weakness, that develops in a distal to proximal fashion. Central to muscle plasticity is the satellite cell (SC), a muscle specific stem cell that, upon activation, facilitates muscle repair and regeneration. To date, SCs have yet to be elucidated in DM1; therefore, the aim of the present study was to extensively characterize the PAX7+ SC population, along with other indices of muscle quality in SkM. DM1 patients (6 women, 5 men) performed stationary cycling 3 times per week for 12wks, with biopsies taken from the Vastus lateralis pre- (PRE) and post-endurance exercise intervention (POST). Age-matched, healthy controls (CTRL) were used for comparison of baseline measures. Type 1 and 2 myofiber-specific PAX7+ cells were significantly greater in DM1 patients (PRE), in comparison to CTRL (2.24- and 1.84-fold, respectively), with type 2 SC content further increasing following training (p<0.05). In addition, protein expression of myogenic regulatory factors PAX7 and myogenin were significantly higher in DM1 compared to CTRL, with no training effects observed. Both immunohistochemical and immunoblotting analysis showed that activated MYOD+/PAX7+ cells did not significantly differ in DM1 vs. CTRL. FISH- IF analysis of CUG repeats show that 30% of SCs in DM1 were positive for these inclusions. Muscle capillarization was significantly lower in type 2 fibers in DM1 vs CTRL, which was fully rescued with training (p<0.05). At baseline, DM1 muscle showed the presence of de novo and fat infiltrated fibres, as well as fibrosis, that were relatively non-existent in the CTRL. In vitro results show patient-derived myoblasts exhibit a proliferation defect. Furthermore, myoblasts showed impairments in both glycolysis and mitochondrial respiration, with the latter being completely normalized to CTRL in myotubes. Our novel findings display an increased, albeit non-functional, SC pool in DM1 SkM indicated by disturbances in the myogenic program and overall poor muscle quality. We show that both SCs and SkM remain responsive to exercise training, suggesting therapeutic potential. We also suggest that mitochondrial dysfunction may underpin these impairments in the myogenic program. / Thesis / Master of Science (MSc) / Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy in adults worldwide affecting 1:8000 individuals, with certain areas in northeastern Quebec having a higher prevalence of 1:600 individuals. DM1 is caused by an autosomal dominant genetic mutation that leads to muscle weakness, respiratory insufficiency, cataracts and cardiac conduction block, ultimately resulting in poor quality of life and shortened lifespan. Preliminary evidence suggests that the maintenance of muscle health can greatly improve quality of life and life-span of these individuals, making an in-depth research focus on this therapeutic intervention extremely important. Optimal muscle health is maintained by the functionality of muscle stem cells, that aid in muscle repair and facilitate adaptations in muscle following exercise interventions. These cells are shown to be dys- or non-functional in various muscular dystrophies which coincide with the observation of poor muscle health. Therefore, the aim of this study was to examine the number and functionality of muscle stem cells, and physiological factors of muscle health in DM1. In addition, we also aimed to explore whether exercise has therapeutic potential to alleviate poor muscle quality in DM1. In general, we found that DM1 patients have a higher proportion of muscle stem cells; however, they are inherently dysfunctional but did respond to exercise. Consistent with the latter observation, we found poor muscle quality metrics in DM1 patients, with aerobic training leading to improvements in muscle health. Altogether, our results provide in-depth analysis that underscores muscle dysfunction observed in DM1 and the benefits of exercise interventions.

La dystrophie myotonique de type 1 (DM1), est une maladie génétique héréditaire affectant environ 1/8000 personnes. Les patients souffrant de DM1 développent essentiellement des troubles musculaires tels qu’une faiblesse et une atrophie musculaire. La cause de la DM1 est expliquée par la mutation du gène "DMPK". Lors de ma thèse, j’ai pu démontrer que l’épissage de l’ARNm BIN1 était altéré dans le muscle DM1. En effet, l’exon 7 de BIN1, qui est absent du muscle normal, est exprimé de façon aberrante chez les patients DM1. En utilisant un modèle murin, j’ai prouvé que l’expression forcée de l’exon 7 de BIN1 altérait simultanément la structure et la fonction du muscle. Nous avons notamment observés une diminution de la taille des fibres musculaires et une augmentation de la faiblesse musculaire, comparé à des souris normales. Par conséquent, ce travail aidera à la compréhension du mécanisme de la maladie et pourrait expliquer les causes de la faiblesse musculaire et de l’atrophie. / Myotonic dystrophy of type 1 (DM1), is an inherited genetic disease affecting around 1 in 8000 person. Patients suffering from DM1 develop essentially muscle disorders such as muscle weakness, muscle loss and atrophy. The cause of DM1 is explained by the mutation of a gene called “DMPK“.During my thesis, I discovered that the alternative splicing of BIN1 mRNA was altered in the muscle of DM1 patients. Indeed, the BIN1 exon 7, which is normally absent in healthy muscle, is aberrantly expressed in DM1 muscle. By using a mouse model, I found that the forced expression of BIN1 exon 7 was responsible of the alteration of both muscle structure and function. Notably, we found a decrease in muscle fibers area (atrophy) and an increase of muscle weakness, compared to wild-type mice. Therefore, this work will help in the understanding of the disease mechanism and could explain the causes of muscle weakness and atrophy, which have never been elucidated to this date.