Ácido Hialurônico (HA) é um componente da matriz extracelular, responsável pela hidratação e manutenção do equilíbrio osmótico tecidual. Concentrações de HA estão elevadas em vários tipos de cânceres, incluindo próstata. Hialuronidases (HAases), são uma família de enzimas relacionadas com a propagação de infecções bacterianas, toxinas de venenos e progressão tumoral. A quebra do HA em pequenos fragmentos (3-25 dissacarídeos) promovidos pela ação das HAases tipo Hyal1, Hyal2 e Hyal3, está relacionada à promoção do câncer através da indução da angiogênese e estímulo a proliferação através de ativação da via tirosina quinase. Algumas isoformas de HAases, descritas como produto de splicing alternativo, possuem atividade enzimática diversificada. A heterogeneidade de expressão das HAases foi identificada em alguns tipos de câncer e pode ser correlacionada com o comportamento diferenciado dos tumores. Para este trabalho estudamos amostras de 55 pacientes submetidos a prostatectomia radical por carcinoma de próstata (CP) . A média de idade foi 66 anos e o tempo médio de seguimento 73,7 meses. Os pacientes foram divididos em dois grupos para análise dos resultados: 1- Escore de Gleason (EG) >=7 (30) e EG <=6 (25). 2- Comportamento tumoral (recidiva-19, e não recidiva-36), considerando o nível sérico de Antígeno Específico da Próstata (PSA) 0,2 ng/mL. O grupo controle foi representado por 11 pacientes com hiperplasia prostática benigna, submetidos à ressecção retropúbica. As HYAL foram identificadas por PCR, com uso de primers específicos para as variantes 1, 2, 3, 4 e 5 e wt da HYAL1, wt da HYAL2, e wt e variantes 1, 2 e 3 da HYAL3. As HYAL mais freqüentemente expressas pelo CP foram HYAL2-wt (65,4%), HYAL1-v1 (63,3%) e HYAL3-wt (47,2%). Em tecidos prostáticos benignos, a HYAL3-v1 foi expressa em 90,9% dos casos, estando presente em 36% dos tumores com EG baixo, e não expressa em tumores com EG alto (p=<0,001). Nos tumores sem recidiva HYAL1-v3 foi expressa em 30,5% dos casos versus 5,2% em casos que recorreram (p=0,041). HYAL3 v2, foi expressa por 33,3% dos tumores que não recorreram e não expressa em tumores que recorreram (p=0,002). Concluímos que a expressão de HYAL1-v3, HYAL3-v1 e HYAL3-v2 está relacionada a tumores mais diferenciados e com menores taxas de recidiva, podendo ser utilizadas como marcadores na prática clínica identificando candidatos a terapias mais conservadoras. / Hyaluronic acid (HA) is a component of the extracellular matrix that hydrates and maintains the osmotic balance of tissues. HA concentration is elevated in several cancers including prostate. Hyaluronidases (HAases) are a family of enzymes related to the spread of bacterial infections, toxins of venoms and probably cancer progression. Small fragments of HA are generated by HAase Hyal1, Hyal2 and Hyal3, stimulating endothelial proliferation and activating mitogen-activated protein kinase pathway. Several isoforms of HAases have been described as a product of alternative splicing, and are responsible for differences in the enzyme activity. The heterogeneity of HAses expression has been identified in tumors and could be related to the differences in their biological behavior. Fifty-five patients submitted to radical prostatectomy for prostate cancer (PC) were the subject of this study. The mean age was 66 years old and the mean follow-up was 73,7 months. Patients were divided into two groups for the analyses: 1- High Gleason score (GE) >=7 (30) and low Gleason score <=6 (25). 2- Tumor behavior; recurrence - 19 and nonrecurrence - 36. Biochemical recurrence was considered when PSA was higher than 0.2 ng/mL. The control was represented by 11 patients submitted to retropubic prostate resection for benign prostatic hyperplasia. The alternative splicing forms of HYAL were identified by PCR, and the primer sequences identified variants 1, 2, 3, 4, 5 e wt of HYAL1, wt of HYAL2, wt and variants 1, 2 and 3 of HYAL3. The HYAL more frequently expressed by PC was HYAL2-wt (65.4%), HYAL1-v1 (63.3%) and HYAL3-wt (47.2%). In benign prostate tissue the main expressed HAase was HYAL3-v1 in 90.9%, being present in 36% of low Gleason score tumors and not expressed by tumors with high Gleason score (p=<0.001). For tumors that not recurred there was expression of HYAL1-v3 in 30.5% of the cases vs. 5.2% in cases that recurred (p=0.041). The same difference was noted regarding the expression of HYAL3-v2, that was expressed by 33.3% of tumors that not recurred and not expressed by tumors that recurred (p=0.002). We conclude that there is a profile of HAase related to low Gleason score and non-recurrent PC that is characterized by expression of HYAL1-v3, HYAL3-v1 and HYAL3-v2 that could be used in clinical practice to choose a better treatment.

No description available.

Myotonic dystrophy (DM) is an inherited disease characterized by myotonia, insulin resistance, cardiomyopathy, and cognitive deficiencies. DM is a triplet repeat disorder, meaning that affected individuals carry anywhere between 50 and thousands of CTG/CCTG repeats in their genetic makeup. When transcribed into RNA, these repeats become “toxic” in the sense that they serve to bind and sequester important RNA binding proteins. One such family of proteins, the Muscleblind-like (MBNL) family, is important in the regulation of alternative mRNA splicing, and thus the sequestration of MBNL proteins leads to a number of mis-splicing events. Many of these events are directly correlated to DM symptoms. While there is no known cure for DM, the use of small molecules to treat symptoms is a well-characterized therapeutic tactic with immense promise. Pentamidine is a small molecule that was found to reverse mis-splicing in both DM cell and mouse models. Mechanistically, this molecule is particularly unique because unlike many small molecules, which physically displace MBNL from the toxic CUG RNA, pentamidine reduces CUG RNA levels, possibly through inhibition of CTG transcription. Chapter I summarizes alternative splicing mechanisms and regulation, defines MBNL protein structure and function, describes DM pathophysiology and molecular mechanism, and finally provides an overview of pentamidine characterization as a small molecule therapeutic. Chapter II reports the development of an in vitro T7 transcription assay, which allowed us to compare the relative efficacy by which pentamidine is able to inhibit the transcription of various repeat and non-repeat DNA sequences. This chapter further reports the characterization of a series of methylene linker analogues of pentamidine, which were also characterized through the T7 transcription assay. Chapter III details our thorough structure-activity relationship investigation of bisbenzamidine analogues of pentamidine, both in in vivo and in vitro models. Chapter IV describes our characterization of actinomycin D, a known transcription inhibitor and chemotherapeutic, within the DM disease framework. Chapter V summarizes these data, which ultimately serve as a proof of concept for the potential of CTG transcription inhibition in therapeutic contexts and broadly describe their application in other repeat diseases. This dissertation contains previously published and unpublished co-authored material. / 10000-01-01

No description available.

In most eukaryotes, alternative splicing is an important regulatory mechanism of gene expression that results in a single gene coding for multiple protein isoforms, thus largely increases the diversity of the proteome. RNA-seq is widely used for genome-wide splicing isoform quantification, and several effective and powerful methods have been developed for splicing analysis with RNA-seq data. However, it remains problematic for genes with low coverages or large number of isoforms. These difficulties may in principle be ameliorated by exploiting correlations encoded in the structured data sources. This thesis contributes to developments of Bayesian methods for splicing analysis by leveraging additional information in multiple datasets with structured prior distributions. First, we developed DICEseq, the first isoform quantification method tailored to time-series RNA-seq experiments. DICEseq explicitly models the correlations between experiments at different time points to aid the quantification of isoforms across experiments. Numerical experiments on both simulated and real datasets show that DICEseq yields more accurate results than state-of-the-art methods, an advantage that can become considerable at low coverage levels. Furthermore, DICEseq permits to quantify the trade-off between temporal sampling of RNA and depth of sequencing, frequently an important choice when planning experiments. Second, we developed BRIE (Bayesian Regression for Isoform Estimation), a Bayesian hierarchical model which resolves the difficulties in splicing analysis in single-cell RNA-seq (scRNA-seq) data by learning an informative prior distribution from sequence features. This method combines the quantification and imputation for splicing analysis via a Bayesian way, which is particularly useful in scRNA-seq data due to its extreme low coverages and high technical noises. We validated BRIE on several scRNA-seq data sets, showing that BRIE yields reproducible estimates of exon inclusion ratios in single cells. Third, we provided an effective tool by using Bayes factor to sensitively detect differential splicing between different single cells. When applying BRIE to a few real datasets, we found interesting heterogeneity patterns in splicing events across cell population, for example alternative exons in DNMT3B. In summary, this thesis proposes structured Bayesian methods to integrate multiple datasets to improve splicing analysis and study its biological functions.

La maladie de Steinert ou dystrophie myotonique de type 1 (DM1), dystrophie musculaire la plus commune chez l’adulte, est causée par l’expansion instable de triplets CTG dans la région 3’ non traduite du gène DMPK (Dystrophia Myotonica Protein Kinase). Cette maladie multisystémique, affectant principalement les muscles squelettiques et le cœur, est liée à l’épissage. En effet, les CUG exp forment des structures secondaires dans le noyau capables de séquestrer la protéine MBNL1, facteur d’épissage alternatif. En parallèle, un autre facteur d’épissage alternatif, CELF1 est stabilisé. La dérégulation de la balance entre ces deux protéines cause des défauts d’épissage, responsables de certains symptômes de la maladie, comme la myotonie, des défauts de conduction cardiaque et une résistance à l’insuline, causés respectivement par l’épissage aberrant du canal chlorure Clcn1, du canal sodique SCN5A et du récepteur à l’insuline IR. De plus, des dérégulations indépendantes de l’épissage sont aussi mises en jeu dans la DM1 mais leur responsabilité dans l’apparition des symptômes de la maladie reste à identifier. Pour identifier des dérégulations transcriptionnelles indépendantes de l’épissage mais liées à la progression et à la sévérité des symptômes, nous avons généré de nouveaux modèles drosophile de la DM1 avec un nombre croissant de répétitions CTG. Ces modèles étudiées au stade larvaire récapitulent les caractéristiques majeures de la DM1 : la formation de foci et une hypercontractilité musculaire. De plus, nous avons identifié dans ce modèle des dérégulations géniques indépendantes de l’épissage mais dépendantes du nombre de répétitions CTG. Notamment, une atténuation de Gbe1, codant pour une enzyme de branchement du glycogène pourrait participer aux phénotypes musculaires. Afin d’étudier les symptômes cardiaques de la maladie qui touchent 80% des patients et représentent la deuxième cause de mortalité, nous avons utilisé le modèle DM1 de drosophile développé dans notre équipe, et réalisé des analyses physiologiques cardiaques sur des mouches adultes qui expriment 960 CTG dans le cœur (Hand>DM1 960 ), un ARNi pour Mbl, l’orthologue de MBNL1, ou qui surexpriment l’orthologue de CELF1, Bru-3. Ces trois modèles DM1 reproduisent les symptômes cardiaques majeurs observés chez les patients comme des défauts de conduction, de l’arythmie (fibrillation) ou encore une cardiomyopathie dilatée. Afin d’identifier des dérégulations géniques susceptibles d’être responsables de ces défauts, nous avons réalisé une analyse transcriptomique par séquençage ARN après collection de l’ARN spécifique du cœur par la technique du TU-tagging. Les gènes dérégulés identifiés dans ces contextes ont été classés en fonction de leur conservation et du niveau de dérégulation. Parmi eux, la surexpression dans le cœur adulte de Straightjacket (Stj), l’orthologue de CACNA2D4 qui code pour une sous-unité d’un canal calcique voltage- dépendant, cause des défauts de conduction et de la fibrillation, mimant ce qui a été observé en contexte DM1 960 et gain de fonction pour Bru-3. Dans l’avenir, nous aimerions confirmer son implication dans la physiologie cardiaque et en particulier dans la DM1 en analysant son expression chez les patients présentant des défauts cardiaques similaires. / The most common muscular dystrophy found in adults, Steinert disease or Myotonic Dystrophy Type 1 (DM1) is caused by an unstable CTG repeat expansion in the 3’ untranslated region of the Dystrophia Myotonica Protein Kinase (DMPK) gene. This multisystemic disease, affecting particularly skeletal muscles and the heart, is called a spliceopathy because it involves the sequestration of the MBNL1 splicing factor by the expanded CUG-carrying transcripts and the stabilization of the CELF1 splicing factor. The misbalance of these two factors is responsible for splicing defects that cause most of the disease symptoms, like myotonia, conduction defects and arrhythmia but also insulin resistance, respectively associated to missplicing of Clcn1, SCN5A and IR. Moreover, DM1 toxicity is also associated to splice-independent deregulations but their link to disease symptoms remain poorly understood. To identify transcriptional deregulations independent of splicing and associated to disease progression and severity, we generated new DM1 Drosophila models with increasing number of CTG repeats. These larval models recapitulated the main DM1 muscular symptoms such as hypercontractility and foci formation and allowed us identifying gene deregulations independent of splicing. Among them, Gbe1 coding for a glycan branching enzyme is attenuated in the DM1 context in a CTG-repeat dependant manner and could participate in the severity of muscle phenotypes. To better understand the causes of cardiac symptoms that represent the second cause of death and affecting 80% of DM1 patients, we took advantage of our DM1 inducible Drosophila model and performed phenotypic analyses on the heart of adult flies expressing: 960 CTG specifically in the heart (Hand>DM1 960 ), a RNAi for the Drosophila MBNL1 orthologue (Muscleblind, Mbl) or overexpressing the CELF1 orthologue (Bruno-3, Bru3). These DM1 adult models display conduction abnormalities, arrhythmicity (fibrillation) and dilated cardiomyopathy (DCM). Thus, these three pathogenic contexts recapitulated collectively the main DM1 cardiac symptoms and prompted us to perform transcriptional profiling to identify symptom’s-associated gene deregulations. To identify new molecular actors responsible for the DM1 associated heart defects, we performed cardiac cell-specific transcriptional analyses by RNA-sequencing, using TU-tagging technique. Then, we selected deregulated candidate genes that could be linked to the particular observed phenotypes and ranked depending on their conservation and deregulation level. Among them, increased expression of Straightjacket (Stj), the CACNA2D4 orthologue, encoding a subunit of voltage- dependent calcium channel results in fibrillation and conduction defects, thus mimicking cardiac symptoms found in DM1 960 and Bru-3 gain of function contexts in which it was up- regulated. Whether identified candidates are deregulated in DM1 patients displaying cardiac abnormalities remains to be tested.

La Dystrophie Myotonique de type 1 (DM1) est cause par l’expansion anormale d’un triplet CTG dans la partie 3’UTR du gène DMPK, entrainant l’agrégation du transcrit mutant dans des inclusions ribonucléoprotéiques appelées foci. D’après plusieurs études structurales sur des courtes répétitions CUG, il a été proposé que les expansions CUG se replient en une structure en tige-boucle qui interfère avec l’activité de plusieurs facteurs lié au métabolisme de l’ARN et altère leur fonction cellulaire. Le facteur d’épissage muscleblind-like 1 (MBNL1) a été identifié par sa capacité à interagir avec les répétitions CUG. In vivo, ces répétitions entrainent la séquestration de cette protéine aboutissant en une déplétion nucléaire. Un autre facteur d’épissage, la CUG Binding protein (CUGBP1), est également impliqué dans la pathologie. Au lieu d’être séquestré par les répétitions, la stabilité protéique de CUGBP1 est augmentée dans les tissus DM1 entrainant un gain d’activité pour ce facteur. La séquestration de MBNL1 et la stabilisation de CUGBP1 résultent en la dérégulation de l’épissage alternatif de plusieurs transcrits musculaires et du cerveau et la réexpression d’isoformes protéiques fœtales dans les tissus adultes. Cependant, de récentes études suggèrent que d’autres facteurs ou voies de signalisation que celles faisant intervenir MBNL1 et CUGBP1 pourraient être impliquées dans la pathologie DM1.Le but de mon travail de thèse a été d’identifier de nouveaux facteurs ayant la capacité d’interagir avec les répétitions CUG. A l’aide d’une purification sur chromatographie d’affinité utilisant un ARN contenant 95 répétitions CUG comme appât, nous avons identifié l’ARN hélicase p68/DDX5. p68 fait partie de la famille des protéines DEAD-box, caractérisée par un core protéique conservé constitué de neufs domaines hautement conservés, dont le motif DEAD, à l’origine du nom de ces protéines. p68 est impliquée dans de nombreux aspects du métabolisme de l’ARN, dont la transcription, l’épissage, l’export, la traduction et la dégradation des ARN. Nous avons montré, que p68 colocalise avec les foci CUG dans un modèle cellulaire exprimant la partie 3’UTR du gène DMPK contenant de longues répétitions CTG. Nous avons identifié que p68 augmente l’interaction de MBNL1 sur les répétitions CUG et une structure secondaire particulière d’un élément régulateur de l’ARN pré-messager cardiac Troponin T (TNNT2), dont l’épissage est dérégulé dans la pathologie. L’insertion de mutations dans le core de l’hélicase de p68 abolit l’effet de p68 sur la fixation de MBNL1 ainsi que la colocalisation de p68 avec les expansions CUG in vivo, suggérant que le remodelage des structures secondaires ARN de manière ATP-dépendante par p68 facilite l’interaction de MBNL1. Nous trouvons également que la compétence de p68 pour réguler l’inclusion de l’exon alternatif 5 de TNNT2 dépend de l’intégrité des sites de fixation de MBNL1.Nous proposons que p68 agit comme un modificateur de l’activité de MBNL1 sur ces cibles d’épissage ainsi que sur les expansions CUG à l’origine de la pathologie. / Myotonic Dystrophy type I (DM1) is caused by an abnormal expansion of CTG triplets in the 3’ UTR of the DMPK gene, leading to the aggregation of the mutant transcript in nuclear RNA foci. Based on structural studies on short CUG repeats, it has been proposed that expanded CUG repeats fold into an imperfect hairpin structure that interferes with the activities of RNA binding proteins and alters their normal cellular function. The muscleblind-like 1 protein (MBNL1) was identified by its ability to bind to CUG repeats. It has been shown that the expanded mutant transcript promotes the sequestration of the MBNL1 splicing factor in nuclear RNA foci. CUGBP1 is another splicing factor that is involved in DM1. Instead of being sequestered by the repeats, the steady-state level of CUGBP1 is increased in DM1 tissues, leading to a gain of activity of the protein. The sequestration of MBNL1 and the up-regulation of CUGBP1 in DM1 results in the misregulation of alternative splicing of a subset of muscle and brain-specific transcripts, leading to the re-expression of fetal isoforms in adult tissues. However, several recent studies suggest that factors or signaling pathways other than MBNL1 and CUGBP1 could be involved in DM1 pathogenesis.The aim of this work was to isolate new factors that bind to CUG repeats. Using an affinity chromatography strategy with an RNA containing 95 pure CUG repeats, we identified the RNA helicase p68 (DDX5). p68 is a prototype of DEAD-box RNA helicase proteins. This family is characterized by a conserved core, consisting of nine conserved motifs including the DEAD signature, which gives rise to the name to these proteins. p68 is involved in many aspects of RNA metabolism including transcription, RNA processing, RNA export, translation and mRNA degradation. We showed that p68 colocalized with RNA foci in cells expressing the 3’UTR of the DMPK gene containing expanded CTG repeats. We found that p68 increased MBNL1 binding onto pathological repeats and the stem-loop structure regulatory element within the cardiac Troponin T (TNNT2) pre-mRNA, splicing of which is misregulated in DM1. Mutations in the helicase core of p68 prevented both the stimulatory effect of the protein on MBNL1 binding and the colocalization of p68 with CUG repeats, suggesting that remodeling of RNA secondary structure through a ATP-dependant manner by p68 facilitates MBNL1 binding. We also found that the competence of p68 for regulating TNNT2 exon 5 inclusion depended on the integrity of MBNL1 binding sites.We propose that p68 acts as a modifier of MBNL1 activity on splicing targets and pathogenic RNA.

During mRNA synthesis, pre-mRNAs must be cleaved and polyadenylated at their 3'-end to be fully mature, before being exported from the nucleus. In yeast, there is a large protein machinery comprised of dozens of proteins that work together to perform these two reactions. Some of these proteins are capable of recognizing and binding key sequence elements in the pre-mRNA, effectively directing where in the transcript the cleavage and polyadenylation occur. In this thesis, recently reported structural findings related to the pre-mRNA 3'-end processing machinery are summarized. Within this machinery, the Cleavage Factor IA (CF-IA) complex is comprised of the Rna14, Rna15, and Pcf11 and Clp1 proteins. Results reported here include the crystal structure of the Rna14-Rna15 complex, which indicates that the Rna14 protein forms a dimer that has inherent conformational variability. The Rna15 protein binds to the C-terminal domain of Rna14, and is connected to the Rna14 HAT domain by a flexible linker, which may indicate that Rna15 functions somewhat independently of the Rna14 HAT domain. The complete CF-IA complex is explored in detail, including protein-protein interactions within the complex and the stoichiometric ratios of CF-IA components. Unlike previous reports, results indicate that CF-IA may form a dimer with a 2:2:2:2 stoichiometry of Rna14:Rna15:Clp1:Pcf11. Also reported are projects unrelated to CF-IA, including the crystal structure of the biotin-dependent alpha(6)beta(6) geranyl-CoA carboxylase (GCC) holoenzyme. Comparison of GCC to the closely related 3-methylcrotonyl CoA carboxylase (MCC) holoenzyme reveals a conserved domain swap in the carboxyltransferase (CT) domains of both enzymes. This domain swap is not present in the related biotin-dependent carboxylases propionyl-CoA carboxylase (PCC) and acetyl-CoA carboxylase (ACC), which may indicate a distinct lineage for biotin-dependent carboxylases that target the γ-carbon. In addition, comparison of the two structures also reveals a conserved Phe191 in MCC that is absent in GCC. Phe191 blocks a key substrate-binding pocket and explains the differences in substrate-specificities between MCC and GCC. The role of Phe191 is tested by site-directed mutagenesis to a Glycine to open the pocket in MCC and by mutating a structurally equivalent Glycine to Phe to close the pocket in GCC. These mutations can convert MCC to a GCC and vice versa.

Il a été démontré au sein du laboratoire du Pr Tazi que les isoformes du gène LMNA issu d’un épissage alternatif jouent des rôles opposés sur le métabolisme lipidique et énergétique (Lopez-Mejia et al., 2014). Ces travaux suggèrent que la modulation pharmacologique de cet épissage pourrait représenter une approche nouvelle et originale dans le traitement de l’obésité. Cette hypothèse a été testée dans les travaux ici présentés en utilisant 2 systèmes de criblage complémentaires, et ceci afin d’identifier un potentiel modulateur de l’épissage présentant un impact sur le métabolisme énergétique. Un composé appelé ABX300 a ainsi été sélectionné pour être testé sur deux modèles murins d’obésité, un modèle de souris génétiquement modifié et un modèle nutritionnel. Son administration journalière a conduit à une perte de poids chez ces animaux. La modulation spécifique de l’épissage du gène LMNA par ABX300 a quant à elle été confirmée à l’aide d’un système rapporteur d’épissage. Les données générées montrent qu’ABX300 interagit directement avec SRSF1 avec pour conséquence son effet sur l’épissage de LMNA. Le travail de thèse ici présenté a consisté à déterminer le mécanisme d’action de la molécule ABX300, ainsi que son impact sur le métabolisme. Les résultats ont montré qu’ABX300 n’a pas d’effet ni sur la différenciation adipocytaire, ni sur le contenu en triglycérides au sein de lignées cellulaires (cellules 3T3-L1 et préadipocytes de tissu adipeux brun). Cependant, des analyses in vivo de « pair-feeding », des analyses PET-scan, et des études en cages métaboliques, ont montré une différence entre les groupes traités et non-traités au niveau de leur prise alimentaire, la consommation d'oxygène et la source énergétique utilisée. Parallèlement une série d'approches transcriptomiques ont permis de mettre en évidence une importante modulation par ABX300 de microRNA dont les cibles sont mitochondriales, et ceci en absence d’une restructuration globale du profil d'épissage.Ces travaux montrent que l’identification de modulateurs de l'épissage alternatif du gène LMNA est une stratégie innovante et prometteuse pour la découverte de molécules bioactives dans le traitement de l’obésité. / The discovery within our laboratory that the different LMNA isoforms play opposite roles on metabolism (Lopez-Mejia et al., 2014), led to the proposal that pharmacologically modulating this splicing could be a novel and original approach for the treatment of obesity. In this thesis I have challenged this proposal by performing two complementary screens in order to identify potential modulators of splicing with impact on energy metabolism. Following this initial screen, a compound termed ABX300 was selected and tested on animal models of obesity. Specific modulation of the LMNA splicing by ABX300 was confirmed using splicing reporters. Our data show that ABX300 interacts directly with SRSF1 to mediate its effect on LMNA splicing.The daily treatment with ABX300 lead to a weight loss in both, genetically modified mouse models and diet induced obesity mouse models. During my PhD I have established the mode of action of ABX300, along with its impacts on metabolism. Results demonstrated that ABX300 did not have an effect on adipocytes differentiation, nor in triglycerides content on in vitro cell lines (3T3-L1 and BAT preadipocytes). However, in vivo analysis, by means of pair-feeding experiments, PET-scan analysis, and metabolic chambers, among others, exhibited differences in between treated and untreated groups regarding food intake, oxygen consumption and fuel source. Concurrently, a series of transcriptomic approaches showed that ABX300 modulates the expression of miR whose targets encode proteins involved in mitochondrial functioning, but did not have an effect on global pre mRNA splicing. This work validates the screening for modulators of the LMNA alternative splicing as a promising strategy for the identification of bio-active small molecules and therefore promotes a complementary approach in the treatment of obesity.

Le syndrome de Usher (USH) est une maladie transmise selon le mode autosomique récessif caractérisée par l’association d’une surdité congénitale (HL) et d’une rétinite pigmentaire (RP), et dans certains cas, d’une aréflexie vestibulaire. Une hétérogénéité clinique et génétique est reconnue. Environ 10 % des cas USH restent non résolus après analyse moléculaire exhaustive des différents gènes. Ces cas incluent les patients qui ne portent aucune mutation dans un des gènes USH connus ainsi que les patients porteurs d’une seule mutation dans un gène USH. Au cours de cette thèse, nous nous sommes intéressés à l’étude des patients porteurs d’une seule mutation dans les gènes USH2A et PCDH15.Dans la première partie de la thèse, nous avons analysé une cohorte de patients avec un phénotype USH2A bien défini : 5 patients pour lesquels une seule mutation à l’état hétérozygote avait été identifiée dans le gène USH2A et un patient porteur d’un variant silencieux en trans d’une mutation non-sens.Pour les 5 patients, nous avons émis l’hypothèse que la seconde mutation, restant à être identifiée, pourrait se trouver dans des régions introniques profondes. Pour cela, nous avons développé une approche de séquençage à haut débit (NGS) de l’ADN pour identifier les variants introniques profonds dans le gène USH2A et évaluer leurs conséquences sur l’épissage. Comme preuve de concept et pour valider l’approche, y compris le pipeline bio-informatique et l’évaluation des outils de prédiction de l’épissage, nous avons analysé un patient porteur d’un pseudoexon (PE) connu dans le gène USH2A. Ensuite, les 5 patients ont été étudiés en utilisant le pipeline défini, ce qui a conduit à l’identification de 3 nouveaux variants introniques profonds chez 4 d’entre eux. Tous les variants ont été prédits comme pouvant avoir un impact sur l’épissage et aboutir à l’insertion de PE. Ces prédictions ont été validées par les essais minigènes. Grâce à cette étude, nous présentons une stratégie innovante pour identifier les mutations introniques profondes, lorsque l’analyse des transcrits n’est pas possible. Par ailleurs, le pipeline bio-informatique développé fonctionne indépendamment de la taille du gène analysé, ce qui permet l’application possible de cette approche à n’importe quel gène. Par ailleurs, un oligonucléotide antisens de type morpholino (AMO) a été évalué in vitro afin de rétablir l’altération d’épissage induite par une des mutations identifiées. Les résultats ont montré un taux d’exclusion élevé du transcrit aberrant et suggèrent une application possible en thérapie moléculaire. Nous avons ensuite effectué des études sur le variant USH2A c.1377T>A, un variant silencieux afin d’évaluer son effet sur l’épissage. L’analyse de l’ARN issu de cellules nasales du patient a montré que ce variant conduit au saut de l’exon 8 dans les transcrits USH2A. Ceci a été confirmé par un essai minigène. En outre, des études préliminaires ont été réalisées en utilisant des outils de prédictions et des essais minigènes pour évaluer l’implication des éléments cis-régulateurs dans le défaut d’épissage observé chez le patient. Dans la deuxième partie de la thèse, nous avons analysé une patiente USH1, pour laquelle une seule mutation avait été identifiée dans le gène PCDH15. Dans ce cas, nous avons combiné la culture des cellules épithéliales nasales avec l’analyse des transcrits PCDH15. Celle-ci a été réalisée par séquençage de cinq RT-PCR chevauchantes. Grâce à cette analyse, nous avons réussi à délimiter une région d’intérêt dans le transcrit, dont l’amplification a échoué exclusivement pour l’allèle porteur de la mutation non identifiée. D’autres analyses ont été effectuées dans la région génomique correspondante par capture ciblée couplée au séquençage NGS et LongRange PCR suivi de séquençage Sanger. Cependant, aucun variant candidat n’a été identifié à ce jour. Nous suggérons l’implication de mécanismes moléculaires complexes qui restent à être caractérisés. / Usher syndrome (USH) is an autosomal recessive disorder characterized by the association of sensorineural hearing loss (HL) and retinitis pigmentosa (RP), and in some cases, vestibular areflexia. Clinical and genetic heterogeneity are recognised. Indeed, three clinical types can be caused by mutations in one of the 10 known genes and USH2A represents the most frequently involved gene.Approximately 10 % of the USH cases remain genetically unsolved after extensive molecular analysis of the different genes, which includes sequencing of the exons and their intronic boundaries, combined to large rearrangements screening by array CGH. These unsolved cases include patients who do not carry any mutation in any of the known USH genes and patients who carry a single USH mutation. During this thesis we focalised on the study of patients carrying a single mutation in USH2A and PCDH15 gene.First, we have analysed a cohort of well-defined USH2A patients: five patients, for whom a single USH2A heterozygous mutation had been identified and one patient carrying a silent variant in trans to a nonsense mutation. For the 5 patients, we supposed that the second mutation remaining to be found could be localised deep in the introns. Indeed, a deep intronic mutation resulting in the inclusion of a pseudoexon (PE 40) in USH2A transcripts had been identified, following RNA analysis from nasal cells. Unfortunately, analysing USH2A transcripts still represent a challenging approach in a diagnostic settings and it is not always possible. To circumvent this issue, we have developed a DNA-Next Generation Sequencing (NGS) approach to identify deep intronic variants in USH2A and evaluate their consequences on splicing. As a proof of concept and to validate this approach, including the bioinformatics pipeline and the assessment of splicing predictor tools, the patient carrying the PE 40 was analysed at first. Then, the 5 patients were studied using the defined pipeline, which led to the identification of 3 distinct novel deep intronic variants in 4 of them. All were predicted to affect splicing and resulted in the insertion of PEs, as shown by minigene assays. Through this study, we present a new and attractive strategy to identify deep intronic mutations, when RNA analyses are not possible. In addition, the bioinformatics pipeline developed is independent of the gene size, implying the possible application of this approach to any disease-linked gene. Moreover, an antisense morpholino oligonucleotide (AMO) tested in vitro for its ability to restore the splicing alterations caused by one of the identified mutation provided high inhibition rates. These results are indicative of a potential application for molecular therapy.In the second case, we have performed studies on the USH2A c.1377T>A silent variant to investigate its effect on splicing. Analysis of RNA from nasal cells of patients showed that this variant led to the skipping of exon 8 in USH2A transcripts. This was confirmed by minigene assay. Moreover, preliminary studies have been performed using prediction tools and minigene assays to assess the involvement of cis-acting elements in causing the aberrant splicing.In the second part of the thesis, we have analysed an USH1 patient, for whom only one mutation had been identified in the PCDH15 gene. In this case, we combined nasal epithelial cells culture with the analysis of the PCDH15 transcripts. This was performed by sequencing five overlapping RT-PCRs. Through this analysis, we were able to delimit a region within the transcript, which failed to be amplified exclusively in the allele carrying the unidentified mutation. Further analyses have been performed in the corresponding genomic region by NGS-target capture and LongRange PCR associated with Sanger sequencing. However, no evident mutation has been identified so far. Therefore, we suggest the involvement of complex molecular mechanisms that remain to be characterised.