Le sarcome d’Ewing est une tumeur pédiatrique de l’os très agressive, généralement causée par une translocation chromosomique aboutissant à la protéine de fusion EWSR1-FLI1 qui dérégule l’expression d’un grand nombre de gènes participant à l’oncogenèse du sarcome d’Ewing. Au laboratoire, nous avons pu mettre en évidence une hétérogénéité intra-tumorale de l’expression d’EWSR1-FLI1 aboutissant à un nouveau modèle de la biologie du sarcome d’Ewing basé sur la coexistence de cellules EWSR1-FLI1high, participant à la prolifération de la tumeur primaire, et de cellules EWSR1-FLI1low, capables de dissémination métastatique. Au cours de ma thèse, je me suis intéressée en particulier aux mécanismes moléculaires sous-jacents aux capacités migratoires et invasives des cellules EWSR1-FLI1low. Nous avons ainsi pu mettre en évidence une diminution des jonctions serrées intercellulaires associée à une augmentation des interactions cellule-matrice chez les cellules EWSR1 FLI1low. Nous avons ensuite révélé le rôle clé des MMP dans l’invasion du sarcome d’Ewing, plus spécifiquement de la MMP2 et de la MT1-MMP qui sont toutes deux réprimées par EWSR1-FLI1 et sont apparues nécessaires à l’invasion des cellules EWSR1-FLI1low. L’un des défis majeurs actuels est de parvenir à visualiser cette sous-population très minoritaire et à suivre la plasticité de l’expression d’EWSR1-FLI1. Pour cela, l’identification de marqueurs des cellules EWSR1-FLI1low est cruciale. Ceci est également important pour déterminer si les chimiothérapies actuelles, qui ciblent plutôt les cellules prolifératives, n’entraînent pas une augmentation de la proportion de ces cellules au sein de la tumeur primaire. Enfin, nos essais infructueux d’utilisation de l’embryon de poulet comme nouveau modèle de la métastase du sarcome d’Ewing in vivo ont souligné la fragilité globale et les limitations de ce type de modèle, indiquant plutôt la nécessité d’améliorer les modèles murins existants. La mise au point de modèles in vivo apparaît en effet primordiale pour mieux disséquer les mécanismes moléculaires de la métastase et permettre le test de drogues susceptibles d’inhiber ce processus. / Ewing sarcoma is a very aggressive pediatric bone tumor generally caused by a chromosomal translocation that leads to the expression of the EWSR1-FLI1 fusion protein. This protein deregulates the expression of a number of genes involved in Ewing sarcoma oncogenesis. In the laboratory, we discovered an intra-tumor heterogeneity of EWSR1-FLI1 expression which lead us to propose a new model for Ewing sarcoma biology based on the coexistence of EWSR1-FLI1high cells, responsible for primary tumor growth, and EWSR1-FLI1low cells, with metastatic dissemination capacities. During my phD, I was especially interested in the molecular mechanisms underlying the migration and invasion capacities of EWSR1-FLI1low cells. We showed a decreased expression of intercellular junctions proteins associated with an increased expression of cell-matrix interaction proteins in EWSR1-FLI1low cells. We then revealed the key role of MMPs in Ewing sarcoma invasion, in particular of MMP2 and MT1-MMP, which are both repressed by EWSR1-FLI1 and were found necessary for invasion of EWSR1-FLI1low cells. One of the current major challenges is to visualize this very small sub-population and to track the plasticity of expression of EWSR1-FLI1. To this end, the identification of markers of EWSR1-FLI1low cell is crucial. This is also important in order to determine if current chemotherapies that primarily target highly proliferative cells do not increase the proportion of these EWSR1-FLI1low cells. Finally, our unsuccessful attempts to use the chick embryo as a new in vivo model of Ewing sarcoma metastasis indicate the need to improve the existing murine models. Indeed, the development of in vivo models appears essential for the dissection of the molecular mechanisms of Ewing sarcoma metastasis and the test of drugs susceptible to inhibit this process.

RNA-bindende Proteine spielen eine zentrale Rolle in der posttranskriptionellen Kontrolle von mRNAs, die zwischen Transkription und Abbau von mRNAs stattfindet. RNA-bindende Proteine beeinflussen Spleißen, Export, Stabilität, Lokalisierung und Translation von mRNAs. FUS, EWSR1 und TAF15 gehören zu der Familie der FET Proteine. Diese wirken an verschiedenen zellulären Prozessen wie Transkription, Spleißen und der Prozessierung von miRNAs mit. Translokationen und Mutationen der FET Proteine führen zu verschiedenen Krankheiten. FUS spielt eine Rolle bei den neurodegenerativen Krankheiten frontotemporale Lobärdegeneration (FTLD) und amyotrophe Lateralsklerose (ALS). In dieser Arbeit wurde die mithilfe von photoaktivierbaren Ribonukleotiden UV-Licht induzierte Quervernetzung und Immunpräzipitation (PAR-CLIP) Methode genutzt, um die RNA-Bindestellen von FUS, EWSR1 und TAF15, einer ALS-verursachenden FUS Mutante und einem anderen, mit ALS in Verbindung stehenden Protein, TARDBP, zu bestimmen. Die RNA-Bindestellen der FET-Proteine lagen größtenteils in Introns. Passend dazu konnte durch knockdown der FET Proteine eine Rolle von FUS und EWSR1 im Spleißen von mRNAs validiert werden. Dem Ubiquitin-Proteasom-System zugehörige RNAs waren unter den sowohl von FUS als auch TARDBP gebundenen mRNAs überrepräsentiert. Dies bestätigt die Annahme, dass Störungen in der Proteindegradation die ALS-Pathogenese beeinflussen. Zusätzlich konnte gezeigt werden, dass FUS und TAF15 bevorzugt UAC-reiche, einzelsträngige RNA-Sequenzen binden. Sequenzierung von mRNAs nach Depletion von FUS, EWSR1 und TAF15 in HEK293-Zellen zeigte einen stabilisierenden Effekt der FET-Proteine auf gebundene mRNAs. Desweiteren scheinen die FET Proteine durch Interaktion mit Promotor-assoziierten, nicht-kodierenden RNAs die Transkription zu beeinflussen. / Post-transcriptional regulation of gene expression takes place at multiple levels between transcription and decay of the mRNA. RNA-binding proteins play a key role in orchestrating splicing, export, stability, localization and translation of mRNAs. FUS, EWSR1 and TAF15 constitute the FET protein family which participates in multiple levels of cellular function. FET proteins have been implicated to function in various cellular processes including transcription, pre-mRNA splicing and miRNA processing. Translocations and mutations in FET proteins lead to diverse pathologies. FUS is involved in neurodegenerative diseases like frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). In this study, Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) was used to determine RNA-targets and binding sites of FUS, EWSR1 and TAF15, an ALS-causing FUS mutant and another ALS-related protein, TARDBP. The identified binding sites of FET proteins were mainly intronic, supporting the involvement of FUS and EWSR1 in splicing, which was validated by FET protein knockdown. Comparison of FUS and TARDBP RNA targets revealed that ubiquitin-proteasome related gene categories were overrepresented, further illustrating that aberrations in protein degradation are implicated in the pathogenesis of ALS. In addition, it was shown that FUS and TAF15 proteins preferentially bind UAC rich, single-stranded RNA sequences. mRNA sequencing after FUS, EWSR1 and TAF15 depletion in HEK293 cells revealed a stabilizing effect on their targets. Interestingly, FET proteins also seem to influence transcription by interaction with promoter-associated noncoding RNAs. In summary, we identified the RNA-targets and binding sites of all human FET proteins in comparison with an ALS-causing FUS mutant and TARDBP. Functional studies revealed an involvement of FET proteins in mRNA stabilization, splicing and transcriptional regulation.

Thesis deals with relationship between histomorphological and molecular-genetic findings of selected salivary gland tumors. Author, as a molecular-cytogeneticist mainly focused on detection of tumor-specific translocations of the salivary gland tumors which can serve as differential diagnostic markers. The thesis is composed as a commented files of authors own publications, and it is divided into four parts. First part deepens the knowledge of salivary adenoid cystic carcinoma. It was proved, that t(6;9)(q22-23;p23-24) resulting in fusion of transcription factors MYB-NFIB, or more rarely t(8;9) resulting in MYBL1-NFIB fusion represent robust differential diagnostic marker of adenoid cystic carcinoma. Further it was proved, that the 1p36 deletion can serve as an unfavorable prognostic indicator of adenoid cystic carcinoma, as the patients with 1p36 deletion had significantly lower survival. Second part summarizes new developments about mammary analogue secretory carcinoma (MASC), which was described by our group as a new salivary tumor entity characterized by translocation t(12;15)(p13;q25) resulting in ETV6-NTRK3 fusion. Another novel observation is a discovery of ETV6-RET fusion in a subset of MASC cases. Further, the first two MASCs of nasal mucosa origin have been described. Third part consists...

Thesis deals with relationship between histomorphological and molecular-genetic findings of selected salivary gland tumors. Author, as a molecular-cytogeneticist mainly focused on detection of tumor-specific translocations of the salivary gland tumors which can serve as differential diagnostic markers. The thesis is composed as a commented files of authors own publications, and it is divided into four parts. First part deepens the knowledge of salivary adenoid cystic carcinoma. It was proved, that t(6;9)(q22-23;p23-24) resulting in fusion of transcription factors MYB-NFIB, or more rarely t(8;9) resulting in MYBL1-NFIB fusion represent robust differential diagnostic marker of adenoid cystic carcinoma. Further it was proved, that the 1p36 deletion can serve as an unfavorable prognostic indicator of adenoid cystic carcinoma, as the patients with 1p36 deletion had significantly lower survival. Second part summarizes new developments about mammary analogue secretory carcinoma (MASC), which was described by our group as a new salivary tumor entity characterized by translocation t(12;15)(p13;q25) resulting in ETV6-NTRK3 fusion. Another novel observation is a discovery of ETV6-RET fusion in a subset of MASC cases. Further, the first two MASCs of nasal mucosa origin have been described. Third part consists...