La récidive et la progression métastatique du cancer du sein ne sont toujours pas curables. Le concept des cellules souches cancéreuses (CSC) pourrait apporter une explication à ces échecs. Les CSC résisteraient aux thérapies conventionnelles (chimiothérapies, radiothérapie) et seraient responsables de la rechute et de la progression du cancer. L'élimination des CSC semble être un pré-requis indispensable pour le traitement des patientes. L'identité et le destin des cellules souches sont finement régulés par des acteurs épigénétiques. Les travaux de cette thèse se sont intéressés aux conséquences de la dérégulation de deux acteurs épigénétiques en particulier : les enzymes HDAC et le long ARN non-codant Xist. Nous avons montré que la modulation épigénétique via l'inhibition des HDAC (HDACi) permet d'éliminer les CSC en induisant leur différenciation. Nous présentons une nouvelle stratégie thérapeutique pour le cancer du sein : la thérapie différenciante. Nous avons déterminé Xist comme étant le biomarqueur prédictif de la réponse aux HDACi. Xist étant un partenaire clé de la plasticité cellulaire, les travaux de cette thèse se sont ensuite intéressés aux conséquences de la dérégulation de Xist dans l'initiation tumorale. Nous avons observé que l'inhibition de Xist favorise la division des cellules souches mammaires normales. Nous proposons un nouveau modèle de l'initiation tumorale où la dérégulation épigénétique est une modification précoce sans conséquence sur l'homéostasie tissulaire mais pourrait être la première étape de la transformation cancéreuse. / These last decades have allowed deciphering the biology of breast cancer and improving the therapeutic management. However, recurrence and metastatic progression of the disease are still not curable. The concept of cancer stem cells (CSC) could provide an explanation for these failures. CSC would resist conventional therapies (chemotherapy, radiotherapy) and would be responsible for both relapse and progression of cancer. The elimination of CSC seems to be an essential prerequisite for the treatment of patients. The identity and fate of stem cells are tightly regulated by epigenetic mechanisms. The work of this thesis investigated the consequences of deregulation of two epigenetic players: HDAC enzymes and long non-coding RNA Xist. We have shown that epigenetic modulation via HDAC inhibitor (HDACi) eliminates the CSC by inducing their differentiation. We present a new therapeutic strategy for breast cancer: differentiation therapy. We determined Xist as the predictive biomarker of response to HDACi. Xist is a key partner of cell plasticity, the work of this thesis therefore interested in the consequences of Xist deregulation in tumor initiation. We observed that Xist inhibition promotes division of normal breast stem cells. We propose a new model of tumor initiation: epigenetic deregulation is an early change without consequence on tissue homeostasis but could be the first step of the cancerous transformation.

L’inactivation d’un des deux chromosomes X dans les cellules d’organismes femelles permet d’assurer un taux similaire des transcrits des gènes liés aux chromosomes X entre les deux sexes. L’ARN non codant Xist d’environ 17000 nts joue un rôle central dans ce processus. Il habille le futur chromosome X inactivé et induit la mise en place de modifications épigénétiques qui permettent d’éteindre l’expression des gènes. Une région d’approximativement 500 nts située à l’extrémité 5’ de l’ARN Xist est nécessaire à l’initiation de l’inactivation. Cette région appelée region des A-repeats contient 8 répétitions d’une séquence de 24 nucléotides. La délétion de cette région provoque un défaut d’inactivation, ce qui souligne son importance dans le processus. Etant donné que la fonction d’un ARN est bien souvent conditionnée par sa structure 2D, mon travail de thèse a consisté à réaliser l’étude expérimentale de la structure 2D de la région des A-repeats, ceci en utilisant des sondes de la structure secondaire des ARN en solution et une méthode de FRET. Nous avons montré que la région des A-repeats se structure selon 2 grandes structures tige-boucle irrégulières formées par l’appariement 2 à 2 des éléments répétés. Par purification des RNP et identification de leurs protéines, nous avons démontré que le complexe PRC2, impliqué dans la mise en place des marques épigénétiques du Xi, se lie à la région des A-repeats. Nous avons également identifié un grand nombre d’autres protéines pouvant avoir un rôle dans l’activité de la région des A-repeats (PTB, KSRP, Sam68, Vigiline, RHA, TIAR, DEK, H1, BRML1, Rod1, Lin28). Leurs implications dans l’inactivation du chromosome X est en cours de vérification. / Silencing of one X chromosome (XCI) in cells of mammalian female ensures sex chromosome dosage compensation between male and female. The 17kb Xist ncRNA plays an essential role in XCI. Its spread along the future inactivated X chromosome is associated with major modifications of the epigenetic status of this chromosome, including histone H3K27 methylations mediated by PRC2 complex. One key part of Xist necessary for XCI initiation is the phylogenetically conserved A region. It lies at the 5’ end of the Xist molecule and contains 8 of a 24-nucleotides motif. Female mouse embryos carrying a mutated Xist deleted for the A region are selectively lost during embryogenesis, which underlines the importance of this element. We performed the first experimental analysis of the structure of the entire A region in solution. By the use of chemical and enzymatic probes and FRET experiments, using oligonucleotides carrying fluorescent dyes, we established a 2D structure for the A region that contains two long stem-loop structures each including 4 repeats which interact together two by two. By immunoprecipitation assays and mass spectrometry analysis, we identified the protein partners of the A region. We demonstrated that the A region associate with PRC2 components which is responsible for the apposition of epigenetic modifications of X inactive chromosome. Others proteins which would have a role in A region function were also identified (PTB, KSRP, Sam68, Vigiline, RHA, TIAR, DEK, H1, BRML1, Rod1, Lin28).

L'inactivation du chromosome X correspond au silence transcriptionnel de l'un des deux chromosomes X dans les cellules des mammifères femelles. Il s'agit d'un mécanisme de compensation du dosage du chromosome X qui assure un taux d'expression des gènes liés aux chromosomes X équivalent entre organismes mâles (XY) et femelles (XX). Elle débute par une accumulation de l'ARN Xist (X inactive specific transcript) sur le chromosome X qui sera inactivé (Xi). Elle est suivie très rapidement par des modifications des histones qui assurent l'établissement, le maintien et la transmission de l'état transcriptionnel inactif de la chromatine. L'ARN Xist comprend plusieurs régions d'éléments répétés et notamment la région des A-repeats, essentielle pour la mise en place de l'inactivation. Mes recherches se sont portées sur l'étude de cette région singulière : sa structure et ses interactions protéiques. La technique de FRET (Fluorescence Resonance Energy Transfer) appliquée à l'ARN nous a permis de confirmer la structure de cette région parmi 3 modèles possibles. Elle se structure en deux tiges-boucles formée par l'appariement 2 à 2 de 4 répétitions successives. Dans une seconde partie, j'ai caractérisé l'interaction de cette région avec certains de ses partenaires protéiques in vitro. La région des A-repeats interagit notamment de manière directe avec les protéines PTB, KSRP et ASF/SF2. Les 2 premières protéines pourraient avoir un rôle dans la stabilité de l'ARN tandis qu'ASF/SF2 serait impliquée dans la maturation de l'ARN X / X-chromosome inactivation is the transcriptional silencing of one of the two X chromosomes in female mammal cells. This mechanism of dosage compensation ensures an equal level of the X-linked genes expression between males (XY) and females (XX). It initiates with the accumulation of the Xist RNA (X inactive specific transcript) on the futur inactive X chromosome (Xi). It is followed by the apposition of epigenetic marks such as histone modifications, that ensure establishment, maintenance and transmission of the inactive state of the chromatin. Xist RNA comprises a number of repeated regions and, in particular to its 5' end the A region, absolutely necessary for the establishment of the X-inactivation. My research was focused on the study of this singular region: its structure and its protein interactions. The FRET method (Fluorescence Resonance Energy Transfer) applied to RNA allowed us to ascertain that the RNA is structured in two long stem-loop structures each including four repeats. In a second part, I characterized the in vitro interaction of this region with some of its protein partners. The A region interacts directly with PTB, KSRP and ASF/SF2 proteins. The first two proteins may have a role in RNA stability whereas ASF/SF2 could be involved in the splicing process

Maintenance of gene dosage is important for proper cellular function and development, as evidenced by the natural silencing of one X-chromosome in mammalian females, and by the embryonic lethality of most autosomal aneuploidy. A notable exception is Down syndrome (DS), which occurs in 1/700 newborns. It has been known for 50+ years that DS is caused by trisomy for chromosome 21 (chr21), yet biological understanding remains wanting; even what cell types and pathways are impacted by chr21 dosage has remained unclear. Given the complexity of DS, better experimental approaches have been needed. This thesis advances understanding of DS pathobiology using an innovative approach that translates the X-inactivation mechanism via the XIST gene, to an inducible system to “silence trisomy” in DS patient-derived iPSCs and their differentiated derivatives. I investigated the most immediate and direct effects of silencing trisomy on mRNAs genome-wide. Initial studies revealed trisomy 21 (T21) impairs early developmental pathways for two major cell type processes: neurogenesis and, surprisingly, angiogenesis. Further analysis of endothelial cells showed chr21 overexpression reduces pathways relating to cell migration, projection, and signaling, and functional assays showed delayed response to angiogenic cues causing a deficit in microvessel formation. The previously unknown cell-autonomous effect of T21 on angiogenesis has broad significance for systems impacted, including brain and heart development, and comorbidities throughout life such as early-onset Alzheimer’s disease. This work also has implications for understanding of dosage sensitivity and genome balance, a fundamental but poorly understood aspect of genome biology.

Due to their underlying genetic complexity, chromosomal disorders such as Down syndrome (DS), which is caused by trisomy 21, have long been understudied and continue to lack effective treatments. With over 200 genes on the extra chromosome, even the specific cell pathologies and pathways impacted in DS are not known, and it has not been considered a viable target for the burgeoning field of gene therapy. Recently, our lab demonstrated that the natural mechanism of dosage compensation can be harnessed to silence the trisomic chromosome in pluripotent cells. Using an inducible XIST transgene allows us to study the effects of trisomy in a tightly controlled system by comparing the same cells with either two or three active copies of chromosome 21. In addition, it raises the prospect that insertion of a single gene into a trisomic chromosome could potentially be developed in the future for “chromosome therapy”. This thesis aims to utilize this inducible system for dosage compensation to study the neurodevelopmental effects of trisomy 21 in vitro, and to answer basic epigenetic questions critical to the viability of chromosome silencing as a therapeutic approach. Foremost, for XIST to have any prospect as a therapeutic, and to strengthen its experimental utility, it must be able to initiate chromosome silencing beyond its natural context of pluripotency. Here I demonstrate that, contrary to the current literature, XIST is capable of initiating chromosome silencing in differentiated cells and producing fully dosage compensated DS neurons. Additionally, I show that silencing of the trisomic chromosome in neural stem cells enhances their terminal differentiation to neurons, and transcriptome analysis provides evidence of a specific pathway involved. Separate experiments utilize novel three-dimensional organoid technology and transcriptome analysis to model DS neurodevelopment in relation to isogenic euploid cells. Overall, this work demonstrates that dosage compensation provides a powerful experimental tool to examine early DS neurodevelopment, and establishes that XIST function does not require pluripotency, thereby overcoming a perceived obstacle to the potential of XIST as a therapeutic strategy for trisomy.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

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Down Syndrome (DS), the most common aneuploidy seen in live-borns, is caused by trisomy for chromosome 21. DS imposes high risks for multiple health issues involving various systems of the body. The genetic complexity of trisomy 21 and natural variation between all individuals has impeded understanding of the specific cell pathologies and pathways involved. In addition, chromosomal disorders have been considered outside the hopeful progress in gene therapies for single-gene disorders. Here we test the feasibility of correcting imbalanced expression of genes across an extra chromosome by expression of a single gene, XIST, the key player in X chromosome inactivation. We targeted a large XIST transgene into one chromosome 21 in DS iPS cells, and demonstrated XIST RNA spreads and induces heterochromatin and gene silencing across that autosome in cis. By making XIST inducible, this allows direct comparison of effects of trisomy 21 expression on cell function and phenotypes. Importantly, XIST-induction during in vitro hematopoiesis normalized excess production of differentiated blood cell types (megakaryocytes and erythrocytes), known to confer high risk for myeloproliferative disorder and leukemia. In contrast, trisomy silencing enhances production of iPS and neural stem cells, consistent with DS clinical features. Further analysis revealed that trisomy 21 initially impacts the endothelial hematopoietic transition (EHT) to generate excess CD43+ progenitors, and also increases their colony forming potential. Furthermore, results provide evidence for a key role for enhanced IGF signaling, involving over-expression of non-chromosome 21 genes controlled by trisomy 21. Finally, experiments to examine trisomy effects on angiogenesis showed no effect on production of endothelial cells, but it remains unclear whether trisomic cells may differ in ability to form vessels. Collectively, this thesis demonstrates proof-of-principle for XIST-mediated “trisomy silencing”. Phenotypic improvement of hematopoietic and neural stem cells demonstrates the value for research into DS pathogenesis, but also provides a foundation of potential for future development of “chromosome therapy” for DS patients.

Ce travail est une édition critique et une traduction annotée en français d’un extrait du Mir’ât al-zamân fî tawârîh al-a‘yân (Miroir du temps dans les histoires des notabilités) de Sibt Ibn al-Gawzî (m. 654 / 1257). L’auteur était un célèbre sermonnaire originaire d’Iraq qui vécut la majeure partie de sa vie en Syrie à l'époque des Croisades. Son œuvre est une vaste histoire universelle qui allait de la Création à l’année de son décès. L’extrait édité porte sur les années 412 à 434/ 1021-1043, qui correspondent dans l’histoire de l’Iraq aux règnes de Musharrif al-Dawla et Galàl al-Dawla, deux émirs de la dynastie iranienne bouyide qui gouverna le pays entre 945 et 1055. Il comporte également de nombreuses informations sur d’autres régions du monde arabo-islamique de l‘époque : Ghazna, l’Egypte, la Syrie, l’Iran, et la Haute-Mésopotamie. Les textes de l‘édition et de la traduction sont en outre précédés d’une biographie actualisée de l’auteur et d’une étude sur les manuscrits du Mir’ât al-zamân en général : en effet, ceux-ci ne reproduisent pas la version originale de l’auteur, qui ne nous est pas parvenue, mais plusieurs abrégés distincts dont les auteurs sont encore, pour la plupart, non identifiés. L’édition s’appuie sur les deux principales versions abrégées existantes de cette œuvre, une courte, déjà éditée mais de manière incomplète et donc révisée ici, et une longue, à ce jour inédite. / This work is a critical edition and a French translation of a part extracted from the Mir’at al-zamân fi tawârikh al-a‘yan (Mirror of the time in the histories of notabilities) of Sibt Ibn al-Gawzi (d. 654/1257). The author was a famous preacher of Iraqi origin and lived the major part of his life in Syria during the Crusades' times. His work is a universal history going back to the Creation down to the author’s death. The edited part deals with the years 412 to 434 / 1021-1043, corresponding in the history of Iraq to the reigns of Musharrif al-Dawla and Galal al-Dawla, two emirs of the Buyid dynasty who rule the country between 945 and 1055. It also contains information about other parts of the Arabic and Islamic world of that time: Ghazna, Egypt, Syria, Iran, and Upper-Mesopotamia. The edition and the French translation are preceded by an up to date biography of the author and a wide study about the Mir’at al-zamân’s manuscripts. The original version of Sibt Ibn al-Gawzi’s work indeed didn’t come down to us and the manuscripts only usually reproduce different abridged versions whose authors are still mostly unknown to us. Our edition provides for this part of the work the two extent abridged versions, one short which has already been edited but in an incomplete way and had to be revised, and one long which is here edited for the first time.

XIST RNA established the precedent for a noncoding RNA that stably associates with and regulates chromatin, however it remains poorly understood how such RNAs structurally associate with the interphase chromosome territory. I demonstrate that transgenic XIST RNA localizes in cis to an autosome as it does to the inactive X chromosome, hence the RNA recognizes a structure common to all chromosomes. I reassess the prevalent thinking in the field that a single protein, Scaffold Attachment Factor-A (SAF-A/hnRNP U), provides a single molecule bridge required to directly tether the RNA to DNA. In an extensive series of experiments in multiple cell types, I examine the effects of SAF-A depletion or different SAF-A mutations on XIST RNA localization, and I force XIST RNA retention at mitosis to examine the effect on SAF-A. I find that SAF-A is not required to localize XIST RNA but is one of multiple proteins involved, some of which frequently become lost or compromised in cancer. I additionally examine SAF-A’s potential role localizing repeat-rich CoT-1 RNA, a class of abundant RNAs that we show tightly and stably localize to euchromatic interphase chromosome territories, but release upon disruption of the nuclear scaffold. Overall, findings suggest that instead of “tethering” chromosomal RNAs to the scaffold, SAF-A is one component of a multi-component matrix/scaffold supporting interphase nuclear architecture. Results indicate that Cot-1 and XIST RNAs form integral components of this scaffold and are required to maintain the chromosomal association of SAF-A, substantially advancing understanding of how chromatin-associated RNAs contribute to nuclear structure.