Les oestrogènes peuvent favoriser la croissance, la promotion et la progression des cancers hormono-dépendants tels que le cancer du sein, de la prostate et des ovaires. Certains métabolites secondaires de plantes constituent une source importante de phyto-œstrogènes, capables de réduire le risque du cancer en antagonisant les fonctions des hormones. La férutinine (FRT), est une phyto-œstrogène biologiquement active extraite des racines de Ferula hermonis, espèce endémique du Liban. Plusieurs études ont été menées sur l'activité œstrogénique et anticancéreuse de la FRT, cependant son activité cytotoxique sur les lignées de cancer œstrogéno-dépendantes n'a pas été élucidée. La FRT est connue pour son effet agoniste vis-à-vis des récepteurs aux œstrogènes a (REa) et agoniste/antagoniste vis-à-vis des REß. Dans un premier temps, la production de la FRT a été optimisée par une hémisynthèse à partir de l'hydrolyse basique de l'extrait brut. Son activité anticancéreuse sur des lignées du sein MCF-7 (REa+, REß+) et MDA-MB-231(REa-, REß-), de la prostate PC-3 (REa+,REß+), DU 145 (REa-, REß+) et 22Rv1 (REa-, REß-) et des ovaires OVCAR-3 (REa+, REß+), SKOV-3 (REa muté, REß+) et IGROV-1 (REa-, REß-) a été testée. Un effet biphasique a été observé sur la prolifération des cellules du carcinome mammaire MCF-7, où son activité proliférative a été corrélée avec la stimulation des REs. La FRT est capable à des concentrations élevées d'inhiber la prolifération des lignées cellulaires cancéreuses et d'induire un arrêt du cycle cellulaire au niveau de la phase pré G0/G1 agissant ainsi via un mécanisme pro-apoptotique. L'efficacité de la férutinine réside dans son pouvoir à cibler spécifiquement les cellules souches/progénitrices cancéreuses chez les lignées cellulaires étudiées qui sont à la base de la réémission tumorale. Cependant, son activité antiproliférative est considérée moyenne puisqu'elle ne peut pas déclencher à des faibles concentrations une activité pure antagoniste des œstrogènes. Les travaux de thèse se sont ensuite focalisés sur la synthèse de composés analogues de la FRT en conservant sa structure indispensable à son activité. Nous avons élaboré un filtre in silico de chimiothèques d'antagonistes potentiels des REs. Ce nouvel outil d'arrimage moléculaire a guidé la synthèse des analogues de la FRT en améliorant leur fixation en position antagoniste dans le site de liaison des REs. L'arrimage moléculaire de la férutinine dans le site actif des REs a confirmé structuralement sa double compétence œstrogénique (agoniste/antagoniste) observée in vitro. Une douzaine d'analogues de la FRT a été synthétisée et testée pour son pouvoir antiprolifératif sur les lignées cancéreuses considérées. Des résultats prometteurs ont été obtenus notamment pour trois analogues sur les lignées cancéreuses mammaires (3c' et 2c'), prostatiques (2c') et ovariennes (3b). Ces composés ont montré une sélectivité vis-à-vis des lignés cancéreuses. Ces analogues constitueront alors des candidats pour une éventuelle plateforme de développement d'agents anticancéreux. / Estrogens are key regulators of cell growth in hormone-dependent cancers such as breast, prostate and ovarian. Phyto-estrogens are a diverse group of plant-derived compounds, exhibiting potential benefits for chemoprevention by antagonizing the function of estrogens. Ferutinin (FRT) is the main active phyto-chemical extracted from the endemic plant of Lebanon, Ferula hermonis. Several studies were conducted on the estrogenic and anti-proliferative activities of FRT; nevertheless, its cytotoxic activity against estrogen-dependent cancers is not yet elucidated. FRT has been reported as agonist to estrogen receptor a (ERa) and agonist/antagonist to ERß. FRT production was first optimized by hemi-synthesis from basic hydrolysate of crude root extract. The anticancer properties of FRT was assessed against breast (MCF-7, MDA-MB-231), prostate (PC-3, DU 145, 22Rv1) and ovarian (OVCAR-3, SKOV-3, and IGROV-1) cancer cell lines. A biphasic effect was observed on the proliferation of mammary MCF-7 cell line, where the proliferative activity was correlated to ER stimulation. FRT inhibited the proliferation of all studied cell lines at high concentrations and induced a pre G0/G1 cell cycle arrest via a pro-apoptotic mechanism of action. FRT targeted the enriched population of cancer stem cells/progenitors which is responsible for tumor reemission. However, its antiproliferative activity is considered weak since it cannot trigger at low concentrations pure estrogen antagonistic activity. This project emphasizes next on the synthesis of FRT analogues by preserving its active structure. We have created an in silico filter of chemical compounds that might act as potential antagonists to ERs. This novel molecular docking tool was used to design FRT derivatives by enhancing their antagonist position inside the binding cavity of ERs. Docking results of FRT in the binding site of ERs confirmed structurally the dual potency that exerts this molecule (agonist/antagonist) in vitro. A list of FRT analogues were synthesized and tested for their anti-proliferative activity against the studied cell lines. Promising results were obtained with three ferutinin analogues on the proliferation of breast (3c' and 2c'), prostate (2c') and ovarian (3b) cancer cell lines. These compounds were also shown to be more selective to cancer cell lines. The cytotoxic properties of these analogues suggest that they could be promoted as potential candidates for useful anticancer therapy.

Glioblastoma multiforme is the most malignant primary brain tumor that affects adults, recognized by the World Health Organization as an aggressive grade IV astrocytoma. Patients diagnosed with this type of tumor are left with a poor prognosis even with the most advanced treatment available. The cancer is quite heterogeneous and is typically categorized into four different subtypes depending on genetic aberrations and patient characteristics. Furthermore, researchers have discovered a subpopulation of glioblastoma cells, known as cancer stem cells, which are thought to be resistant to current therapies and responsible for tumor reoccurrence and relapse. Previous studies, in addition to this one, have found that the differentiation of glioblastoma cells downregulate nestin protein expression, the selected stem cell marker, and upregulate glial fibrillary acid protein expression, the selected differentiation marker, using immunofluorescence. Thus, one alternative treatment option is to understand the mechanism underlying the differentiation of cancer stem cells. Four cell cultures representative of each glioblastoma subtype will be endogenously tagged using the genome editing system, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9). The representative stem cell marker, nestin, will be tagged with a green fluorescent protein, while the chosen differentiation marker, glial fibrillary acid protein, will be tagged with a red fluorescent protein. Several drugs were screened to analyze whether the drugs had a differentiation effect on the glioblastoma cells. As a result, strong evidence indicated that bone morphogenetic protein four upregulated glial fibrillary acid protein expression levels to the same extent as the differentiation control media using 5% fetal bovine serum. The goal of this study is to establish a method to directly monitor the differentiation process of glioblastoma cells as a novel molecular screening method. In this case, all glioblastoma cells, even the ones resistant to treatment, can be eliminated through an initial “pre-treatment” by forcing differentiation of cancer stem cells, making the cells more susceptible to the chemotherapy drugs. In the long run, glioblastoma patients would have a chance at a more positive prognosis; a longer life that is free of glioblastoma. / Master Thesis in Applied Biotechnology

La présence de métastases est un facteur de mauvais pronostic dans les cancers solides et une meilleure compréhension de la dissémination tumorale est nécessaire afin d'améliorer la prise en charge de ces formes avancées. Les cellules tumorales circulantes (CTC) représentent un intérêt majeur dans la pathologie tumorale, d'une part sur le plan clinique en tant que marqueur prédictif et pronostique et d'autre part sur le plan de la compréhension des mécanismes impliqués dans la formation des métastases. Les CTC sont rares et hétérogènes et restent mal caractérisées, et ce, particulièrement dans le cancer colorectal. Une partie de ces cellules aurait un phénotype de cellules initiatrices de tumeur (CIT) leur permettant de former des métastases, de résister aux traitements et par conséquent d'être responsables des rechutes. Une meilleure connaissance des CTC possédant un phénotype de CIT représente donc un enjeu majeur. L'objectif de ce travail a été d'identifier et de caractériser les CTC avec un potentiel de cellules initiatrices de tumeur dans le cancer colorectal en se basant sur les propriétés fonctionnelles des CIT. Nous avons ainsi, pour la première fois, pu établir deux modèles permettant de répondre à cet objectif. D'une part des lignées de CTC avec un fort potentiel de CIT obtenues à partir d'échantillons sanguins de patients atteints de cancer colorectal, et d'autre part, nous avons mis en place un modèle murin de dissémination tumorale par xénogreffe orthotopique permettant d'isoler les CTC. / Liver or lung metastases represent a poor prognosis in colorectal cancer patients and better understanding tumor spreading became essential to improve patient care. Circulating tumor cells (CTC) is considered as a promising tool, both as prognostic marker and as tool to study mechanisms involved in metastasis development. CTCs are rare and heterogeneous and remain poorly characterized especially in colorectal cancer. It is accepted that at least some of the CTC have a tumor initiating cell (TIC) phenotype that could be responsible for metastasis, chemoresistance and consequently lead to relapse. A deep characterization of CTC became thus an urgent unmet need. The aim of this work was to identify and characterize CTC with TIC properties in colorectal cancer, on the basis of their functional properties. To reach this aim, we established for the first time and characterized CTC lines from blood sample of colorectal cancer patient, and we also developed an orthotopic xenograft mouse model in which tumoral cells are circulating in the blood.

Transforming growth factor β (TGF-β) and bone morphogenetic protein (BMP) signaling pathways are involved in many physiological processes during embryonic and adult life. TGF-β promotes epithelial to mesenchymal transition (EMT). We identified a gene target of TGF-β signaling, encoding the salt-inducible kinase 1 (SIK1). A potential substrate of this kinase, the polarity protein Par3, is an established regulator of tight junction assembly. SIK1 associates with Par3, can potentially phosphorylate Par3 and leads to its degradation, contributing to tight junction disassembly. Glioblastoma multiforme (GBM) is a common malignancy in the central nervous system, characterized by high heterogeneity, invasiveness, and resistance to therapy. One of the causes of heterogeneity and therapy-resistance is the existence of glioblastoma stem cells (GSCs). TGF-β signaling promotes self-renewal while BMP signaling induces differentiation of GSCs. Snail is a potent inducer of the EMT in carcinomas. However, in the context of GBM, Snail induces BMP signaling and represses TGF-β signaling through interaction with SMADs, the signaling mediators of TGF-β and BMP. In conclusion, Snail differentially regulates the activity of the opposing BMP and TGF-β pathways, thus promoting an astrocytic fate switch and repressing stemness in GSCs. Although profound changes in cell polarity is a hallmark of invasive malignancies, little is known about the role of the polarity machinery in tumor suppression. Patient transcriptomic data suggested low Par3 expression, correlating with poor survival of the GBM patients. Par3 silencing decreased the GSC self-renewal capacity and enhanced their invasiveness. Transcriptomic analysis indicates that loss of Par3 leads to downregulation of genes encoding mitochondrial enzymes that generate ATP. These results support a novel role of Par3 in GBM, beyond its contribution to junctional contacts between cells. Another regulator of TGF-β and BMP signaling is the liver kinase B1 (LKB1). According to GBM patient mRNA analysis, high levels of LKB1 correlate with poor prognosis. Silencing of LKB1 in GSCs impairs invasion and self-renewal capacity due to downregulation of genes involved in these processes. Moreover, loss of LKB1 induces mitochondrial dysfunction, leading to decreased ATP levels. Collectively, this thesis has delivered a group of novel regulatory pathways that control critical aspects of cancer cell polarity, invasion and stemness.

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.

Les glioblastomes sont des tumeurs au pronostic défavorable. L’échec des thérapies est lié à la présence de cellules souches cancéreuses (CSCs), résistantes aux traitements ; la caractérisation de ces cellules et l’identification de biomarqueurs sont donc primordiales. Le calcium contrôle de nombreux processus cellulaires ; parmi les éléments majeurs de la signalisation calcique, la Calmoduline (CaM) est impliquée dans différentes pathologies, dont des cancers, et est un puissant régulateur de l’état physiologique d’une cellule. CaM interagit avec de nombreuses protéines impliquées dans la régulation de l’homéostasie calcique de la cellule. Nous avons cherché à identifier et caractériser des antagonistes de CaM, inhibant différentiellement ces interactions. L’utilisation de ces antagonistes en tant que perturbateurs de l’homéostasie calcique a permis de mettre en évidence un marqueur caractérisé des CSCs de glioblastomes. D’autre part, l’étude comparée du protéome membranaire de CSCs issues de glioblastomes a permis de mettre en évidence la surexpression de clusters de différenciation et protéines impliquées dans la signalisation calcique. Ces protéines sont de potentiels marqueurs moléculaires des CSCs de glioblastome. / Glioblastomas are malignant tumor of poor prognosis. Therapeutic failure might be supported by cancer stem cells (CSCs); characterization of these cells and biomarkers identification are of most importance. Calcium controls numerous cellular process; beyond major elements of calcium signaling, Calmodulin (CaM) is involved in different pathologies and tumors, and is a powerful regulator of cell physiological state. CaM interacts with a plethora of proteins involved in cell calcium homeostasis regulation. We aimed at identifying and characterizing CaM antagonists, capable of differentially inhibiting these interactions. The use of these antagonists in calcium homeostasis disturbance led to the identification of a characterized marker of glioblastomas CSCs. In another approach, the comparative study of glioblastomas CSCs membrane proteome uncovered the overexpression of differentiation clusters and proteins involved in calcium signaling. These proteins are potential molecular biomarkers for glioblastomes CSCs.

Bei verschiedenen Krebs-Typen kann die molekulare Behandlung der Krebs-Stammzellen ein effektives Ziel sein, die Therapie-Resistenz und die Metastasierung der Tumore zu hemmen. Basaler Brustkrebs enthält Zellen mit Stammzell-Eigenschaften; hingegen sind rationale Therapien gegen diese Zellen nur wenige etabliert. Ich zeige in meiner Doktorarbeit, dass Rezeptor-Tyrosinkinase-Met-Signalvermittlung die Aktivität der Hippo-Komponente YAP im basalem Brustkrebs verstärkt. Weitere Analysen zeigten erhöhte YAP-Aktivität in den Krebsstammzell-Populationen. Durch Verwendung genetischer und pharmakologischer Methoden konnte ich zeigen, dass die Interferenz mit YAP die Tumor-Bildung verzögert und die luminal-basale Transdifferenzierung verhindert sowie das Krebsstammzell-Überleben reduziert. Gen-Expressions-Analysen von YAP-Knockout-Brustdrüsen zeigten eine starke Reduzierung der Expression der β-Catenin-Zielgene, was indiziert, dass YAP für nukleare β-Catenin-Aktivität essentiell ist. Ich habe weiter gefunden, dass nukleares YAP mit β-Catenin und TEAD4 interagiert und an gemeinsamen regulatorischen Gene-Regionen überlappt. Die Analyse von proteomischen Daten von primären Brustkarzinomen des Menschen zeigte eine signifikante Hoch-Regulation der YAP-Signatur in basalem im Vergleich zu andern Brustkarzinom-Typen, was suggeriert, dass YAP-Aktivität auf den basalen Brustkrebs limitiert ist. Unsere Daten beleuchten die Wichtigkeit von YAP als essentiellen Tumor-Initiator und Krebs-Stammzell-Regulator beim basalen Brustkrebs und zeigt, dass dessen Aktivität als Prognose-Faktor wichtig ist, wenn man basalen mit luminalem Brustkrebs vergleicht. Dies suggeriert, dass Behandlung des YAP/TEAD4/β-Catenin-Komplexes mit neuen, spezifischen Pharmaka, die die Wissenschaftler in Akademie- und Industrie-Instituten im Moment entwickeln, eine potentielle therapeutische Richtung darstellen, um basalen Brustkrebs in der Zukunft zu behandeln. Dies ist der wichtigste Aspekt meiner Doktorarbeit. / In various cancer types, targeting cancer stem cells (CSCs) can serve as an effective approach for limiting therapy resistance and metastasis. While basal breast cancers encompass cells with CSC features, rational therapies remain poorly established. Here, I show that receptor tyrosine kinase (RTK) Met signalling promotes the activity of the Hippo component YAP in basal breast cancer. Further analysis revealed enhanced YAP activity within the CSC population. Utilising both genetic and pharmaceutical approaches, I show that interference of YAP activity delays tumour formation, prevents luminal to basal trans-differentiation and reduces CSC survival. Gene expression analysis of YAP knock-out mammary glands revealed a strong decrease in β-catenin target genes, suggesting that YAP is required for nuclear β-catenin activity. Mechanistically, I find that nuclear YAP interacts and overlaps with β-catenin and TEAD4 at common gene regulatory regions. Analysis of proteomic data from primary breast cancer patients identified significant upregulation of the YAP signature in basal compared to other breast cancers, suggesting that YAP activity is limited to basal breast cancers. Our data highlight the importance of YAP as a crucial tumour initiator and cancer stem cell regulator in basal breast cancer and demonstrates that its activity has prognostic value, when comparing basal with luminal breast cancers. This suggests that targeting the YAP/TEAD4/β-catenin complex through specific new drugs, which researchers in academia and industry are presently developing, is a potential therapeutic avenue for treating basal breast cancers in the future. This is the most important aspect of my thesis.

Therapy resistance of malignant cells represents the main reason responsible for the failure of cancer therapy. The growth of malignant cells at primary tumour sites but most importantly the dissemination of tumour cells and their growth at secondary sites, are the main reasons why patients eventually succumb to the disease. Even novel immune-based therapies find their limitation in most tumour types. The therapy resistance is mediated by the tumour cells but also by other cellular components of the tumour microenvironment. Understanding the tumour cells mechanisms and the tumour microenvironment features responsible for therapy resistance enables the development of novel therapeutic strategies. Here, we show that ionizing irradiation, 5-azacytidine, and IFNγ treatments induced expression of suprabasin (SBSN) and therapy-resistant low-adherent phenotype in cancer cells. Knockdown of SBSN resulted in suppression of the phenotype. Next, we identified aberrantly elevated SBSN in the bone marrow of a subgroup of myelodysplastic syndromes (MDS) patients. SBSN was expressed by myeloid-derived suppressor cells (MDSCs) and showed significant anti-correlation with T cell abundance and CCL2 levels, hence promises a prognostic value in clinical use. We compiled the most of the relevant knowledge of SBSN...

(EN) Analogously to normal stem cells within the tissues, cancer stem cells (CSCs) have been proposed to be responsible for maintenance and growth of tumours. CSCs represent a small fraction of cells within the tumour, which is characterised by self-renewal capacity and ability to give rise to a tumour when grafted into immunocompromised mice. Cells with increased stemness properties are believed to be responsible for tumour resistance, metastases formation and relapse after tumour treatment. The first part of this work concentrates on resistance of the tumours, which is often associated with increased expression of ATP-binding cassete (ABC) transporters pumping chemotherapeutics out of the cells. For the purposes of this study, we utilized an in vitro model of CSCs, based on cultivation of cells as 3D "spheres". Expression profiling demonstrates that our model of CSCs derived from breast and prostate cancer cell lines express higher mRNA level of ABC transporters, particularly ABCA1, ABCA3, ABCA5, ABCA12, ABCA13, ABCB7, ABCB9, ABCB10, ABCC1, ABCC2, ABCC3, ABCC5, ABCC8, ABCC10, ABCC11 and ABCG2 among the cell lines tested. The protein level of ABC transporters tested in breast CSCs showed higher expression of ABCB8, ABCC1, ABCC2, ABCC10 and ABCG2 but downregulation of ABCB10 and ABCF2 proteins....

L’infection chronique par Helicobacter pylori touche plus de la moitié de la population mondiale et est la principale cause connue de l’adénocarcinome gastrique. La metformine, un antidiabétique oral, est de plus en plus étudiée pour ses propriétés antitumorales dans de nombreux types de cancers. Cependant, ses effets potentiels ont très peu été étudiés dans le cancer gastrique. Des expériences réalisées sur des lignées cellulaires cancéreuses gastriques et des tumeurs de patients amplifiées par xénogreffe chez la souris (PDX), ont permis de confirmer les propriétés antitumorales de la metformine. La metformine, en traitement préventif et curatif, diminue la capacité de formation des tumorsphères, l’expression des marqueurs de CSC gastriques, et la capacité d’auto-renouvellement propre aux CSC. Dans un second temps, nous avons montré que la metformine est capable d’inhiber la croissance bactérienne de H. pylori invitro et in vivo. Enfin, les effets de l’infection par H. pylori ont été étudiés sur la voie de signalisation mTOR par la réalisation d’une analyse transcriptomique et de western-blots sur des lignées cellulaires gastriques. Ceci a permis de démontrer que H. pylori inhibe le complexe mTORC1.Pour conclure, ce travail de thèse a permis i) de démontrer la capacité de la metformine à cibler les CSC gastriques, ii) de découvrir une nouvelle propriété antibactérienne de la metformine vis-à-vis de H. pylori, iii) de démontrer que H. pylori inhibe la voie de signalisation mTOR. / Chronic infection with Helicobacter pylori affects more than half of the world's population and is the main known cause of gastric adenocarcinoma. Metformin is an oral antidiabetic drug used to treat type 2 diabetes patients, and is being increasingly studied for its antitumoral properties in several cancer types. However, its potential effects in gastric cancer have not been thoroughly studied. Experiments performed on gastric cancer cell lines and patient-derived gastric carcinoma xenografts (PDX), have confirmed the antitumoral properties of metformin. Metformin, in preventive and curative treatment, decreases the tumorsphere formation, the expression of gastric CSC markers and the self-renewal capacity of CSC. In a second time, we have shown that metformin is able to inhibit the bacterial growth of H. pylori in vitro and in vivo. Finally, the effects of the H. pylori infection have been studied on the mTOR signaling pathway using a transcriptomic analysis and western blots, performed on gastric cancer cell lines. These show the ability of H. pylori to inhibit mTORC1.To conclude, this thesis work allowed i) to demonstrate the ability of metformin to target gastric CSCs, ii) to discover a new antimicrobial property of metformin against H. pylori, iii) to demonstrate that H. pylori inhibits the mTOR signaling pathway.