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Cell phenotypic transitions, or cell fate decision making processes, are regulated by complex regulatory networks composed of genes, RNAs, proteins and metabolites. The regulation can take place at the epigenetic, transcriptional, translational, and post-translational levels to name a few. Epigenetic histone modification plays an important role in cell phenotype maintenance and transitions. However, the underlying mechanism relating dynamical histone modifications to stable epigenetic cell memory remains elusive. Incorporating key pieces of molecular level experimental information, we built a statistical mechanics model for the inheritance of epigenetic histone modifications. The model reveals that enzyme selectivity of different histone substrates and cooperativity between neighboring nucleosomes are essential to generate bistability of the epigenetic memory. We then applied the epigenetic modeling framework to the differentiation process of olfactory sensory neurons (OSNs), where the observed 'one-neuron-one-allele' phenomenon has remained as a long-standing puzzle. Our model successfully explains this singular behavior in terms of epigenetic competition and enhancer cooperativity during the differentiation process. Epigenetic level events and transcriptional level events cooperate synergistically in the OSN differentiation process. The model also makes a list of testable experimental predictions. In general, the epigenetic modeling framework can be used to study phenotypic transitions when histone modification is a major regulatory element in the system. Post-transcriptional level regulation plays important roles in cell phenotype maintenance. Our integrated experimental and computational studies revealed such a motif regulating the differentiation of definitive endoderm. We identified two RNA binding proteins, hnRNPA1 and KSRP, which repress each other through microRNAs miR-375 and miR-135a. The motif can generate switch behavior and serve as a noise filter in the stem cell differentiation process. Manipulating the motif could enhance the differentiation efficiency toward a specific lineage one desires. Last we performed mathematical modeling on an epithelial-to-mesenchymal transition (EMT) process, which could be used by tumor cells for their migration. Our model predicts that the IL-6 induced EMT is a stepwise process with multiple intermediate states. In summary, our theoretical and computational analyses about cell phenotypic transitions provide novel insights on the underlying mechanism of cell fate decision. The modeling studies revealed general physical principles underlying complex regulatory networks. / Ph. D.

L’invasion cellulaire est un phénomène clé du développement tumoral au cours duquel les cellules réalisent une transition épithélio-mésenchymateuse (TEM) caractérisée par des changements d’expression de gènes clés dans la régulation de l’adhérence et de la morphologie cellulaire. L’expression de ces gènes est sous le contrôle de voies de signalisation, qui lors du processus de tumorigenèse sont dérégulées. La dérégulation de ces voies est multifactorielle et peut-être initiée par une activation de récepteurs présents à la membrane plasmique.Dans ce contexte, nous avons mis en évidence que les flotillines sont d’importants régulateurs de l’activation de ces récepteurs et des voies de signalisation en aval qui conduisent à l’induction de la TEM. Les flotillines 1 et 2 sont des protéines ubiquitaires très conservées. Le niveau d’expression des flotillines est accru dans de nombreux cancers invasifs et ceci est un facteur de mauvais pronostic. En condition physiologique, non surexprimées, les flotillines sont majoritairement à la membrane plasmique. Surexprimées les flotillines induisent la formation d’endolysosomes ayant une faible activité de dégradation, dans lesquels elles sont retrouvées.Mes travaux montrent que l’augmentation de l’expression des flotillines dans des cellules normales mammaires est suffisante pour induire le processus de TEM, processus clé de l’invasion tumorale. De plus nous montrons que la surexpression des flotillines génère une voie de trafic vésiculaire que nous nommons UFIT (Upregulated flotillin Induced Trafficking pathway) et qui affecte le trafic de plusieurs récepteurs membranaires connus pour participer à l’activation des voies oncogéniques inductrices de la TEM. Dans le cas particulier d’un de ces récepteurs, AXL, cible thérapeutique dans les cancers du sein, nous montrons que la surexpression des flotillines régule son endocytose et l’adresse dans les endosomes de signalisation riches en flotillines tout en le protégeant de la dégradation. Ces travaux apportent donc des explications nouvelles quant au rôle des flotillines dans le processus d’invasion cellulaire conduisant à la formation des métastases. / Tumor cell invasion and consecutive metastasis formation are the main cause of death in cancer patients. One crucial process of tumor cell invasion is the epithelial to mesenchymal transition (EMT), a reversible process during which polarized epithelial cells convert into motile mesenchymal cells. This process is characterized by gene expression changes involved, in particular, in the perturbation of cell adhesion, polarity and cytoskeletal structures.Flotillin 1 and 2 are two ubiquitous and highly conserved membrane proteins that assemble in large oligomers, known to participate in membrane protein clustering and endocytosis. Flotillins are upregulated in many invasive cancers and are considered as markers of poor prognosis. At physiological expression level, flotillins are mainly located at the plasma membrane. The cellular distribution of upregulated flotillins is dramatically modified with a strong enrichment in vesicular compartments that we characterized as non-degradative-endolysosomes.During my PhD project, we identified that flotillins are key EMT inducer. We upregulated flotillins in normal mammary cells and demonstrated that it is sufficient to promote EMT. Using several global comparative analyses (transcriptomic, phosphokinase arrays), we showed that flotillin upregulation activates key oncogenic signaling pathways and plasma membrane receptors. We identified that flotillin overexpression induces a trafficking pathway that we named UFIT-pathway (Upregulated flotillin Induced Trafficking pathway), which promotes the endocytosis of several cargos, amongst them membrane receptors involved in the activation of oncogenic pathways.Our results suggest that the UFIT pathway generates flotillin-positive endolysosomes acting as as “signalosome compartments” involved in the activation of signaling pathways stimulating EMT and cellular invasion.

Squamous cell carcinoma of the head and neck (HNSCC) is an extremely common and devastating disease with a bleak prognosis. Despite intensive research, survival rates have not improved over the past 30 years principally due to untreatable recurrent/metastasising disease. Feline oral squamous cell carcinoma (FOSCC) is an equally common disease in cats with an even less favourable prognosis than humans. Human and feline squamous cell carcinomas share similar etiopathogenesis, molecular markers, tumour biology and treatment thus making FOSCC an excellent model for HNSCC. Epithelial to mesenchymal transition (EMT), under the direction microRNAs (miRNAs/mirs) could be a key driver in oncogenic transformation and chemoresistance. The aim of this study was to induce resistance to characterise the EMT/resistance phenotype and to investigate whether common miRNA-mediated pathways are present in HNSCC and FOSCC that drive this phenomenon. We used epidermal growth factor (EGFR)-inhibitor gefitinib to induce resistance in HNSCC and FOSCC and investigated the associated EMT-related molecular changes. In vitro and in vivo invasive and migratory properties of both species were explored to determine whether resistance and/or EMT status conferred a functional advantage. We determined the miRNA expression pattern during acquisition of resistance to gefitinib in both species by next generation sequencing and screened candidate miRNAs as potential therapeutics. We found that gefitinib-resistance produced a previously unrecognised biphasic response that consisted of two distinct phenotypes, a highly invasive mesenchymal phenotype during early resistance, and a more epithelial phenotype associated with established resistance. The biphasic nature of this transition may prove critical in establishing effective therapeutic targets and the timing of treatment to overcome resistance or in preventing local invasion or metastatic spread of squamous cell carcinoma. We found that the major anti-apoptotic PI3K/AKT pathway was activated in transitioning and resistant cells of both species as demonstrated upregulation of AKT, pAKT and c-FLIP together with inactivation of PTEN by phosphorylation. This indicates that avoidance of apoptosis may be a major pathway in resistance that could be targeted therapeutically. We showed that three miRNAs were differentially expressed in both gefitinib-resistant human and feline cell lines: miR-107 was downregulated, and miR-551b and miR-574 were upregulated. These microRNAs provide potential therapeutic targets in the fight against drug resistance in head and neck cancer although much further research needs to be conducted to elucidate the complex network of interactions that may be affected by targeting these powerful regulatory molecules.

Epithelial to Mesenchymal Transition (EMT) is a dynamic process by which a distinct change in the phenotype and function of epithelial cells render them as mesenchymal cells. Characteristics of mesenchymal cells include the ability to invade, increased migratory kinetics and heightened resistance to apoptosis. Therefore, there is a strong need to fully understand the mechanism for the induction of EMT in pathological conditions such as carcinoma progression. Recent advances highlight two pivotal contributors, soluble growth factor (gf) signals, and mechanical signals, in the process. However, to date, no clear mechanism exists linking the two in epithelial transdifferentiation. Transforming Growth Factor-β1 (TGF-β1), a gf known to induce EMT in breast cancer formation, induces EMT on rigid surfaces and apoptosis on compliant surfaces. It is our belief that a combination of mechanical signals, gf signals, and the type of extracellular matrix (ECM) proteins assembled by cells together drive the process of EMT. Here we investigated the role of the ECM protein fibronectin (FN) in EMT. Upon assembly into elastic, insoluble fibrils through cell-generated forces which become larger on stiffer surfaces, FN is able to serve as a gf delivery system. We examined the following hypothesis: Increased tissue stiffness drives FN assembly, which exposes cryptic binding sites for various gfs, such as TGF-β1, and creates a high concentration of these gfs at the cell surface, which in turn drives EMT. In this project we investigated three aims: (1) evaluate the effect of inhibiting FN fibrillogenesis and gf localization on TGF-β1-induced EMT, (2) assess the effect of TGF-β1 concentration on spatial patterning of ECM dynamics, cell phenotype and adherens junctional force, and (3) probe the role of the FN matrix in TGF-β1-induced spatial patterning of EMT. Results showed that both inhibition of FN fibril assembly and blocking the gf binding site on fibrils significantly attenuated the downstream effects of EMT. In microcontact patterns of epithelial colonies, increasing gf concentration led to spatial patterning of FN fibrils, cell phenotype and cell-cell junctional force. Elimination of FN fibrils effectively attenuated TGF-β1-induced spatial patterning. The knowledge acquired through these studies serves as an addition to an increasingly important body of work aimed at elucidating how physical changes within the microenvironment regulate physiology and pathology. By establishing a novel mechanism by which gf signaling induces EMT through interaction with the extracellular matrix, this research serves to combat the development and initiation of pathological phenomena, such as metastasis.

Notch signaling plays a key role in development, tissue homeostasis, and cancer. High expression levels of Notch signaling components are associated with aggressive disease and poor patient prognosis in breast cancer. Mesenchymal‐epithelial transition factor (MET) is a receptor tyrosine kinase with an established prognostic significance correlating with poor disease outcome in breast cancer patients as a result of high metastatic rate. We performed expression array analysis to identify candidate Notch target genes; we identified and validated MET as a target of NOTCH1 signaling in breast cancer. We found that NOTCH1 knockdown significantly reduces MET promoter activity, as well as expression levels of MET transcript and protein. The mechanism of NOTCH1 regulation of MET expression will be the focus of future work. To further identify candidate target genes of NOTCH1 signaling, we generated and validated a NOTCH1 antibody for use in chromatin immunoprecipitation experiments.

Notch signaling plays a key role in development, tissue homeostasis, and cancer. High expression levels of Notch signaling components are associated with aggressive disease and poor patient prognosis in breast cancer. Mesenchymal‐epithelial transition factor (MET) is a receptor tyrosine kinase with an established prognostic significance correlating with poor disease outcome in breast cancer patients as a result of high metastatic rate. We performed expression array analysis to identify candidate Notch target genes; we identified and validated MET as a target of NOTCH1 signaling in breast cancer. We found that NOTCH1 knockdown significantly reduces MET promoter activity, as well as expression levels of MET transcript and protein. The mechanism of NOTCH1 regulation of MET expression will be the focus of future work. To further identify candidate target genes of NOTCH1 signaling, we generated and validated a NOTCH1 antibody for use in chromatin immunoprecipitation experiments.

El mal pronòstic en una neoplàsia epitelial està associada a l'adquisició de característiques mòbils o invasives per part de les cèl·lules canceroses. Aquesta transformació morfològica es denomina transició epiteli-mesènquima (TEM). Snail és un factor de transcripció implicat en aquest procés, responsable de reprimir l'expressió de l'E-cadherina. Aquest treball demostra que Snail té la capacitat de reprimir l'expressió de MUC1 i VDR a través de la seva unió directa a caixes de reconeixement situades en els diferents promotors proximals. A més, la sobreexpressió d'Snail en diverses línies cel·lulars provoca un augment dels nivells d'ARNm de ZEB1 i un increment de l'activitat del seu promotor. L'activitat del promotor mínim d'Snail i els seus nivells d'ARNm depenen de la senyalització d'ERK. Finalment, hem demostrat que Snail i WT1, un regulador positiu de l'expressió de l'E-cadherina, competeixen per unir-se al promotor de l'E-cadherina i regular la seva transcripció. / The poor prognosis in epithelial neoplasia is associated with the acquisition of motile or invasive properties by the cancerous cells. This morphological transformation is often referred to as epithelial to mesenchymal transition (EMT). The Snail transcription factor is involved in this process by repressing the expression of E-cadherin. In this study we demonstrate the capacity of Snail to repress both MUC1 and VDR transcription by direct binding to specific sequences within their proximal promoter. Moreover, Snail overexpression in several cell lines induces ZEB1 mRNA and increases its promoter activity. The activity of the Snail minimal promoter is dependent on the ERK signaling pathway. Finally, we have demonstrated that Snail and WT1, a positive regulator of E-cadherin expression, compete for the binding to the E-cadherin promoter in order to regulate its transcription.

Η επιθηλιακή προς μεσεγχυματική μετατροπή (EMT – epithelial to mesenchymal transition) είναι ένας τύπος επιθηλιακής πλαστικότητας που χαρακτηρίζεται από μακράς διάρκειας φαινοτυπικές και μοριακές αλλαγές στο επιθηλιακό κύτταρο ως αποτέλεσμα μιας διαδικασίας διαφοροποίησης προς κύτταρο μεσεγχυματικού τύπου. Η μοριακή αυτή διεργασία φαίνεται πως είναι θεμελιώδης κατά την μετάσταση επιθηλιακών καρκίνων και αποσκοπεί στην απόκτηση από τα καρκινικά κύτταρα φαινοτυπικών χαρακτήρων που τους δίνουν την δυνατότητα διείσδυσης στους ιστούς. Το ΕΜΤ, εκτός από την μετάσταση, αποτελεί βασική διεργασία τόσο στην εμβρυική ανάπτυξη όσο και στις παθολογικές καταστάσεις της φλεγμονής και της επούλωσης. Στόχος της παρούσας εργασίας είναι μια πλοήγηση μέσα από την βιβλιογραφία που αφορά το φαινόμενο ΕΜΤ και τις επιμέρους διεργασίες που το πλαισιώνουν. Στην πρώτη ενότητα θα γίνει παρουσίαση των μορίων που αναλαμβάνουν τον ρόλο της σηματοδότησης του φαινομένου το οποίο στη συνέχεια εξελίσσεται μέσα από την ενεργοποίηση δεδαλώδων σηματοδοτικών μονοπατιών. Θα παρακολουθήσουμε ακόμα την μετάδοση του σήματος μέσω των κομβικών μορίων αυτών των μονοπατιών ως τον πυρήνα όπου το σήμα απαρτιώνεται αλληλεπιδρώντας με μεταγραφικούς παράγοντες που ρυθμίζουν την έκφραση πρωτεϊνών σχετιζόμενων με την μετατροπή του επιθηλιακού κυττάρου. Στην δεύτερη ενότητα της εργασίας θα γίνει αναφορά στις δομικές και λειτουργικές αλλάγές του επιθηλιακού κυττάρου που του εξασφαλίζουν την μεταναστευτική δυναμική. Πιο συγκεκριμένα θα παρακολουθήσουμε πως το επιθηλιακό κύτταρο χάνει τη συνοχή του με το ‘περιβάλλον’ του εκφεύγοντας ταυτόχρονα της απόπτωσης. Επιπλέον θα εξετάσουμε την αναδιαμόρφωση του κυτταροσκελετού και την έκφραση νέων πρωτεϊνών με σπουδαία συμμετοχή στο φαινόμενο. Τέλος θα γίνει αναφορά στην φαινοτυπική μετατροπή που επιφέρει το φαινόμενο ΕΜΤ στο στρώμα που περιβάλλει τον καρκίνο και πως αυτή με τη σειρά της συνεισφέρει στα δίαφορα μοριακά γεγονότα που συνιστούν το φαινόμενο. Η μετάσταση είναι μια ραγδαία εξέλιξη στην αδυσώπητη πορεία του καρκίνου. Η κατανόησή της λοιπόν σε μοριακό επίπεδο είναι ζήτημα νευραλγικής σημασίας που ξεφεύγει απο τα πλαίσια του απλού ακαδημαϊκού ενδιαφέροντος. Ο χειρισμός των μοριακών μηχανισμών για τον έλεγχο της μετάστασης θα μπορεί να αποτελέσει το στοίχημα για την ΄΄μοριακή χειρουργική΄΄ του μέλλοντος. / Epithelial to mesenchymal transition (EMT) is a type of epithelial cell plasticity which is characterized by long lasting phenotypic and molecular modifications of the epithelial cell as a result of a transforming procedure leading to a cell of mesenchymal type. This molecular procedure seems to be pivotal for the metastasis of epithelial cancers and its attribution to the epithelial cells is the gain of phenotypic characters which enable them to invade the tissues. EMT apart from metastasis is also an important molecular phenomenon during embryogenesis and inflammation. The target of this project is a scan through the recent bibliography about EMT. Specifically the project’s first part is going to present the molecules that induce the phenomenon followed by the activation of the complicated signaling pathways of the cell. These paths which are consisted of nodal molecules lead the sing towards the nucleus where it interacts with transcription factors. The conclusion is the regulation of the transcription of some important genes for the phenotypic alteration of the epithelial cell to a cell with mesenchymal characters. The next subject with which this project is going to deal is the thorough presentation of the alterations of the epithelial cell. These include basically the abolishment of the adherence junctions and the reconstruction of the cytoskeleton with the formation of new structures such as filopodia and lamellipodia which endows the cell with the potential of kinesis. Additionally the transformed cells produce new proteins like N-cadherin and vimentin. They also modify the production of a family of proteins with unique importance for the EMT, the so called metalloproteinases. Moreover the cell which has gone through the impact of EMT phenomenon has the ability to induce neovascular formation and at the same time acquires molecular mechanisms to avoid the programmed cell death, known as apoptosis. Finally the transformed epithelial cell implies a phenotypic modification even to the surrounding stroma of the cancer with which the epithelial cells constitute a functional harmonic unit. From one hand the modification of the stroma activates it and the activated stroma from the other hand implies an intense impact to the most molecular subjects that are related to EMT. Metastasis is a rapid development in the ominous course of cancer. The effort to deceive the molecular basis of this phenomenon is not a subject of simple academic interest since the exploit of the molecular mechanisms so as to gain the control of metastasis could be the ‘bet’ for a futuristic ‘molecular surgery’.