Thèses sur le sujet « Stem cell heterogeneity »

Le muscle squelettique adulte a une capacité de régénération remarquable, pouvant guérir après des traumatismes répétés. Cette propriété dépend de la présence de cellules souches musculaires (SCMu), qui sont pour la plupart quiescentes dans des conditions homéostatiques mais qui s'activent après une blessure, réintègrent le cycle cellulaire et prolifèrent pour donner naissance à des myoblastes qui fusionneront pour restaurer les fibres endommagées. De nombreuses études ont étudié les états transitoires que les SCMu empruntent de l'entrée du cycle cellulaire à la différenciation. Malgré le fait que plusieurs souris rapportrices génétiquement modifiées aient été générées pour examiner ces événements, l'initiation de la différenciation, qui est généralement définie par l'expression du facteur de régulation myogénique Myogenin, est difficilement appréciable à cause du manque de souris rapportrice fiable. Par conséquent, nous avons développé une nouvelle lignée rapportrice où la différenciation des cellules myogéniques exprimant le facteur de transcription Myogenin peut être marquée par l'expression d'une protéine fluorescente tdTomato. Cette nouvelle lignée de souris knock-in nous a permis d'analyser la cinétique de l'expression de Myogenin lors de la différenciation cellulaire in vitro et d'effectuer des expériences préliminaires in vivo par imagerie intravitale. De plus, bien que toutes les SCMu de souris soient caractérisées par l'expression du facteur de transcription Pax7, plusieurs études ont décrit des différences de prolifération, de capacité de transplantation et de sensibilité à la maladie entre les SCMu des muscles crâniens et des membres. Pour étudier les réseaux de régulation des gènes qui régissent cette hétérogénéité fonctionnelle, nous avons combiné des analyses transcriptomiques sur cellules uniques avec des approches de biologie cellulaire utilisant des lignées de souris rapportrices pour identifier les régulateurs clés qui confèrent des propriétés distinctes aux SCMu à haute-performance (extraoculaires) et à faible-performance (tibialis antérieur) en quiescence et lors de l'activation. Nous avons identifié un retard dans la différenciation des SCMu extraoculaires en culture, accompagné par l'expression de facteurs de remodelage de la matrice extracellulaire et de récepteurs membranaires distincts et nous avons validé l'expression de certains de ces candidats au niveau protéique. Des analyses informatiques avancées ont mis en évidence la dynamique sous-jacente au maintien d'une population de progéniteurs dans les SCMu extraoculaires, contrôlée par un réseau singulier de facteurs de transcription formant un module de molécules co-régulées. En conclusion, ces études apportent de nouvelles informations sur les mécanismes qui octroient des propriétés différentes des cellules souches musculaires venant d'emplacements anatomiques distincts
Adult skeletal muscle has a remarkable regenerative capacity, being able to recover after repeated trauma. This property depends on the presence of muscle stem cells (MuSCs), which are mostly quiescent in homeostatic conditions, re-enter the cell cycle after injury and proliferate to give rise to committed myoblasts that will eventually fuse to restore the damaged fibres. Numerous studies have investigated the cell state transitions that MuSCs undergo from cell cycle entry to differentiation. Although several genetically modified reporter mice have been generated to study these events, detailed studies on the initiation of differentiation, which is generally defined by expression of the myogenic regulatory factor Myogenin, have been hampered by the lack of a reliable reporter mouse. Therefore, we developed a fluorescent reporter line where differentiating myogenic cells expressing Myogenin are marked by the expression of a tdTomato fluorescent protein. This novel knock-in mouse line allowed us to monitor the kinetics of Myogenin expression during cell differentiation in vitro, and perform preliminary experiments on the behaviour of myogenic cells in vivo by intravital imaging. Although all mouse MuSCs are characterised by the expression of the transcription factor Pax7 and they share several properties, some studies have reported differences in proliferation, engraftment ability, and sensitivity to disease of MuSCs from cranial and limb muscles. To investigate the gene regulatory networks that govern this functional heterogeneity, we have integrated single-cell transcriptomic analyses with cell biology approaches using mouse reporter lines to identify key regulators that confer distinct properties to high performing (extraocular muscles) and lower performing (limb, Tibialis anterior muscle) MuSCs in quiescence and activated states. We identified a delayed lineage progression of extraocular MuSCs in culture that was accompanied with the expression of distinct extracellular matrix remodelling factors and membrane receptors, and we validated the expression of some of these candidates at the protein level. Advanced computational analyses highlighted the dynamics underlying the maintenance of a stem-like progenitor population in extraocular MuSCs, controlled by a singular network of transcription factors acting as a co-regulating module. Taken together, these studies provide novel insights into the mechanisms underlying the differential properties of muscle stem cells in distinct anatomical locations

Le carcinome spinocellulaire (SCC) est le 2ème cancer de la peau le plus fréquent avec plus d’un million de nouveaux patients diagnostiqués dans le monde chaque année. On retrouve également des SCCs associés à un pronostic plus sombre au niveau de la tête, du cou, de la cavité orale et de l’œsophage. Des travaux récents ont démontré l’existence de cellules souches cancéreuses (CSCs) dans les SCCs cutanés mais les mécanismes moléculaires contrôlant leurs fonctions restent indéterminés. Dans une première étude, nous avons montré que Sox2, un facteur de transcription (TF) associé aux cellules souches, est détecté de manière hétérogène dans une grande majorité des papillomes et des SCCs chez la souris et chez l’humain. La délétion conditionnelle de Sox2 dans l’épiderme réduit drastiquement l’apparition de tumeurs démontrant le rôle clé de Sox2 dans l’initiation tumorale. En utilisant une souris génétiquement modifiée Sox2-GFP knock-in, nous avons démontré que les cellules tumorales Sox2+ sont enrichies en cellules propagatrices de tumeurs dont la proportion augmente au fur et à mesure des transplantations sériées. L’ablation des cellules Sox2+ dans les papillomes et les SCCs conduit à une importante régression des tumeurs, indiquant que ces cellules ont un rôle crucial dans le maintien des tumeurs. La délétion conditionnelle de Sox2 dans des papillomes et SCCs préexistants provoque également une régression majeure des tumeurs, soulignant le rôle essentiel de Sox2 dans la régulation des fonctions des cellules tumorales. Une analyse transcriptionnelle et des expériences d’immunoprécipitation de chromatine nous ont permis de mettre en évidence un réseau de gènes associés à des fonctions essentielles des cellules tumorales et régulés par Sox2 dans les tumeurs primaires in vivo. Dans une 2ème étude, nous avons montré que les SCCs issus de l’épiderme inter-folliculaire (IFE) présentent en général un caractère différencié alors que ceux issus du follicule pileux (HF) présentent fréquemment des caractéristiques de transition épithélio-mésenchymateuse (EMT). En réalisant une analyse transcriptionnelle et épigénétique, nous avons démontré que les différentes cellules à l’origine expriment un réseau de gènes spécifiques et présentent une accessibilité différentielle à des sites de liaison d’importants TFs associés soit à un phénotype épithélial soit à l’EMT. Ces résultats démontrent que l’état transcriptionnel et épigénétique de la cellule à l’origine amorce spécifiquement les tumeurs vers le processus d’EMT. L’ensemble de ces résultats souligne des mécanismes cruciaux à l’établissement de l’hétérogénéité tumorale et seront essentiels pour parvenir à des pronostics affinés et au développement de nouvelles thérapies ciblées dans le traitement du cancer.
Skin squamous cell carcinoma (SCC) is the second most frequent skin cancer with more than a million new patients affected every year throughout the world. It is also the predominant cancer of the head, neck, oral cavity and esophagus, associated with a poor prognosis. Recent studies have identified cancer stem cells (CSCs) in skin SCC but the molecular mechanisms controlling their functions remain unclear. In a first study, we show that Sox2, a transcription factor (TF) associated with stemness, is expressed in a heterogeneous manner in the vast majority of benign and malignant skin tumors in mouse and human. Sox2 conditional deletion in the epidermis impairs tumor development showing that Sox2 plays a crucial role in tumor initiation. Using a Sox2-GFP knock-in mouse model, we show that Sox2-expressing tumor cells are greatly enriched in tumor-propagating cells, which further increase upon serial transplantations. Lineage ablation of Sox2-expressing cells in primary benign and malignant SCCs leads to tumor regression, consistent with the critical role of Sox2-expressing cells in tumor maintenance. Conditional Sox2 deletion in pre-existing skin papilloma and SCC leads to tumor regression, supporting the essential role of Sox2 in regulating cancer cells functions. Using transcriptional profiling and chromatin immunoprecipitation, we uncovered a gene network controlling many cancer hallmarks regulated by Sox2 in primary tumour cells in vivo.In a second study, by targeting the same oncogenic mutations to distinct skin compartments, we show that interfollicular epidermis (IFE)-derived SCCs are generally well-differentiated, while hair follicle stem cells (HFSCs)-derived SCCs frequently exhibit features of epithelial-mesenchymal transition (EMT). Using transcriptional and epigenetic profiling, we show that IFE and HF tumor-initiating cells harbor distinct chromatin landscapes and gene regulatory networks associated with tumorigenesis and EMT. These different chromatin landscapes correlate with the differential accessibility of key epithelial and EMT TFs binding sites in the cancer cell of origin. These findings demonstrate that cell type-specific chromatin and transcriptional states differentially prime tumours towards EMT.Altogether, these results highlight crucial mechanisms for the establishment of tumor heterogeneity which will be relevant for better prognostic assessment and the development of novel targeted therapies for cancer treatment.
Doctorat en Sciences biomédicales et pharmaceutiques (Médecine)
info:eu-repo/semantics/nonPublished

Colorectal tumors are not homogeneous entities but rather composed of a mixture of cells with different phenotypes, reminiscent of healthy intestinal epithelium cell types. Intestinal epithelium is one of the organs with highest self-renewal rate, maintained by a pool of highly proliferating stem cells located at the base of the crypts. Daughters of the stem cells abandon the crypts and differentiate as they move up the villi, in a process that takes no longer than six days. Recent findings suggest that colorectal cancers (CRCs), like normal intestine, rely on a stem cell hierarchy for its growth. Cancer stem cells, identified by LGR5 gene expression, are at the apex of this hierarchy, and are thought to be the drivers of CRC expansion and metastasis. This thesis is focused on characterizing the growth dynamics of the different tumor compartments and identifying the cells that fuel tumor growth. Moreover, we have also tried to elucidate which is the cell of origin of metastasis. To complete this project we have first developed new models to study human disease, as most of the previous work relied on genetically modified mouse models to reproduce the disease. Here, we have combined patient-derived organoid 3D cultures and CRISPR/Cas9 genome editing techniques to insert fluorescent reporter proteins under the control of our genes of interest. This has allowed us to visualize different tumor cell types in vivo using LGR5, KRT20 and EMP1 as markers for stemness, differentiation and invasion respectively. In addition, we have also set up a system to follow the progeny of the abovementioned populations in vivo in intact tumors. We have identified the different tumor compartments by subcutaneously injecting modified human organoids into immunosuppressed mice. Flow cytometry purification and reinjection into secondary hosts of stem-like and differentiated-like cells has enabled us to discover that cancer cells retaining stem cell characteristics are more proficient in tumor initiation than the rest of the tumor. Nevertheless, lineage tracing of the abovementioned genes in an intact tumor cell environment shows how both stem and differentiated progenies are able to give rise to long lasting clones and thus equally fuel tumor growth. Furthermore, we have observed plasticity arising from both cell types, indicative that the cellular hierarchy is disrupted during tumor progression. In addition, we have defined EMP1 as a putative gene marker for invasive cells. EMP1-High cells are a differentiated subset of tumor cells that harbor migratory properties and secrete myeloid recruiting chemokines to the tumor site. Myeloid cells have been shown to contribute to all steps of metastasis in several cancer types. We hypothesize that this EMP1+ subpopulation is the one that disseminates from the primary tumor and initiates metastasis. For metastatic studies, we have resorted to mouse derived tumor organoids that allow the growth of primary and metastatic disease in fully immunocompetent ice, and we have set up new models to study disease relapse in metastatic sites upon primary tumor removal Taken together, our data provides new insights on the mode of tumor growth in advanced human colorectal carcinomas and suggests that stem cell traits are not required for tumor growth neither metastatic spread, contrary to what was initially though based on mouse adenoma studies.
Els tumors colorectals no són una entitat homogènia sinó que estan formats per una barreja de cèl·lules de fenotips variats, reminiscents dels tipus cel·lulars de l’epiteli intestinal sa. Estudis recents suggereixen que el creixement del càncer colorectal (CCR), igual que el de l’intestí normal, està mediat per una jerarquia amb origen en cèl·lules mare. Les cèl·lules mare del càncer, identificades per l’expressió del gen LGR5, es troben a l’àpex de la jerarquia i impulsen l’expansió del CCR i la metàstasis. Aquesta tesi se centra en caracteritzar la dinàmica d’expansió dels diferents compartiments tumorals i en identificar les cèl·lules que en mantenen el creixement. També hem intentat elucidar quina és la cèl·lula d’origen de la metàstasi. Per a realitzar aquest projecte primer hem desenvolupat nous models per estudiar la malaltia humana, combinant el cultiu d’organoids derivats de pacients i l’edició genòmica mitjançant CRISPR/Cas9. Això ens ha permès visualitzar diferents tipus cel·lulars tumorals in vivo usant LGR5, KRT20 i EMP1 com a marcadors de cèl·lula mare, cèl·lula diferenciada i cèl·lula invasiva, respectivament. Addicionalment, també hem establert un sistema per seguir la progènie de les poblacions mencionades. Hem descobert que tant el compartiment de cèl·lules mare com el diferenciat són capaços de donar lloc a una progènie que persisteix en el temps, suggerint que ambdós tipus cel·lulars contribueixen al creixement tumoral. A més a més, hem observat plasticitat entre els dos compartiments, cosa que indica que la jerarquia cel·lular es perd durant el desenvolupament del tumor. Finalment, mitjançant l’ús d’EMP1 com a marcador de cèl·lules invasives hem identificat un subgrup de cèl·lules diferenciades amb propietats migratòries i amb potencial per reclutar cèl·lules mieloides. La nostra hipòtesi és que la població EMP1+ és la que dissemina del tumor primari i inicia la metàstasi. En resum , les nostres dades suposen una nova visió en l’estudi del mode de creixement del càncer de colon d’estadis avançats en humà, i suggereixen que els trets de cèl·lula mare no són necessaris per creixement tumoral ni la disseminació metastàtica, contràriament al que es pensava inicialment, degut als estudis realitzats en adenoma de ratolí.

Stem cell-based therapies have been proposed as promising for the maintenance, regeneration, or replacement of malfunctioning tissues, but suffer from limitations mainly due to scarce cell availability and clinical safety concern related to cell quality. Optimization of stem cell expansion process is an engineering challenge, besides a biological issue. Aim of the work presented is to develop the experimental technology and the rational insight to understand and control stem cell expansion in vitro, in terms of both average and distributed properties of the cell population produced. A rational analysis of the main phenomena involved in a cell culture was achieved, underlining the sources of stem cell heterogeneity in both conventional culture systems and stirred bioreactors. From an experimental point of view, two types of bioreactors were designed, developed, and prototyped. The first, a microliter bioreactor array, was designed based on thermoconvective mixing; this experimental setup is particularly convenient for multiparametric optimization of cell culture conditions. The second, a six-well suspension bioreactor with a working volume of 10 ml/well, was designed and fabricated for coarse process optimization or, alternatively, for small-scale stem cell production; an improved setup was developed to perform stem cell cultures under hypoxia conditions. Both devices were advantageously used to culture human cord blood-derived hematopoietic stem cells, which were then characterized according to the currently available biological assays. In order to rationally optimize the stem cell expansion process, a computational model, based on a population balance approach, was developed, that takes into account receptor and receptor-ligand complex distribution in the cell sample. The model fairly describes intrinsic intra- and inter-generational heterogeneity arising from the process of cell division. These findings could give interesting feedback to experimental design and to define the operative conditions for bioreactor cultures, in order to minimize extrinsic and intrinsic heterogeneity, and to make a step towards a clinically safe and reliable human hematopoietic stem cell expansion process.
E' stato prospettato l'impiego di cellule staminali per terapie volte al mantenimento, alla rigenerazione o alla sostituzione di tessuti malfunzionanti. Tuttavia non sono ancora state risolte alcune limitazioni legate principalmente alla scarsa disponibilità di cellule staminali e ai problemi di sicurezza clinica connessi alla qualità cellulare. L'ottimizzazione del processo di espansione cellulare è un sfida ingegneristica, oltre che biologica. Scopo di questa tesi è lo sviluppo di una tecnologia sperimentale e di un quadro razionale che consenta di comprendere e controllare l'espansione di cellule staminali in vitro, sia considerando le proprietà medie che la loro distribuzione nella popolazione cellulare prodotta. E' stata realizzata un'analisi razionale dei principali fenomeni coinvolti nella coltura cellulare, ponendo in evidenza le fonti di eterogeneità sia nei sistemi di coltura convenzionali che nei bioreattori mescolati. Da un punto di vista sperimentale, sono stati progettati e sviluppati due tipi di bioreattori fino a realizzarne dei prototipi. Il primo, un sistema di bioreattori di volume dell'ordine dei microlitri, è stato progettato basato su un meccanismo di termoconvezione; questo apparato sperimentale è particolarmente adatto per un'ottimizzazione multiparametrica delle condizioni di coltura. Il secondo, un bioreattore in sospensione multipozzetto con un volume operativo di 10 ml/pozzetto, è stato pensato e costruito per un'ottimizzazione di processo meno dettagliata o, alternativamente, per una produzione su piccola scala di cellule staminali; una versione più avanzata è stata sviluppata per effettuare colture di cellule staminali in condizioni di ipossia. Entrambi i dispositivi sono stati vantaggiosamente utilizzati per coltivare cellule staminali ematopoietiche, ricavate da cordone ombelicale umano, che sono poi state caratterizzate secondo i metodi di analisi biologica convenzionali. Per ottimizzare razionalmente il processo di espansione delle cellule staminali, è stato sviluppato un modello computazionale, basato su un bilancio di popolazione, che tiene conto della distribuzione di recettori e di complessi recettore-ligando nel campione cellulare. Il modello descrive ragionevolmente l'eterogeneità intrinseca, intra- e intergenerazionale, derivante dal processo di divisione cellulare. Questi risultati possono dare un riscontro positivo in fase di progettazione degli esperimenti e di definizione delle condizioni operative a cui effettuare colture in bioreattore, al fine di minimizzare l'eterogeneità estrinseca e intrinseca della popolazione cellulare e di effettuare un ulteriore avanzamento verso un processo di espansione di cellule staminali umane clinicamente sicuro ed affidabile.

Jarid2 is required for the genomic recruitment of the polycomb repressive complex-2 (PRC2) in embryonic stem cells. However, its specific role during late development and adult tissues remains largely uncharacterized. In this first part of my thesis, we show that deletion of Jarid2 in mouse epidermis reduces the proliferation and potentiates the differentiation of postnatal epidermal progenitors, without affecting epidermal development. In neonatal epidermis, Jarid2 deficiency reduces H3K27 trimethylation, a chromatin repressive mark, in epidermal differentiation genes previously shown to be targets of the PRC2. However, in adult epidermis Jarid2 depletion does not affect interfollicular epidermal differentiation but results in delayed hair follicle (HF) cycling as a consequence of decreased proliferation of HF stem cells and their progeny. We conclude that Jarid2 is required for the scheduled proliferation of epidermal stem and progenitor cells necessary to maintain epidermal homeostasis. Several human and mouse solid tumors, including squamous cell carcinomas (SCC), contain a population of Cancer Stem Cells (CSCs). CSCs are characterized by their unique ability to initiate and propagate the tumor; however, very little is known about their capacity to disseminate to distant organs and give rise to metastasis. CSCs display a great functional and molecular heterogeneity, and it has been proposed that different CSC subclones might exist to either maintain the primary tumor or to metastasize in distant sites. However, the identity of these heterogeneous populations of CSCs, as well as their molecular and functional characteristics for most type of tumors remains to be elucidated. Using a novel xenograft system that we have developed to study human head and neck squamous cell carcinoma, we have identified a labelretaining (LRC) population inside the cancer stem cell pool defined by the high expression of CD44 and high activity of Aldh1. Unexpectedly, tumor LRC harbor poor initiating potential, and are more sensitive to chemotherapy than their proliferating counterparts. Intriguingly, tumor LRCs are defined by a unique transcriptome signature previously linked with bone and lung identity, two major sites of SCC metastasis, suggesting they might be involved in the colonization of distant tissues by SCC tumors. We have also identified surface molecules, including CD36 and CD37, that are uniquely expressed by tumor LRCs, that can be used as surrogate markers to isolate and characterize them from primary human SCCs. Based on this signature, we could demonstrate that the presence or absence of this population in the primary tumor of a large cohort of patients with cutaneous SCC is highly predictive of the metastatic occurrence. In addition, several markers exclusively expressed by tumor LRCs can be targeted with drugs currently in clinical trials for the treatment of other diseases. We are testing whether some of these therapeutical strategies are effective to preventing or reducing the metastatic potential of SCC tumors.
Jarid2 es necesario para la localización genómica del complejo represor polycomb repressive complex-2 (PRC2) en células stem embrionarias. Sin embargo, la función de Jarid2 en las últimas fases del desarrollo embrionario y su papel en la función de los tejidos adultos no ha sido aún caracterizada en profundidad. En esta primera parte de mi tesis doctoral, mostramos que la deleción de Jarid2 en la piel de ratón no afecta al desarrollo de la epidermis, pero reduce la proliferación y potencia la diferenciación de las células progenitoras epidermales en neonatos. La piel de los ratones neonatos Jarid2-KO muestra niveles reducidos de la marca represora de la cromatina, H3K27me3, en genes necesarios para la diferenciación de las células progenitoras. En cambio, en piel adulta la depleción de Jarid2 no afecta la diferenciación de la epidermis, pero sí que resulta en una reducción del número de células stem activas de los folículos pilosos, lo que desemboca en el retraso del crecimiento de los folículos. Por lo tanto, nuestros resultados demuestran que Jarid2 es necesario para la activación y diferenciación de diferentes células stem del compartimento queratinocítico de la piel necesarios para mantener la homeostasis epidermal. Diversos tipos de tumores sólidos humanos y de ratón, incluyendo carcinomas de células escamosas (SCCs del inglés: Squamous Cell Carcinomas), contienen una población de células madre cancerosas (CSCs del inglés Cancer Stem Cells). Las CSCs se caracterizan porque pueden iniciar y propagar el tumor; sin embargo, se conoce muy poco sobre su capacidad de alcanzar órganos lejos del tumor primario y de formar metastasis. Las CSCs pueden ser muy heterogéneas tanto a nivel funcional como molecular, y se ha propuesto que podrían existir diferentes subclones sea para mantener el tumor primario, sea para formar metástasis. No obstante, no se conoce por ahora ni la identidad de estas poblaciones heterogéneas de CSCs, ni sus características a nivel funcional o molecular. Usando un nuevo sistema de xenoinjerto que hemos desarrollado en nuestro laboratorio para estudiar SCC de cabeza y cuello, hemos identificado una población que es capaz de retener el marcaje con el tiempo (LRC de inglés: Label-retaining Cells), dentro de la población total de CSSs, definidas como células dentro del tumor que muestran alta expression de CD44 y alta actividad de Aldh1. En contra de lo que esperábamos, las LRC del tumor tienen dificultad para iniciar tumores por sí solas y son más sensibles a tratamientos de quimioterapia cuando las comparamos con otras células más proliferativas. Por otra parte, las LRC del tumor se pueden definir con un transcriptoma único que ha sido relacionado anteriormente con hueso y pulmón, que son dos de los órganos donde los SCC forman metástasis preferentemente. Esto sugiere que podrían estar involucradas en la colonización de órganos alejados del SCC primario. Hemos identificado también moléculas de superficie, incluyendo CD36 y CD37, que se expresan exclusivamente en las LRC de tumor y que se pueden usar como marcadores para aislar y caracterizar las LRC de SCCs primarios humanos. Basándonos en estos marcadores, hemos podido demostrar que la presencia o no de esta población en el tumor primario predice la formación de metástasis en pacientes con SCC cutáneos. Además, diversos marcadores que hemos identificado como únicos en LRC de tumor, son diana de fármacos ya usados en la actualidad en ensayos clínicos para tratamiento de otras enfermedades. En la actualidad estamos probando si alguno de estos tratamientos puede ser efectivo para prevenir o reducir el potencial de formar metástasis en SCC.

Carbonic anhydrase IX (CA9) is strongly induced by hypoxia and its overexpression is associated with poor therapeutic outcome in cancer. The function of CAIX is to catalyze the reversible hydration of CO2 to bicarbonate and a proton. This helps hypoxic tumours to maintain a more neutral intracellular pH (pH_i) promoting survival, but produces a more acidic extracellular (pH_e) which promotes invasion and metastasis. Recent evidence has expanded on the role of hypoxia and CAIX by relating them to stem cell niches. In this study, taking advantage of the transmembrane location of CAIX, we show for the first time, a direct marked heterogeneity in response to hypoxia within each tumour cell population studied, associated with major biological differences. Based on CAIX expression pattern under hypoxic conditions, we identify, isolate and characterize two distinct populations of tumour cells, one that express CAIX and the other that does not. Interestingly, we discover that the CAIX positive population is enriched with cells expressing cancer stem cell markers. These include ALDHA1, IGF1, LIN28 and genes involved in epithelial-mesenchymal transition (EMT) and multi-drug resistance (i.e. WNT2, TWIST1, and ABCC2). Accordingly, CAIX+ve cells show higher self-renewal capacity and form tumours significantly faster compared to the CAIX-ve population. Importantly, functional suppression of CAIX in vitro and in vivo, in two breast cancer cell lines resulted in the downregulation of breast cancer stem cell signatures, suggesting that CAIX is not just a marker of stemness but also a regulator of stemness. The molecular mechanism underlying the differential expression of CAIX in the two populations is not HIF-1α-dependent, but instead driven by hypoxia-induced reorganization of chromatin structure. In line with this, we provide experimental evidence showing that the genomic locus encoding CA9 has a more “open” and transcriptionally active chromatin structure in CAIX+ve cells, and a condense and transcriptionally silent chromatin structure in the CAIX-ve cells. Given that HIF induces the transcription of CA9 by binding to hypoxia response elements (HREs) in its promoter we show a significant reduction in binding of HIF to the CA9 promoter of the negative population. We suggest that the reduce HIF binding is a result of the compact chromatin structure of CA9 promoter of the negative cells. Analysis of the transcriptome of the positive and negative populations suggests a symbiotic relationship between these two subpopulations and their environment, likely required to promote tumour growth. This is based on the following observations: Firstly, we identified that CAIX-ve cells express high levels of cytokines and based on this, we suggest that the cytokines secreted by CAIX-ve cells may transmit paracrine signals that regulate the CAIX+ve cells, thus providing a wider hypoxia tolerant microenvironment to protect the stem cell population. Secondly, we identified a metabolic heterogeneity between the CAIX+ve and CAIX-ve cells. The CAIX+ve cells show an upregulation of genes implicated in oxidative phosphorylation, TCA cycle and fatty acid synthesis. Whereas in CAIX-ve cells there is an upregulation of genes implicated in autophagy and mitophagy. Given the above together with the upregulation of oxidative phosphorylation and TCA cycle in the CAIX+ve cells, we proposed the existence of a metabolic symbiosis between the CAIX+ve and CAIX-ve cells. We postulate that the catabolic process such as autophagy and mitophagy in the CAIX-ve cells may results in the overproduction of high-energy metabolites such as lactate, glutamine and ketone bodies which in turns they are been utilized by CAIX+ve cells to fuel mitochondria respiration. Finally, we also demonstrated that in the CAIX+ve cells mTORC1 signaling is upregulated, and contributes to the regulation of CAIX expression. Given the role of mTORC1 in stem cell maintenance and EMT as well as the interdependence of mTORC1 and CAIX expression in the CAIX+ve cells we suggest that mTORC1 signaling may be the critical factor by which CAIX regulates stemness. Interestingly, the subpopulations show a differential sensitivity to HDAC inhibitors, NaBu and SAHA as treatment of MCF7 breast cancer cell line and HCT116 colon cancer cell line leads to elimination of the CAIX+ve population. This is not driven by the downregulation of HIF-1α, the major transcriptional regulator of CAIX. In contrast, we demonstrate that SAHA causes downregulation mTORC1. This suggests that SAHA-induced downregulation of CAIX expression could be due to its effect on mTORC1 pathway. Of wider significance, our findings show that tumours are not homogenous in their response to hypoxia, and distinct signal transduction networks regulate different populations of cells within the tumour. This highlights the need for the utilization of biomarkers, which reveal distinct functional hypoxia profiles of human cancers, and permit the stratification of tumours. Furthermore, the identification of epigenetic regulation of the histones in response to hypoxia for highly selective gene regulation, provides a connection between the epigenetic mechanisms under environmental stress and cancer progression, and is model for development of novel epigenetic cancer therapeutic drugs.

Les Cellules Stromales / Souches Mésenchymateuses (CSM) ont un grand potentiel pour de nombreuses applications. Elles sont les cellules les plus utilisées pour les essais cliniques développant des thérapies cellulaires. L’efficacité thérapeutique des CSM est influencée par leur amplification in vitro et d’autres facteurs tels que les paramètres liés au donneur de cellules. Pour améliorer les thérapies à base de CSM, cette étude a ciblé l’étude de leur hétérogénéité grâce à leurs marqueurs de surface, qui permettent de mutualiser la caractérisation des cellules et la possibilité de trier des cellules vivantes. Le premier objectif de ce travail a été de décrire la variabilité des CSM entre et au sein d’échantillons venant de moelle osseuse de donneurs d’âges différents. Le deuxième objectif a été de développer une méthode de tri pour séparer les CSM selon leur expression de CD146 et de comparer les cellules triées. La troisième partie du travail a eu pour objectif de mieux connaître les marqueurs de surface des CSM sénescentes. Les résultats de cytométrie en flux sur les CSM sont soumis à de fortes fluctuations, mais certaines régularités ont pu être mises en évidence. Un ensemble de marqueurs de surface a pu être associé avec l’âge des donneurs : CD146, CD71, CD105, CD44. De plus, des liens entre l’expression de CD146, CD140b et CD71 ont été observés avec la capacité de prolifération des CSM. Des CSM de moelle osseuse provenant de donneurs d’âges différents et à différentes étapes de culture ont pu être triées avec succès selon leur expression de CD146 par une méthode immunomagnétique. Le comportement des CSM triées était encore hétérogène mais il a pu être observé que les CSM exprimant plus fortement CD146 avaient plus souvent de meilleures capacités de différentiation et de migration et étaient moins sénescentes que les cellules exprimant plus faiblement CD146. Une étude protéomique a montré que la plupart des protéines de surface détectées avaient tendance à être moins représentées sur les cellules sénescentes à l’exception de CD157. Les CSM à différentes étapes de culture jusqu’à la sénescence réplicative ont ensuite été suivies par cytométrie en flux. Cette dernière étude a révélé d’importantes fluctuations entre les différents passages, soulignant la difficulté associée à l’utilisation de ces marqueurs. Les marqueurs CD146, CD71, CD140b et CD157 méritent d’être suivis pour le contrôle qualité des CSM provenant de moelle osseuse
Mesenchymal Stromal / Stem Cells (MSC) hold great potential and are currently the most used in clinical trials with cell-based treatments. MSC quality and therapeutic effectiveness are influenced by in vitro expansion but also by other factors such as donor parameters. To ameliorate the success rate of MSC therapies, this study focused on MSC heterogeneity. To put together cell characterization and ways to act when facing cell heterogeneity, this work was oriented toward the study of surface markers that can be monitored on living cells, and can serve to sort them. The first objective was to describe initial MSC surface markers variability between and within different bone marrow MSC samples from donors of different ages. The second objective was to develop a sorting method to separate MSC according to CD146 expression and compare the sorted cells. The third objective was to widen MSC surface markers knowledge by focusing on senescent MSC. Surface markers of early passage and replicative senescent cells were compared with proteomics and flow cytometry. Flow cytometry results on MSC were shown to be submitted to strong fluctuations. However, some regularities were strong enough to stand out. A group of surface markers were found to be associated with donor age: CD146, CD71, CD105, CD44. CD146, CD140b and CD71 were also correlated with proliferation rate. CD146 expression had the particularity to be relatively stable in culture and turned out to be the most heterogeneously expressed when looking at cell population within the samples. Cultivated MSC from bone marrow coming from donor of different ages and at different culture steps were sorted successfully according to CD146 expression with immunomagnetic method. MSC behavior remained heterogeneous after sort but it could still be observed that most CD146high cells had more often better differentiation and migration capacities and were less senescent than their CD146low counterpart. Proteomics study showed that almost all surface proteins expression tended to decrease on replicative senescent MSC, except one marker that increased: CD157. MSC at different stages of culture until replicative senescence were then studied by flow cytometry. This study revealed strong fluctuation in marker expression between different passages, highlighting again the variability of MSC behavior and the difficulty to predict it. CD146, CD71, CD140b, CD157 and SSC deserve to be followed for MSC quality control

Previous work from our laboratory in the mdx mouse model of Duchenne muscular dystrophy (DMD) demonstrated that a fraction of muscle stem cells (i.e., satellite cells) (MuSCs) progressively lose the expression of myogenic markers during the progression of the disease. In the process of characterizing this aberrant behaviour, we serendipitously discovered that MuSCs might be separated into two distinct subpopulations based on the expression of the GPI-anchored surface protein CD90. Crucially, this separation does not correlate with a divergence from the myogenic lineage; instead, it separates the pool of MuSCs into two subpopulations, both maintaining myogenic properties in healthy muscles. These two newly identified subpopulations do not overlap with any previously reported subpopulation and may be prospectively isolated; present a different response in terms of kinetics of activation and differentiation during the regenerative process induced by acute muscle damage; show a different propensity to enter in GAlert state upon distal injury; display dissimilar pAMPK activity and contain a different amount of mitochondria; are present in different proportions in distinct muscle groups; differentially express ECM encoding genes during quiescence. Moreover, one of the two subpopulations can give rise to the other and therefore appears to be upstream in the lineage hierarchy. Notably, loss of function experiments, in which CD90 was downregulated in MuSCs, diminish the difference in activation displayed by the two subpopulations. This demonstrates that CD90 is a molecular determinant of MuSCs functional diversification. Importantly, although the two subpopulations of MuSCs are numerically similar in healthy limb muscles, one of the two subpopulations is lost with time in dystrophic mdx mice. Based on these data, we are hypothesizing that an imbalance between the two newly identified subpopulations may impair regeneration in the dystrophic muscles. These observations not only increase our knowledge of the molecular and cellular dynamics that are controlling normal and pathological muscle homeostasis but also open the possibility that restoring the proper functional equilibrium between subpopulations of MuSCs may counteract the progression of the dystrophic disease.

La leucémie myéloïde chronique est une hématopoïèse maligne clonale, caractérisée par l'acquisition de la translocation t (9;22) conduisant au chromosome Ph1 et à son homologue l'oncogène BCR-ABL, dans une cellule souche hématopoïétique très primitive. La LMC est un modèle de thérapies ciblées, car il a été démontré que la preuve de la faisabilité du ciblage de l'activité tyrosine kinase (TK) BCR-ABL à l'aide d'inhibiteurs de TK (TKI) entraîne des réponses et des rémissions majeures. Cependant, les problèmes actuels rencontrés dans ces thérapies sont la résistance des cellules souches leucémiques primitives et leur persistance qui serait liée à l'hétérogénéité des cellules souches au moment du diagnostic, ce qui conduit à la sélection clonale de cellules résistant aux thérapies TKI. J'ai appliqué la technologie de l'analyse du transcriptome des cellule uniques aux cellules de la LMC en utilisant un panel de gènes impliqués dans différentes voies, combinée à l'analyse d'inférence de trajectoire au modèle d'expression des gènes. Les résultats ont montré un état transitoire des cellules souches comprenant des gènes embryonnaires identifiés dans les cellules de la LMC au moment du diagnostic, ce qui pourrait contribuer à la résistance et à la persistance de la LSC. En outre, l'oncoprotéine Bcr-Abl est la tyrosine kinase constitutivement active produite par le gène chimérique BCR-ABL dans la leucémie myéloïde chronique (LMC). Les cibles transcriptionnelles de Bcr-Abl dans les cellules leucémiques n'ont pas été étudiées de manière approfondie. Une expérience de transcriptome utilisant la lignée cellulaire UT7 hématopoïétique exprimant BCR-ABL, a identifié la surexpression du facteur d'élongation eucaryote kinase 2 (eEF2K) qui joue un rôle majeur dans la survie des cellules en cas de privation de nutriments. Dans l'ensemble, les données suggèrent que la surexpression de eEF2K dans la LMC est associée à une sensibilité accrue à la privation de nutriments
Chronic myeloid leukemia is a clonal hematopoietic malignancy, characterized by the acquisition of the t (9;22) translocation leading to Ph1 chromosome and its counterpart BCR-ABL oncogene, in a very primitive hematopoietic stem cell. CML is a model of targeted therapies as the proof of concept of the feasibility of targeting the tyrosine kinase (TK) activity BCR-ABL using TK inhibitors (TKI) has been shown to lead to major responses and remissions. However, the current problems encountered in these therapies are primitive leukemic stem cells resistance and their persistence which is thought to be related to the heterogeneity of the stem cells at diagnosis leading to clonal selection of cells resisting to TKI therapies. I have applied the technology of single cell transcriptome analysis to CML cells using a panel of genes involved in different pathways combined with trajectory inference analysis to the gene expression pattern. The results showed a transitional stem cell states including embryonic genes identified in CML cells at diagnosis which could contribute to LSC resistance and persistence. Furthermore, the oncoprotein Bcr-Abl is the constitutively active tyrosine kinase produced by the chimeric BCR-ABL gene in chronic myeloid leukemia (CML). The transcriptional targets of Bcr-Abl in leukemic cells have not been extensively studied. A transcriptome experiment using the hematopoietic UT7 cell line expressing BCR-ABL, has identified the overexpression of eukaryotic elongation factor kinase 2 (eEF2K) which plays a major role in the survival of cells upon nutrient deprivation. Overall, the data suggest that overexpression of eEF2K in CML is associated with an increased sensitivity to nutrient-deprivation

On admet communément que les tumeurs proviennent de cellules échappant aux contrôles homéostatiques qui sous-tendent les structures histologiques saines et que le phénotype d’une cellule n’est pas le résultat de processus génétiques et biochimiques déterministes mais la conséquence stochastique de réseaux de régulation intra- et intercellulaires. Ce doctorat vise à étudier quantitativement l’homéostasie phénotypique de populations cellulaires et à présenter une approche à la question fondamentale, mais jusqu’alors jamais étudiée, concernant l’autonomie versus le contrôle collectif du devenir des cellules. Nous avons étudié sur le long terme, par cytométrie de flux et dans des conditions 2D puis 3D, le niveau d’expression de CD24 et CD44 de deux lignées cellulaires de cancer du sein (SUM149-PT et SUM159-PT). Trois phénotypes ont été isolés (CD24-/CD44+, CD24+/CD44+, CD24-/CD44-), ce dernier n’avait pour le moment pas été documenté dans la littérature. Le comportement phénotypique des sous-populations CD44-low et CD44-high a été caractérisé en évaluant leur proportion et en analysant leur spectre de fluorescence. Ainsi nous avons observé des comportements périodiques d’apparition et de disparition de pool de cellules caractéristiques des lignées et une re-diversification des phénotypes pour chacune des sous-population. Seule la population issue de CD24-/CD44- re-diversifiée présente le même équilibre que la population initiale non triée. En 3D, le processus de re-diversification a été observé dans les tumorsphères issues de CD24-/CD44+ et CD24+/CD44+. Les cellules CD24-/CD44- n’ont pas ce potentiel mais survivent néanmoins à l’anoïkis. Ces comportements laissent penser qu’il existe une coordination intercellulaire régulant l’équilibre des proportions phénotypiques. Pour découvrir les règles sociales régissant l’organisation spatiale inter-phénotypique, nous avons mis en place un rapporteur des variations du niveau d’expression endogène des marqueurs d’intérêt et élaboré un modèle théorique d’interactions cellulaires. Ce travail a conforté notre hypothèse selon laquelle il s’établit des règles sociales inter-cellulaires déterminant l’expression phénotypique à l’échelle uni- et pluricellulaire
It is commonly accepted that tumors arise from cells that escape the homeostatic controls which underlie the healthy histological structure and that cell phenotype is not the result of deterministic biochemical and genetic processes, but rather the stochastic and dynamic outcome of multiple intra- and intercellular regulation networks. This PhD aims to quantitatively study the phenotypic homeostasis of the cell populations and to present an approach to the fundamental question, never heretofore studied, regarding the autonomy versus collective control of cell fate. We studied in the long run, using flow cytometry and in 2D and 3D conditions, the level of expression of CD24 and CD44 of two breast cancer cell lines (SUM149-PT and SUM159-PT). Three phenotypes were isolated (CD24-/CD44+, CD24+/CD44+, CD24-/CD44-), the latter had not previously been documented in the literature. The phenotypic behavior of CD44-low and CD44-high subpopulations has been characterized by assessing their proportion and analyzing the fluorescence map. Thereby, we observed both a periodic behavior of appearance and disappearance of pool of cells characteristics of each cell lines and a phenotypic re-diversification for each subpopulation. Only the resulting population derived from CD24-/CD44- provided the same balance as the original unsorted population. 3D re-diversification process was observed in tumorspheres from CD24-/CD44+ and CD24+/CD44+. The cells CD24-/CD44did not have that potential but nonetheless outlived anoikis. These behaviors suggest that there is an inter-cell coordination regulating the balance of phenotypic proportions. To discover the social rules regulating inter-phenotypic spatial organization, we have set up a reporter of the endogenous variations of CD24 and CD44 and developed a theoretical model of cell interactions. This work has confirmed our hypothesis that inter-cellular social rules are determining the phenotypic expression at both the uni- and multicellular scales

Cell-to-cell variation in expression of pluripotency- and lineage-determining factors has been proposed to be integral to the process of cell fate commitment in pluripotent cells both in vitro and in vivo. Understanding the sources of this heterogeneity in pluripotent stem cells promises greater insight into the mechanisms underlying cell fate choice. I identify mitochondrial membrane potential as an axis of heterogeneity in mouse embryonic stem cell populations, and show that high mitochondrial membrane potential marks cells that are in a stable self-renewing state. Partial overlap with previously described metastable subpopulations is demonstrated through gene expression analysis. I present evidence that similarly to previous findings in HeLa, heterogeneity in mitochondrial membrane potential is associated with variation in global transcription rate in mESCs. The direct impact of global transcription rate on differentiation propensity is demonstrated through manipulation of RNA Pol II transcription elongation rate. Mitochondrial variability is therefore likely a functionally relevant source of extrinsic gene expression variability in mouse embryonic stem cells.

The normal mammary gland contains “stem cells” with extensive in vivo growth and bi-lineage differentiation potential and a surface phenotype of basal cells (BCs). BCs also contain cells with more limited growth and differentiation activity in vitro. An analogous luminal-restricted progenitor (LPs) subset has surface characteristics of both basal and luminal cells. I hypothesized that the growth and differentiation activity displayed by individual mammary epithelial cells from both subsets would be highly diverse, and that the properties of tumours produced from these cells would be affected by their cell of origin. To address this hypothesis, I first developed a lentiviral-mediated barcoding strategy that involves transducing each cell with a unique 27-base pair non-coding DNA sequence so that the number of its clonal progeny can be inferred from high-throughput sequencing data obtained on the progeny of bulk-transduced populations. The use of “spiked-in” control cells carrying a known barcode provided an internal calibration for clone size calculations and allowed clones of ≥100 cells to be reliably detected. Application of this strategy to normal mouse and human mammary cells identified expected bi-lineage clones but an unanticipated predominance of lineage-restricted clones produced in primary transplants. These experiments also revealed that many clones apparent in secondary hosts were not detected in the primary hosts, indicating their origin from cells with very delayed growth activity. Application of the barcoding strategy to normal human BCs and LPs transduced with lentiviruses encoding KRASG¹²D ± PI3KCAH¹⁰⁴⁷R ± TP53R²⁷³C showed tumour formation in subsequently transplanted immunodeficient mice was rapid (within 8 weeks) and efficient from both cell types (8-12/18 donors, 1/200-1/4,000 transduced cells). However, tumours generated from LPs contained larger clones than tumours generated from BCs. Surprisingly, none of the LP-derived tumours were ERα⁺ (typical of luminal-like breast cancers) whereas 60% of the BC-derived tumours were. Earlier analysis of xenografts of similarly transduced cells revealed changes in both the number and phenotype of the cells present. Taken together, these findings underscore the diverse regenerative activity of normal mammary cells and provide definitive evidence that the cell of origin can affect the properties of human breast tumours generated using identical oncogenes.

The mammalian blood-forming system sustains physiologically required levels of mature blood cells by supporting their continuous generation from a rare population of undifferentiated, self-sustaining pluripotent hematopoietic "stem" cells (HSCs). Throughout adult life HSCs are located primarily in the bone marrow. Traditionally, the study of HSCs within larger populations of cells has hampered the direct observation of any unique differentiation or self-renewal properties that might distinguish individual members of the HSC compartment. To circumvent this, I analyzed the number and types of progeny generated from single purified HSCs both in cultures initiated with a single cell and in irradiated mice injected with a single cell. In a first set of experiments of this type, I demonstrated that two growth factor cocktails with the same mitogenic and antiapoptotic activity on HSCs in vitro could have remarkably disparate effects on their concomitant self-renewal behaviour, even within the span of a single cell cycle. In addition, I used high-resolution video monitoring of single purified HSCs cultured in microwell arrays to identify cellular features that were associated with HSC self-renewal in vitro. These parameters include longer cell-cycle times than those of their differentiating progeny and an absence of uropodia on the majority of cells within the clone during the final 12 hours of culture. When combined, these parameters improved by a factor of 2-3-fold the identification of clones found to contain daughter HSCs with longterm in vivo reconstituting ability. Finally, from longitudinal and serial WBC analyses performed on a large number of recipients of single purified HSCs, I found that the adult HSC compartment could be resolved into 4 HSC subtypes, 2 of which stably and autonomously propagate their initial unique patterns of WBC reconstitution through many self-renewal divisions in vivo. I also found that, in vitro, HSCs could rapidly acquire less competitive in vivo reconstitution programs although remarkable symmetry was retained in the reconstitution programs acquired by the daughter HSCs generated in the first 4 days in vitro. These findings provide evidence of intrinsically determined heterogeneity in the differentiation and self-renewal properties of individual HSCs.
Medicine, Faculty of
Medical Genetics, Department of
Graduate

Human embryonic stem cells display several features of heterogeneity in culture. This heterogeneity is poorly understood and may impair differentiation protocol efficiency. There is increasing evidence that stem cell heterogeneity is dynamic and affects lineage fate decisions whilst cells are still pluripotent. The aim of this project was to develop new approaches for understanding the heterogeneity of cells within the pluripotent stem cell compartment that influences stem cell fate decisions. Understanding the rules governing stem cell heterogeneity would open up opportunities to manipulate these features for the improved application of differentiation protocols or within regular cell culture maintenance. Two novel methods for the interrogation of pluripotent stem cell heterogeneity have been developed in this thesis. The first approach examines pluripotent stem cell dynamics by modelling the population fluctuations of the sensitive pluripotency marker SSEA3 of a pluripotent Embryonal Carcinoma (EC) cell line, NTera2. The model generated explained the heterogeneity dynamics of SSEA3 within NTera2 and in a predictive manner that also revealed candidate substate populations. The second approach developed was the application of Raman spectroscopy for the non-invasive assessment of heterogeneity within and between stem cell populations according to biochemical signatures. These studies showed that a hyperspectral, grid based, approach proved sensitive for examination of cell biochemistry and furthermore, this approach was used to address biological questions. Raman Spectroscopy proved sensitive enough to notice differences between cell lines, between differentiated and undifferentiated cells, between intracellular compartments, and could discriminate between different pluripotent cells associated with differing lineage biases. This work therefore represents a development in both our understanding of pluripotent stem cell dynamics and the potential for using both modelling and Raman spectroscopy to analyse this phenomenon.

Breast cancer is a heterogenous disease, composed of tumour cells with differing gene expressions and phenotypes. Tumour heterogeneity has several important consequences for breast cancer including: (i) making classification by morphological and expression analysis more difficult because of the diversity within single tumours with the consequence that the majority of cells of the tumour will dominate this classification whether or not these cells are critical for diagnosis or treatment; (ii) treatments may fail to eradicate tumours simply by failing to eliminate one of the cell subtypes within the tumour; and (iii) differing abilities of the cell subtypes for dissemination and metastasis. Recently, a rare subpopulation of cells within tumours has been described with the ability to initiate and sustain tumour growth, to resist traditional therapies and to allow for secondary tumour dissemination. These cells are termed tumour-initiating cells or cancer stem cells, or alternatively, in the case of breast cancer, breast cancer stem cells. The therapeutic targeting of these cells has the potential to eliminate residual disease and may become an important component of a multi-modality treatment of cancer. Presented here is an investigation into: (i) ways to functionally and phenotypically identify breast cancer stem cells; (ii) the role of breast cancer stem cells in disease from both clinical samples and using xenograft assays; and (iii) the potential to target these cells.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Physical Sciences
Science, Environment, Engineering and Technology
Full Text

Le glioblastome (GBM) est la tumeur cérébrale primaire la plus agressive comportant une sous-population de cellules souches tumorales (CSG). Elles sont capables d’auto-renouvellement, de prolifération, de différenciation en cellules exprimant les marqueurs neuraux et de trans-différenciation en cellules de types vasculaires. Dans ce contexte, j’ai dérivé et caractérisé plusieurs lignées de CSG à partir de biopsies de patients. Puis j’ai évalué l’impact des peptides thérapeutiques transmembranaires développés au laboratoire, visant les plateformes de récepteurs de neuropiline-1 et de plexine-A1 surexprimées dans les CSG. Les deux peptides diminuent la croissance des CSG in vitro et in vivo. Finalement, j’ai développé un outil génétique fluorescent permettant de suivre le destin des CSG en direct. Basé sur l’expression de 4 rapporteurs fluorescents contrôlés par des promoteurs spécifiques des types cellulaires, il permet d’identifier l’hétérogénéité de ces cellules en différenciation
The glioblastoma multiforme (GBM) is the most aggressive primary brain tumor and includes a subpopulation of tumoral stem cells (CSG). Those cells can self-renew, proliferate and differentiate by expressing specific neural markers and/or transdifferentiate into vascular-like cells. In this context, my work consisted first to produce and characterize several CSG lines from patient biopsies to constitute a bank of cell lines with different properties. We also evaluated the impact of in house therapeutic transmembrane peptides targeting the neuropilin-1 / plexin-A1 receptor platforms overexpressed in GBM. We thus showed that both targeting peptides decrease the growth of GSC in in vitro and in vivo models. Finally, I developed an inducible mosaic expression system to track the live differentiation of CSG. This system is based on the expression of four different fluorescent reporters controlled by the activity of cell type specific promoters

Oligodendrocytes are the myelinating cells of the central nervous system (CNS), whose function is to optimise neuronal transmission and preserving axonal integrity. Oligodendrocytes are derived from a stem cell population, called oligodendrocyte progenitor cells (OPCs). Oligodendrocyte lineage cells (OLCs) have been implicated in the pathophysiology of various diseases including not only demyelinating diseases (eg. Multiple Sclerosis (MS) or Pelizaeus-Merzbacher disease (PMD)), but also psychiatric disorders (eg. schizophrenia or Rett syndrome (RTT)). Regardless of the type of disease, understanding the underlying fundamental biology of the oligodendrocyte lineage cells is pivotal to develop therapeutic strategies. In the mouse embryonic forebrain OPCs are generated in consecutive waves from distinct brain regions along a spatiotemporal gradient; with ventral OPCs emerging before dorsal OPCs. The developmentally distinct OPCs, and their progenies, persist in the brain throughout life. To investigate whether ventrally and dorsally derived OLCs fulfil different functions in the adult brain, dorsally derived OPCs were ablated in development using a \textit{Sox10}-driven diphtheria toxin fragment A (DTA) mouse model. As dorsally derived OPCs populate the cortex, locomotor coordination and cognition were investigated following dorsal OPC ablation. Mice ablated of the dorsal OPC population do not show a significant deficit in learning and attentional function. In contrast, ablated mice show an impaired locomotor coordination, while general vigilance, gait, balance and sensation are comparable to control groups. The locomotor coordination disabilities are a result of alterations of brain, not spinal cord homeostasis, as only a neglect able number of OLCs in the spinal cord are affected by the ablation model. In addition, no signs of neuronal cell death or chronic inflammatory response was detected in response to the ablation. As the oligodendrocyte numbers are similar between control and ablated animals, the locomotor coordination phenotype can also not be explained by reduced number of oligodendrocytes. However, clustering analysis following single-cell Drop-sequencing uncovered a heterogeneity of oligodendrocyte (OL) subpopulations in the motor cortex. Whilst some OL subpopulations are of mixed developmental origin, others are exclusively formed by either ventrally or dorsally derived OLs, arguing that dorsal oligodendrocyte subpopulations are crucial for homeostatic brain function. In the absence of dorsal OPCs, ventral OPCs are not capable of forming dorsal oligodendrocyte subpopulations in response to dorsal OPC ablation. In conclusion, my results indicate a functional heterogeneity of developmentally-distinct oligodendrocytes in physiological brain function.

Acute myeloid leukaemia (AML) is the most frequent leukaemia in adults, and still represents a disease with an unmet medical need, with 50-60% of patients relapsing within 3 years after diagnosis. AMLs are characterised by a high degree of intra-tumour heterogeneity, both at the biological and the genetic level, which is critical for tumour maintenance and response to treatments. Biologically, AMLs are organised hierarchically, with rare stem-like cells (leukaemia stem cells, LSCs) endowed with the unique properties of self-renewal and differentiation. Genetically, AMLs harbour patient-specific combinations of different driver mutations, which are organised within individual cases in sub-clones with distinct growth properties. We hypothesized that tumour maintenance and relapse in AMLs are driven by the selective expansion of quiescent sub-clones within the LSC population, which serve as the genomic and functional reservoir of the tumour. The experimental strategy we employed to test this hypothesis is based on the xenotransplantation of human leukaemias, the implementation of an in vivo clonal tracking approach, the functional isolation of leukaemic subpopulations with diverse proliferation histories and whole-exome sequencing (WES) of bulk and isolated leukaemic subpopulations. Our aims were to assess the proliferative hierarchy of LSCs and to examine their intrinsic genetic heterogeneity. We identified two functional LSC classes, quiescent and cycling, that are in equilibrium in the tumour and largely share the same clonal architecture. We further observed that genetic leukaemic clones appear to consist of a high number of individual LSCs, the majority of which exhaust upon serial transplantation. Finally, by genetic analyses of isolated leukaemic subsets, we were able to detect a specific enrichment for rare mutations in the quiescent compartment of two patient xenografts. Our data indicate that tumour evolution is sustained by the quiescent LSC pool and suggest that their highly proliferating counterpart has a finite lifespan. We expect that the results of our studies will provide new insights into the mechanisms of disease progression and treatment response in AML, and potentially reveal novel therapeutic approaches.

Les glioblastomes sont les tumeurs primitives cérébrales les plus fréquentes chez l’adulte et les plus agressives. L’objectif de cette thèse était de mieux comprendre l’hétérogénéité qui caractérise les glioblastomes et qui pourrait être en partie responsable de leur mauvais pronostic. Ainsi, nous avons mis en évidence une corrélation entre une localisation tumorale et un profil moléculaire particulier. De plus, l’utilisation de deux lignées cellulaires souches de glioblastomes établies au laboratoire, nous a permis de réaliser le criblage d’une banque chimique et de proposer la proscillaridine A, appartenant à la famille des glycosides cardiaques, comme un agent anti-tumoral potentiel. Par ailleurs, nous avons identifié une sialyltransférase, la ST8Sia III, comme responsable de la biosynthèse de l’antigène souche A2B5. La surexpression de la ST8Sia III par les cellules souches cancéreuses fait d’elle une possible cible thérapeutique. L’ensemble des travaux rapportés ici contribue à améliorer les connaissances sur la gliomagenèse, à proposer des cibles thérapeutiques potentielles et de nouvelles stratégies de traitement des glioblastomes
Glioblastomas are the most frequent and aggressive primary brain tumors in adult. This thesis aimed to better understand the heterogeneity that characterizes glioblastomas and which could be partly responsible for their poor prognosis. We highlighted a relationship between tumor location and a specific molecular profile. Further, using two glioblastoma stem cell lines, we realized the screening of a chemical library and we proposed the proscillaridin A, a cardiac glycoside, as a new anti-tumoral molecule. Besides, we identified a sialyltransferase, ST8sia III, which produces A2B5 antigen. Overexpression recording in cancer stem cells, suggested that ST8Sia III could be considered as a potential therapeutic target. All this work contributes towards a better understanding of gliomagenesis and points out potential therapeutic targets. At last, we propose new therapeutic strategies in glioblastoma

Les cellules cancéreuses ayant des propriétés souches, appelées cellules souches cancéreuses (CSCs), sont au sommet de l'organisation hiérarchique des tumeurs et sont soupçonnées d'être responsable des rechutes et de la formation de métastases. Cependant, nous nous sommes demandé comment ces cellules sont-elles capables de supporter le stress métabolique lié à l'oncogène et de croitre dans un environnement nutritif défavorable distinct de celui d'une tumeur établie ? Nous avons mis en évidence dans ce travail le rôle de la réponse aux glucocorticoïdes dans le contrôle de la plasticité mammaire et l'induction d'une plasticité métabolique nécessaire au maintien du potentiel tumorigène des CSCs. Nous avons montré qu'en régulant la reprogrammation cellulaire via l'induction du gène MAFB, les glucocorticoïdes contrôlent le caractère souche des cellules épithéliales malignes en activant la voie de biosynthèse des hexosamines. L'efficacité anabolique de ces cellules est alors augmentée, favorisant le développement de la tumeur et des métastases. Ensemble, nos résultats suggèrent que l'inhibition de l'activité métabolique des glucocorticoïdes pourrait être une stratégie pour éliminer les CSCs et traiter les tumeurs mammaires
Cancer cells with stemness properties - generally designated cancer stem cells (CSCs) - are at the apex of the hierarchical organisation of tumours and are believed to drive tumour recurrence and metastasis formation. However, how they perform these neoplastic activities in a nutritive environment that is distinct from the one in an established tumour is unknown. Here, we unveil the prominent role of glucocorticoid activity in the control of mammary cancer cell plasticity and the induction of metabolic pliancy necessary for the tumorigenic potential of CSCs. By regulating MAFB-dependent cell reprogramming, glucocorticoids control stemness traits in malignant epithelial cells. As an integral part of this regulation, glucocorticoids activate the hexosamine biosynthetic pathway and rewire the metabolism of CSCs. The anabolic efficiency of these cells increases then, fostering tumour and metastasis development. Together, our findings suggest that inhibition of glucocorticoid metabolic activity could be an original strategy for CSC eradication and tumour treatment

Amniotic fluid stem cells (hAFSC) are emerging as a potential therapeutic approach for various disorders. The low number of available hAFSC requires their ex vivo expansion prior to clinical use, however, during their in vitro culture, hAFSC quickly reach replicative senescence. The principal aim of this study was to investigate the aging process occurring during in vitro expansion of hAFSC, focusing on the redox control that has been reported to be affected in premature and physiological aging. My results show that a strong heterogeneity is present among samples that reflects their different behaviour in culture. I identified three proteins, namely Nox4, prelamin A and PML, which expression increases during hAFSC aging process and could be used as new biomarkers to screen the samples. Furthermore, I found that Nox4 degradation is regulated by sumoylation via proteasome and involves interactions with PML bodies and prelamin A. Since various studies revealed that donor-dependent differences could be explained by cell-to-cell variation within each patient, I studied in deep this phenomenon. I showed that the heterogeneity among samples is also accompanied by a strong intra-population heterogeneity. Separation of hAFSC subpopulations from the same donor, using Celector® technology, showed that an enrichment in the last eluted fraction could improve hAFSC application in regenerative medicine. One of the other problems is that nowadays hAFSC are expanded under atmospheric O2 concentration, which is higher than the O2 tension in their natural niches. This higher O2 concentration might cause environmental stress to the in vitro cultured hAFSCs and accelerate their aging process. Here, I showed that prolonged low oxygen tension exposure preserves different hAFSC stemness properties. In conclusion, my study pointed different approaches to improve in vitro hAFSC expansion and manipulation with the purpose to land at stem cell therapy.

L'incidence, le coût et l'issue fatale dans un nombre encore trop élevé de cas font du cancer un problème majeur en santé publique. Malgré les progrès réalisés dans le développement de thérapies ciblées, la plupart des cancers rechutent, vraisemblablement à cause de l'échappement des cellules souches cancéreuses (CSC) qui survivent et régénèrent la tumeur. L'enjeu clinique en cancérologie aujourd'hui est d'éliminer les cellules souches cancéreuses en épargnant les cellules souches normales. Pour atteindre cet objectif, il est primordial de comprendre leurs mécanismes spécifiques de transformation. Nous évaluons dans mon équipe de recherche l'implication du microenvironnement dans la transformation et la résistance des CSC épithéliales, à travers les effets de facteurs solubles et de contacts cellulaires : l'enzyme CD10, et la voie des BMPs (Bone Morphogenetic Proteins).Notre équipe étudie le rôle du dialogue permanent entre la CS normale et son microenvironnement qui régule la prolifération, et la survie des CS. Nous utilisons la glande mammaire et la prostate comme systèmes modèles car ces deux types d'épithélium présentent des similitudes, ce qui nous permet d'aborder la question de l'apparition et la résistance des CSC dans deux modèles tumoraux correspondants. Des dérégulations de la voie des BMPs, comme de l'enzyme CD10 sont observées dans ces tumeurs. Enfin, nous cherchons à comprendre comment les dérégulations de la voie des BMPs apparaissent, en s'intéressant principalement aux facteurs pouvant modifier directement le microenvironnement, tels que les polluants présents dans l'environnement (bisphénols, benzoapyrène)
It has been shown for a number of cancers that a cell population characterized by stem cell (SC) properties and therapeutic resistance is likely responsible for relapse several years after treatment. Current therapies kill most of the tumor cells, but fail to eradicate the so-called cancer stem cells (CSC). Therefore a complete cure of the disease will require the eradication of the tumor-sustaining CSC. We propose to study these CSC in the context of breast cancer as the existence of CSC as already been highlighted in this epithelia.CD10 is a membrane enzyme able to cleave several peptide of the microenvironment (such as oxytocin, bombesin, enkephalin.. ) that can also interact with intracellular signalling pathway through its direct interaction with PTEN. Our results, and those of the literature, indicate that CD10 enzyme controls the fate of SC and is deregulated in normal breast and cancerous tissues. We showed that CD10 membrane expression allows the maintenance of immature cells partly through its enzymatic function that inhibits mammary stem cells differentiation. As CD10 has been described in breast cancer initiation, progression and resistance, we then decided to test the role of CD10 in tumor context. Our strategy consists in flow cytometry cell sorting for CD10+/CD10- cells to compare the functional properties of both sub-population. Only CD10+ cells are able to regenerate both CD10+ and CD10- subpopulations, and CD10+ cells exhibit higher expression of immature genes. Interestingly, modulating CD10 using stable expression of CD10 in our models and Sh strategies do not mimick the normal functions of CD10, indicating that CD10 could be more a marker of a certain population with immature properties prone to transformation rather than a driver. To better characterize the role of CD10 in luminal breast transformation, we developed a new human mammary model, initiated from immature cells to obtain transformed luminal epithelial cells and their resistant counterpart. We observed a higher level of CD10 expression during mammary epithelial cell transformation process. We then performed a microarray on CD10+ and CD10- subpopulations. Preliminary analysis seems to confirm that CD10 is a potential marker for a stem cell population prone to transformation rather than a direct driver of the cell transformation

Les syndromes myélodysplasiques (SMD) forment un groupe de pathologies clonales de la cellule souche hématopoïétique (CSH) caractérisées par une hématopoïèse inefficace. La présence d’au moins une anomalie génétique (anomalie cytogénétique ou mutation somatique) est observée dans plus de 90% des cas. Ainsi, plusieurs clones moléculaires pouvaient coexister au moment du diagnostic de la maladie. Dans les SMD avec délétion du chromosome 5 (del(5q)), il a récemment été montré que les anomalies étaient présentes dès le stade de la CSH. Dans les SMD, la pénétrance des anomalies génétiques décrites est incomplète. De plus, peu de choses sont actuellement connues sur l’ordre d’apparition des mutations et leur impact fonctionnel sur les différents clones moléculaires dans le cas des SMD non-del(5q). Grâce au séquençage d’exome entier (WES) de patients ne présentant aucune mutation dans les gènes décrits dans les SMD, nous avons décrit l’existence de mutations dans les gènes BCOR et BCORL1, chez respectivement 4,2% et 0,8% des patients. Les mutations du gène BCOR arrivent tardivement au cours de l’évolution de la maladie et affectent le pronostic des patients. Des approches à l’échelle unicellulaire nous ont également permis d’observer que la majeure partie des mutations identifiées chez les patients sont retrouvées dès le stade CD34+CD38-. Chez les patients, plusieurs clones moléculaires coexistent à ce stade. De plus, les mutations des gènes de l’épissage et de la régulation épigénétique sont fréquemment acquises en premier dans les cellules hématopoïétiques les plus immatures des patients porteurs de SMD. Nous avons observé que certaines mutations, acquises secondairement, sont réparties inégalement dans les différents compartiments hématopoïétiques et peuvent avoir un impact sur la différenciation hématopoïétique. Enfin, nous montrons que la répartition des clones moléculaires évolue au cours du temps. En réponse au traitement par Lenalidomide, on observe également une évolution rapide de l’architecture clonale qui peut être liée au statut de réponse des patients. Ces résultats tendent à confirmer l’hétérogénéité génétique mais aussi fonctionnelle des SMD. Nous avons pu identifier de nouvelles mutations impliquées secondairement dans la physiopathologie des SMD. Il existe une dominance clonale précoce dans les SMD du fait de l’acquisition de toutes les mutations dans les cellules hématopoïétiques immatures. Cependant, les différentes populations hématopoïétiques peuvent présenter des génotypes différents. Enfin cette architecture est variable au cours de l’évolution de la maladie
Myelodysplastic syndromes (MDS) are a group of clonal disorders of the hematopoietic stem cell (HSC) characterized by ineffective hematopoiesis. At least one genetic abnormality (cytogenetic abnormality or somatic mutation) is observed in more than 90% of cases. Thus, it has been observed several molecular clones which could coexist at diagnosis of the disease. In MDS with deletion of chromosome 5 (del (5q)), it has recently been shown that defects were present in the HSC. In MDS, the penetrance of genetic abnormalities described is incomplete. In addition, little is currently known about the order of appearance of mutations and their functional impact on different molecular clones in the case of non-del (5q) MDS. Through the whole exome sequencing (WES) of patients without mutation in the genes described in MDS, we described the existence of mutations in genes BCOR and BCORL1, in respectively 4.2% and 0.8% of patients. Mutations in the gene BCOR were acquired lately during the course of the disease and affect the prognosis of patients. Approaches at the single cell level have also allowed us to observe that most of the mutations identified in patients are found at the immature differentiation stage CD34+CD38-. In patients, several molecular clones could coexist at this stage. In addition, mutations in gene splicing and epigenetic regulation are frequently first acquired in the most immature hematopoietic cells of MDS patients. We found that certain mutations, acquired in a second time, are distributed unevenly in different hematopoietic compartment and may have an impact on hematopoietic differentiation. Finally, we showed that the distribution of molecular clones evolves over time. In response to treatment with Lenalidomide, it has also been observed a rapid evolution of clonal architecture that can be linked to patient response status. These results tend to confirm the genetic but also functional heterogeneity in MDS. We have identified new mutations involved in the pathogenesis of MDS. We observed an early clonal dominance in MDS because of the acquisition of all mutations in immature hematopoietic cells. However, different hematopoietic populations can have different genotype. Finally, the architecture of mutations could be modifying during the course of the disease

Les glioblastomes (GBMs) sont des tumeurs cérébrales au pronostic défavorable. La résistance aux thérapies actuelles et la rechute des GBMs pourraient être due à l'existence de cellules aux propriétés souches. L'objectif de ma thèse a été la caractérisation des cellules souches de GBMs (CSGs) isolées à partir de tumeurs. L'analyse du profil souche et de pluripotence des CSGs a montré qu'elles sont maintenues dans un état souche par SOX2 et que COL1A1 et IFITM1 peuvent être des cibles thérapeutiques potentielles. L'étude de la radiosensibilité des CSGs à travers l'analyse des courbes de clonogénicité a mis en évidence deux groupes dont un «atypique» pouvant être composé de sous-populations de cellules aux radiosensibilités différentes qu'il conviendra de caractériser. L'étude de la réparation a mis en évidence deux autres groupes dont un ayant un fort potentiel de réparation qui exprime plus fortement le gène RAD51 après irradiations. Le traitement par un inhibiteur spécifique de RAD51 ralentirait la capacité de réparation de ces cellules. Malgré cette hétérogénéité, l'inhibition de la voie Hedgehog (HH) par un vecteur glucuronylé de la cyclopamine, activé par le microenvironnement tumoral, inhibe la prolifération et l'auto-renouvellement des CSGs in vitro et ralentit la croissance tumorale in vivo. La voie HH semble être une cible thérapeutique intéressante commune à toutes les CSGs. Néanmoins, il est nécessaire de prendre en compte l'hétérogénéité dans les populations tumorales pour le développement de la médecine personnalisée
Glioblastomas (GBMs) are brain tumors with a poor prognosis. Their resistance to current therapies and the occurrence of tumor relapse may be related to the existence of cells bearing stem cell characteristics. The aim of this PhD research was to characterize glioblastoma stem cells (GSCs) having been isolated from tumors. Analysis of the stemness and pluripotency profiles of GSCs indicated that their stemness states are maintained by SOX2 and that COL1A1 and IFITM1 may be potential therapeutic targets. Clonogenic studies of GSC radiosensitivity underscored the presence of two groups, one of them composed of sub-populations of cells with different degrees of radiosensitivity that have yet to be fully characterized. Study of DNA repair capacity highlighted two additional groups including one with high repair potential overexpressing the RAD51 gene after 4Gy. However, treatment with RAD51 inhibitor is likely to slow down repair of GSC lesions. Notwithstanding GSC heterogeneity, in our study inhibition of the Hedgehog pathway (HH) by a cyclopamine glucuronid prodrug, activated by the tumor microenvironment, inhibited in vitro proliferation and self-renewal in all the GSCs tested and slowed down tumor growth in vivo. Hence, HH pathway appears to be conserved among GSCs and constitutes an interesting potential therapeutic target. With regard to the development of personalized medicine, it is nevertheless highly advisable to take into account the pronounded heterogeneity of tumor populations

The natural daily cycles of light and dark have played a fundamental role in shaping the development of an adaptive intrinsic clock mechanism which allows organisms to coordinate the function of multiple organs by setting the correct circadian timing of cellular processes ensuring proper homeostasis. In mammalian skin, homeostasis is maintained by epidermal stem cells (epSCs). EpSCs localize to specialized niches where they undergo cycles of quiescence and proliferation. Several pathways are known to play essential roles in epSC function; however, how are these pathways spatiotemporally coordinated, and why not all stem cells within the niche behave in the same manner, is still poorly understood. We have analyzed the role of the molecular circadian clock in fine-­‐tuning the behavior of epidermal stem cells. Using a fluorescent circadian reporter mouse model, we demonstrate that the dormant epidermal stem cell compartment contains two co-­‐existing populations of stem cells in different clock states. Global comparative transcriptome analysis indicated that each clock population corresponds to a distinct predisposition state of response towards stem cell activating and dormancy cues. We provide evidence that the core circadian transcription factors BMAL1 and CLOCK bind to regulatory elements in the promoters of several of these stem cell homeostatic genes, thus being directly responsible for creating these two stem cell clock states. Unbalancing this clock driven equilibrium of epSCs in vivo resulted in progressive changes in the response of stem cells to activating or dormancy cues, which led to a progressive premature tissue aging, and a significant reduction in the development of cutaneous squamous cell carcinomas. Thus, our results indicate that the molecular clock machinery fine-­‐tunes the spatiotemporal behavior of epidermal stem cells within their niche, and that perturbation of this mechanism affects tissue homeostasis and the predisposition to neoplastic transformation.
Los ciclos naturales de luz y oscuridad han sido determinantes en el desarrollo de un reloj molecular intrínseco que permite coordinar la función de múltiples órganos para mantener la homeostasis global del organismo. La homeostasis del compartimento queratinocítico de la piel depende de una población de células troncales adultas epidermales (epSCs). Las epSCs están localizadas en nichos específicos y especializados desde dónde responden a las necesidades de repoblación celular del tejido mediante la alternancia de fases de quiescencia y proliferación. Varias rutas de señalización regulan el comportamiento de las epSCs; sin embargo, aún no entendemos bien porqué no todas las epSCs se comportan de la misma manera dentro de un mismo nicho troncal, y cómo están coordinadas a nivel espacio-­‐temporal. Hemos analizado el impacto del ritmo circadiano sobre las función de las epSCs. Mediante un ratón reportero fluorescente del ritmo circadiano hemos demostrado que el nicho troncal quiescente contiene dos poblaciones de epSCs en diferentes fases de su reloj molecular. El análisis comparativo global del transcriptoma de ambas poblaciones indicó que las dos poblaciones corresponden a dos estados opuestos de predisposición a responder a estímulos de activación y quiescencia. Mostramos resultados que demuestran que los factores de transcripción circadianos Bmal1 y Clock regulan directamente la expresión de genes que regulan el comportamiento de las epSCs. La arritmia in vivo en las epSCs resultó en una pérdida progresiva de la homeostasis tisular, un envejecimiento prematuro y una reducción significativa en el desarrollo de tumores escamosos de piel. Por lo tanto, nuestros resultados indican que la maquinaria del reloj molecular permite a las epSCs a anticiparse y coordinar su respuesta a estímulos locales del nicho, lo que constituye un mecanismo esencial para su correcta función en el tejido

RESUMO: Uma vasta diversidade celular pode ser observada no sistema nervoso animal. Na mosca da fruta são os neuroblastos (NB), células estaminais multipotentes, que geram todos os neurónios do indivíduo adulto. Estes dividem-se assimetricamente gerando células filhas que de seguida se dividem originando neurónios ou células da glia. Há mais de 30 anos que as linhagens de NBs são estudadas como modelo para entender os mecanismos moleculares básicos por detrás do desenvolvimento neuronal. Estudos mostram que diferentes genes ligados à especificação celular podem ser diferencialmente expressos entre as variadas linhagens. Como resultado, diferentes subtipos neuronais são então gerados a partir de cada NB. No entanto, ainda não temos um entendimento global de todas as instruções genéticas necessárias em cada linhagem para a construção do sistema nervoso central do adulto. De modo a contribuirmos para o seu estudo, recentemente o nosso laboratório revisitou a especificação da diversidade neuronal utilizando o método de sequenciação de célula-única, um método que permite a identificação de heterogeneidade celular. Neste trabalho, dados de sequenciação de célula-única de linhagens de NBs foram analisados com recurso a métodos bioinformáticos. Isto levou à identificação de todos os tipos celulares característicos das linhagens de NBs. Através da comparação dos perfis de expressão das várias categorias celulares, foi possível identificar múltiplos genes que se encontravam diferencialmente expressos ao longo da diferenciação das linhagens de NBs. Incluídos estavam vários genes conhecidos como estando envolvidos na especificação das linhagens de NBs, mas também alguns genes que ainda não foram estudados neste contexto. Além disto, também observámos uma notável heterogeneidade entre NBs e neurónios. Curiosamente, vários genes que foram identificados como estando diferencialmente expressos entre os NBs da larva, também apresentam este padrão no embrião. Isto apoia a ideia de que a identidade e os programas transcricionais das várias linhagens são conservados desde a fase de neurogénese do embrião até à larva. Por último, a expressão de alguns genes marcadores que tinham sido identificados como estando heterogeneamente expressos foi também validada in vivo. No geral, este trabalho poderá providenciar estudos futuros um mapa dos genes potencialmente envolvidos no desenvolvimento de linhagens de NBs e na criação da diversidade neuronal.
ABSTRACT: Vast cellular diversity can be observed in the animal nervous system. In the fruit fly, multipotent neural stem cells, neuroblasts (NB), represent the fundamental unit for the production of all neurons of the adult. These divide asymmetrically to give rise to daughter cells which then produce neurons or glia. For more than 30 years, Drosophila NB lineages have been a powerful model for neurodevelopmental studies, which has allowed the identification of conserved basic molecular mechanisms. Previous work has shown that various fate determinant genes are differentially expressed in between lineages, which results in the production of diverse sets of neurons by each NB in a stereotyped manner. However, we still lack a global understanding of all genetic instructions necessary in each lineage for the construction of the adult central nervous system. To try to contribute to this ultimate goal, our lab has revisited the specification of neuronal diversity through single-cell technologies, a powerful method to identify cellular heterogeneity. Specifically, in this work, we have curated a dataset of single-cell sequencing of larval NB lineages through bioinformatic methods. This allowed the identification of populations of cells that seem to match all the NB lineage cell types. By comparing the transcriptomic profiles of these cell types, we have identified multiple genes that become differentially expressed along NB lineage development. This included known NB lineage fate regulators, but also unstudied genes within this context. Furthermore, we have observed notable expression heterogeneity within NBs and neurons. Interestingly, we found that multiple genes differentially expressed between larval NBs show the same expression pattern in embryonic NBs. This supports the idea that NB lineage identity programs are conserved from embryo to larval neurogenesis. Finally, we have also validated in vivo the expression of a few marker genes which were found to be distinctively expressed among NBs. Overall, this work should provide future studies with a useful molecular blueprint of players potentially driving NB lineage development and the generation of neuronal diversity.

High-grade serous ovarian cancer (HG-SOC) is the most lethal gynecologic malignancy. Although most respond to initial therapy, the vast majority of patients eventually recur and die of their disease. Understanding intra-tumor cellular heterogeneity and inter-patient variability is necessary to effectively cure HG-SOC. The work described in this thesis should help to speed the progress of ovarian cancer research in several ways. First, I generated a robust xenograft model that recapitulates the cellular heterogeneity of HG-SOC. In addition, I performed gene expression profiling on a subset of xenografts and showed that they recapitulate the inter-patient diversity of this disease. Second, I applied this model to pre-clinical testing of a folate-targeted imaging agent and showed that it can identify metastatic studding by PET/CT and fluorescence imaging. Using my xenograft model, I investigated the properties of tumor-initiating cells (TIC) and demonstrated that TIC in HG-SOC are rare. Furthermore, although CD133 marks most TIC, heterogeneity in the phenotype is observed within individual tumors and between different patients. Finally, I used a transformative technology, CyTOF, to develop a novel pipeline for prioritization of candidate TIC markers, as well as for characterization of cellular heterogeneity in primary HG-SOC samples.

Prostate cancer (PCa) is heterogeneous containing phenotypically diverse cells. It is unclear whether these phenotypically different PCa cells are functionally distinct and possess divergent tumorigenic potential. Androgen signaling plays important roles in differentiation and survival of malignant PCa cells, and prostate specific antigen (PSA) as one of the androgen signaling target genes is used as a biomarker of AR signaling to assess tumor progression and evaluate therapeutic efficiency in clinic. Here we present evidence for discordant AR and PSA expression resulting in AR⁺/PSA⁺, AR⁺/PSA⁻, AR⁻/PSA⁻, and AR⁻/PSA⁺ PCa cells in human tumors. We also show that prostate tumor PSA mRNA levels inversely correlate with poor clinical outcomes and patient survival. By employing a lentiviral reporter system, we have fractionated bulk PCa cells into PSA⁺ and PSA⁻[superscript '/lo'] cell populations, with the former being AR⁺/PSA⁺ and the latter containing both AR⁺/PSA⁻ and AR⁻/PSA⁻ cells. The PSA⁺ and PSA⁻[superscript '/lo'] PCa cells demonstrate distinct molecular, cellular, and tumor-propagating properties. PSA⁻[superscript '/lo'] PCa cells are quiescent and refractory to stresses including androgen deprivation, exhibit high clonogenic potential, and possess long-term tumor-propagating capacity. They preferentially express stem cell genes and can undergo asymmetric cell division to generate PSA⁺ cells. Of great clinical interest, PSA⁻[superscript '/lo'] PCa cells can initiate robust tumor development and resist androgen ablation in castrated hosts, and they harbor highly tumorigenic castration resistant PCa cells. In contrast, PSA⁺ PCa cells possess more limited tumor-propagating capacity, undergo symmetric division, and are sensitive to castration. Systemic androgen levels dynamically regulate the relative abundance of PSA⁺/PSA⁻[superscript '/lo'] PCa cells in the tumors, which in turn impact the kinetics of tumor growth. Further studies reveal that the PSA⁻[superscript '/lo'] PCa cell population harbors several overlapping but nonidentical tumorigenic subsets including ALDH⁺, CD44⁺, and [alpha]2[beta]1⁺ cells and ALDH⁺CD44⁺[alpha]2[beta]1⁺ can further enrich castration resistant PCa cells. These observations together suggest that heterogeneous PCa cells are organized as a tumorigenic hierarchy. Our results have important implications in understanding how different subpopulations of PCa cells manifest differential responses to current androgen deprivation therapy (ADT).
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Tese de doutoramento do Programa Interuniversitário de Doutoramento em Envelhecimento e Doenças Crónicas, apresentada à Faculdade de Medicina da Universidade de Coimbra
Glioblastoma (GBM) is the most malignant primary tumor of the central nervous system. Despite all efforts, the median survival time for GBM patients remains approximately between 12 to 15 months under therapy. GBM is a diffuse astrocytoma, highly proliferative, angiogenic, and locally invasive, that develops resistance to the alkylating agents used in chemotherapy, such as temozolomide (TMZ), which is considered part of the gold standard treatment. This limited success appears to be related with several mechanisms, namely: 1) the occurrence of gene mutations, that cause permanent activation and/or inhibition of several molecular signalling pathways involved in tumor growth and proliferation, such as protein kinase C (PKC) activation, cell survival, tumor suppressor genes and apoptosis; 2) the presence of a population of cells known to be chemo and radioresistant, the glioma stem-like cells (GSCs), that are responsible for generating tumor heterogeneity and recurrence after therapy, and; 3) the inexistence of a specific therapeutic target for non-GSCs and GSCs that would permit the development of more specific therapeutic approaches for this neoplasia. Therefore, in this work we aimed to: 1) study the PKC activation contribution to the aggressiveness of GBM, emphasizing the importance of combined therapeutic protocols, including TMZ with PKC inhibitors, namely tamoxifen (TMX); 2) characterize the GSCs and study their plasticity to understand glioma stem-like cells state and its differentiation properties, in order to contribute to the prevention of tumor recurrence; and 3) evaluate the potential of specific cell surface markers as therapeutic targets to non-GSCs and GSCs, allowing the accessibility of therapeutic agents most exclusively to the tumor niche, by a liposome-mediated drug delivery approach. First, using two GBM cell lines, the U87 and U118 cells, we observed that the combination of TMX and TMZ alters the phosphorylation status of PKC, by western blot. We found that TMX is an inhibitor of the p-PKC and that this combination is more effective in the reduction of proliferation and in the increase of apoptosis than each drug alone, by flow cytometry, which presents a new therapeutic strategy in GBM treatment. We then concluded that the combination of TMX and TMZ seems to potentiate the effect of each other in GBM cell lines. In order to study the heterogeneity between GBM cells and further understand the variability in the chemotherapeutic response, we next isolated and characterized a human GBM cell line, termed GBM11, obtained by surgical biopsy from a patient bearing a recurrent GBM, and compared the effect of TMX in monotherapy and in combination with TMZ on this GBM cell line with that observed in U87 and U118 cell lines. We observed that the effect of TMX plus TMZ or with TMX alone on GBM11 cells proliferation, death or migration capability, by flow cytometry and scratch assays, was similar, suggesting that, for recurrent tumors, the best choice of second-line treatment may be TMX alone, which may also reduce putative side effects of combined treatment with TMZ. The chemo- and radioresistance of GBM are also due to GSCs which contribute to tumor growth and relapse, highlighting this cell population as a main focus for GBM therapeutic research. We considered that the understanding of GBM stem state plasticity is of utmost importance to identify the mechanisms involved in GSCs resistance to therapy, which may justify tumor recurrence and so, constitute a step forward to the identification of new approaches to treat GBM. Our results demonstrated that, in four GBM cell lines and in the respectively GSC lines, the plasticity of the GBM stem-like cell state is based on the modulation of specific markers expression associated with this state, such as SOX2 or as Connexin 46 and 43, through immunofluorescence, western blot and PCR real time assays. Moreover, by immunohistochemistry analyses, we observed that this dynamic expression is in accordance with the upregulation of these stem-like cell markers in human samples of higher glioma grades, namely GBM, compared to lower grades, suggesting a direct correlation with the poor prognosis of GBM patients. As so, due to the plasticity of the stem-like cells status, the strategy of targeting both GSCs and non-GSCs may represent a promising approach in order to overcome tumor aggressiveness, and eventually to avoid the known chemotherapeutic side effects, which could improve the survival time and quality of life of GBM patients. In this regard, we next evaluate the potential of the cell surface nucleolin (NCL), described as overexpressed in cancer cells, as a target to specifically recognize non-GSCs and GSCs, taunting a possible therapeutic target for drug delivery in two different GBM cell lines. For that, we used a previously designed F3-peptide-targeted sterically stabilized pH-sensitive liposome (SLpH), which specifically recognizes nucleolin, as a tool to target overexpressed-nucleolin cells. Overall, we showed that NCL overexpression ensures an efficient drug delivery in both cells with stem-like and non-stem-like phenotypic characteristics, by flow cytometry assays, which could validate NCL as a potential therapeutic target in GBM. Altogether, our results showed: 1) a synergistic effect of TMX and TMZ in GBM cell lines and a more efficient effect of TMX alone in recurrent GBM compared to the combined therapy; 2) the plasticity of stem-like cell state through the reversibility of stem-like cell markers expression, and the identification of putative markers associated with this reversibility, the SOX2 and Cx46 and 43, which constitutes a step closer to the understanding of stem cell behaviour; and 3) that the success of targeting both non-GSCs and GSCs, through the nucleolin target, may be the basis for developing a specific treatment for GBM.
O Glioblastoma (GBM) é o tumor primário mais maligno do sistema nervoso central. Apesar de todos os esforços, o tempo médio de sobrevivência para doentes com GBM permanece aproximadamente entre os 12 a 15 meses sob terapia. O GBM é um astrocitoma difuso, altamente proliferativo, angiogénico e localmente invasivo, que desenvolve resistência aos agentes alquilantes utilizados na quimioterapia, como a temozolomida (TMZ), que é considerada parte do tratamento padrão. Este sucesso limitado parece estar relacionado com vários mecanismos, tais como: 1) a ocorrência de mutações genéticas que causam ativação permanente e / ou inibição de várias vias de sinalização molecular envolvidas no crescimento e proliferação de tumores, como a ativação da proteína cínase C (PKC), na sobrevivência celular, na inibição de genes supressores de tumores e apoptose; 2) a presença de uma população de células conhecidas como quimio- e radiorresistentes, as células de glioma do tipo estaminal (GSCs), que são responsáveis ​​pela heterogeneidade tumoral e recorrência após a terapia e; 3) a inexistência de um alvo terapêutico para não-GSCs e GSCs que permita o desenvolvimento de abordagens terapêuticas mais específicas para esta neoplasia. Assim, neste trabalho, objetivámos: 1) estudar a contribuição da ativação da PKC para a agressividade do GBM, enfatizando a importância de protocolos terapêuticos combinados, incluindo a TMZ com inibidores de PKC, nomeadamente o tamoxifeno (TMX); 2) caraterizar as GSCs e estudar a plasticidade das propriedades destas células estaminais do GBM, no sentido de compreender o estado estaminal do glioma e, consequentemente, entender as propriedades de diferenciação, contribuindo para a recorrência do tumor; e 3) avaliar o potencial de marcadores de superfície celular específicos, como alvos terapêuticos para as não-GSCs e GSCs, a fim de permitir a acessibilidade de agentes terapêuticos mais exclusivamente ao nicho do tumor, por meio de uma abordagem de administração de fármacos mediada por lipossomas. Inicialmente, usando duas linhas celulares de GBM, a U87 e a U118, observámos que a combinação de TMX e TMZ altera o estado de fosforilação da PKC, por western blot. Descobrimos que o TMX é um inibidor da p-PKC e que esta combinação é mais eficaz na redução da proliferação e no aumento da apoptose do que cada fármaco em monoterapia, através de ensaios de citometria de fluxo, o que pode representar uma nova estratégia terapêutica no tratamento do GBM. Concluímos, então, que a combinação de TMX e TMZ potencializa o efeito entre si nas linhas celulares de GBM. No sentido de estudar a heterogeneidade entre células de GBM e compreender melhor a variabilidade da resposta à quimioterapia, isolámos e caracterizámos uma linha celular de GBM humana, denominada GBM11, obtida através de uma biópsia cirúrgica de um doente com glioblastoma recorrente, e comparámos o efeito do TMX em monoterapia e em combinação com a TMZ, nesta linha celular, com o observado nas linhas celulares U87 e U118. Na verdade, observámos que o efeito do TMX e TMZ ou do TMX sozinho nas células de GBM11 sobre a proliferação celular, morte ou capacidade de migração, através de ensaios de citometria de fluxo e migração, era semelhante, o que pode sugerir que, para os tumores recorrentes, como o caso do GBM11 previamente tratado com TMZ, a melhor escolha do tratamento de segunda linha pode ser apenas TMX, a fim de reduzir os efeitos secundários putativos do tratamento combinado com TMZ. A quimio- e a radiorresistência do GBM devem-se, também, à existência de GSCs, que contribuem para o crescimento tumoral e recorrência destacando-se, assim, esta população celular como o foco principal da investigação terapêutica no GBM. Consideramos que a compreensão da plasticidade do estado estaminal no GBM é de extrema importância para identificar os mecanismos e fatores envolvidos na resistência das GSCs à terapia, o que pode justificar a recorrência do tumor e, portanto, constituir um progresso na identificação de novas abordagens terapêuticas. Os nossos resultados demonstraram, em quatro linhas celulares de GBM e nas respetivas linhas de GSCs, a plasticidade do estado estaminal com base na modulação da expressão de marcadores específicos associados, tais como o SOX2 e outros marcadores como a Conexina 46 e 43, através de ensaios de imunofluorescência, western blot e PCR em tempo real. Além disso, através de ensaios de imunohistoquímica, verificámos que essa expressão dinâmica está de acordo com a regulação positiva destes marcadores celulares em graus superiores de amostras humanas de glioma, nomeadamente no GBM, comparativamente a graus inferiores, sugerindo uma correlação direta com o mau prognóstico de doentes com GBM. Assim, devido à plasticidade do estado estaminal, a estratégia de atingir designadamente ambas as GSCs e não-GSCs pode representar uma abordagem importante no sentido de diminuir a agressividade do tumor e, eventualmente, evitar os efeitos colaterais quimioterapêuticos conhecidos, o que pode melhorar o tempo e a qualidade de vida de doentes com GBM. Neste sentido, avaliámos o potencial da nucleolina (NCL) de superfície celular, descrita como estando sobre-expressa nas células tumorais, como um alvo terapêutico para o reconhecimento específico de ambas as não-GSCs e GSCs, contribuindo para a entrega direcionada de fármacos encapsulados em nanopartículas, em duas linhas celulares de GBM. Para isso, utilizámos um lipossoma previamente desenhado, sensível ao pH e estericamente estabilizado, contendo na sua constituição um péptido F3, capaz de reconhecer especificamente a nucleolina constituindo, assim, uma ferramenta- alvo para as células com sobre-expressão de nucleolina. Em suma, demostrámos que a sobre-expressão de nucleolina per se pode identificar ambas as não-GSCs e GSCs, através de ensaios de citometria de fluxo, mediando a entrega direcionada intracelular, o que pode validar a NCL como um potencial alvo terapêutico no GBM. Em conclusão, o presente estudo demonstrou: 1) um efeito sinergístico do TMX e TMZ em linhas celulares de GBM e um efeito mais eficiente do TMX em monoterapia numa situação de GBM recorrente em comparação com a terapia combinada; 2) a plasticidade do estado estaminal através da reversibilidade da expressão dos marcadores de células do tipo estaminal e a identificação de dois marcadores putativos associados a essa reversibilidade, o SOX2 e a Cx46 e 43, constituindo um passo mais próximo na compreensão do comportamento das células estaminais; e 3) que o sucesso em atingir especificamente células não-GSCs e GSCs, através da sobre-expressão de nucleolina, poderá ser a base de desenvolvimento de um tratamento específico para o GBM.
Conselho Nacional de Desenvolvimento Tecnológico (CNPq), Brasil; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brasil; Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ); Pró-Saúde - Associação Beneficente de Assistência Social e Hospitalar, Brasil; FEDER/COMPETE/ FCT PTDC/EBB-EBI/120634/2010 e PDTC/QUI-BIQ/120652/2010

Glioblastoma (GBM) is the most common high-grade brain tumor diagnosed in patients who are more than 50 years of age. The standard of care treatment is surgery, followed by radiotherapy and chemotherapy. The median life expectancy of patients is only between 12 to 15 months after receiving current treatment regimes. Hence, identification of new therapeutic compounds and gene targets are highly warranted. This thesis describes four interlinked studies to attain this goal. In study 1, we explored drug combination effects in a material of 41 patient-derived GBM cell (GC) cultures. Synergies between three compounds, pterostilbene, gefitinib, and sertraline, resulted in effective killing of GC and can be predicted by biomarkers. In study 2, we performed a large-scale screening of FDA approved compounds (n=1544) in a larger panel of GCs (n=106). By combining the large-scale drug response data with GCs genomics data, we built a novel computational model to predict the sensitivity of each compound for a given GC. A notable finding was that GCs respond very differently to proteasome inhibitors in both in-vitro and in-vivo. In study 3, we explored new gene targets by RNAi (n=1112) in a panel of GC cells. We found that loss of transcription factor ZBTB16/PLZF inhibits GC cell viability, proliferation, migration, and invasion. These effects were due to downregulation of c-MYC and Cyclin B1 after the treatment. In study 4, we tested the genomic stability of three GCs upon multiple passaging. Using molecular and mathematical analyses, we showed that the GCs undergo both systematic adaptations and sequential clonal takeovers. Such changes tend to affect a broad spectrum of pathways. Therefore, a systematic analysis of cell culture stability will be essential to make use of primary cells for translational oncology. Taken together, these studies deepen our knowledge of the weak points of GBM and provide several targets and biomarkers for further investigation. The work in this thesis can potentially facilitate the development of targeted therapies and result in more accurate tools for patient diagnostics and stratification.

Glioblastoma is the commonest form of brain neoplasm and among the most malignant forms of cancer. The identification of a subpopulation of self-renewing and multipotent cancer stem cells within glioblastoma has revealed a novel cellular target for the treatment of this disease. The role of developmental cell signaling pathways in these cell populations remains poorly understood. Herein, we examine the role of the Notch signaling pathway in glioblastoma stem cells. In this thesis we have demonstrated that the canonical Notch pathway is active in glioblastoma stem cells and functions to inhibit neuronal lineage commitment in a subset of patient derived glioblastoma stem cells in vitro. Gamma secretase (γ-secretase) small molecule inhibitors or dominant-negative co-activators inhibit glioblastoma stem cell proliferation and induce neuronal lineage commitment in a fashion that synergizes with Wingless pathway activation via GSK-3β blockade. Our data suggest that subsets of patient samples show a Notch gene expression profile that predicts their abilities to undergo neuronal lineage differentiation in response to γ-secretase small molecule inhibitors. Additionally, the data suggests that Notch may perturb the relative fractions of cells undergoing symmetric division, in favour of asymmetric division, limiting clonal expansion from single cells. These data may have important implications for treating human glioblastoma, and suggest that in addition to inhibition of proliferation, influencing lineage choice of the tumor stem cells may be a mechanism by which these tumors may be pharmacologically inhibited.

Like with many cancers, a single ovarian tumor can display remarkable diversity in genetics, epigenetics, expression profiles, microenvironment and cell differentiation and plasticity. This so-called intratumoral heterogeneity (ITH) is thought to greatly increase mortality by enabling tumors to adapt quickly to therapy, metastasize, and recur, thus the study of ITH holds great clinical significance. Clonal evolution and cancer stem cell (CSC) theory are two models for the initiation and propagation of a tumor, which offer differing views on the way that ITH is developed and maintained. In the clonal evolution model, cancer arises from a single cell and, through genetic instability, proliferates into a diverse population of daughter cells, which develop additional mutations and undergo Darwinian selection under the influence of the tumor microenvironment. Each cell of the clonal evolution model may be capable of initiating a tumor independently. In CSC theory, cancer arises from the transformation of a stem cell that has the capacity to self-renew and differentiate into a diverse population of daughter cells. Each cell is NOT capable of tumorigenesis as most are terminally differentiated and do not harbor self-renewing capabilities. According to CSC theory, small, rare subpopulations of CSCs persist throughout chemotherapy and are responsible for repopulating the heterogeneous tumor post-treatment. The hypothesis that CSCs may play a role in ovarian cancer progression is the subject of this thesis. Many studies have detected the presence of stem cell markers and dysregulated stem cell signaling pathways in ovarian cancer, but doubts remain as to the existence of ovarian CSCs; critics have pointed out inherent flaws in experimental designs meant to identify and characterize CSCs. For example, the presence of cancer cells which express the stem cell marker CD133 has been correlated to both positive and negative impacts on prognosis. Further challenging the study of ovarian CSCs is the lack of consensus on the true cell of origin for ovarian cancer - whether it be from the fallopian tube epithelium or ovarian surface epithelium, or elsewhere in the peritoneal cavity - this will have important implications for the identification and characterization of tumorigenic ovarian CSCs. Advocates of clonal evolution theory have put forth incredible effort to reveal the extent of inter and intra-tumoral heterogeneity in ovarian cancer, and from these data there has arisen a general consensus that cancer cell populations do evolve in a step-wise fashion, accumulating additional mutations over time. The involvement of cancer stem cells in this progression and how exactly they fit in (as a cell of origin or arising from genetic mutations), as well as their significance for different cancer types, is a question worth answering. Despite the challenges facing the study of ovarian CSCs, the clinical impact of cells with stem-like properties has been repeatedly demonstrated, especially with regard to metastatic processes and chemoresistance. Moreover, new drugs which target stem cell pathways have proven effective in the treatment of ovarian cancer. The existence of a rare subset of cells that have enhanced tumor-initiating properties is apparent in ovarian cancer, and more work is needed to characterize the unique identifiers and behavior of these cells in vivo. Future experiments involving lineage tracing promise to deepen our understanding of the nature of ovarian CSCs and address whether normal stem cells might serve as the cell of origin.

Dissertação de mestrado em Bioinformática
Cell behavior differs even under identical micro-environmental conditions, resulting in cell heterogeneity. This phenomenon can transform a well producing bacterial population which is exposed to production-like stress conditions into subpopulations with reduced or even stopped product formation properties. As a step towards understanding population heterogeneity it is necessary to apply sophisticated techniques, such as a combination of fluorescence activated cell sorting (FACS) and mass spectrometry (MS) resulting in proteomic information on the subpopulation level rather than on the whole population level. The proteome of Pseudomonas putida KT2440 subpopulations were analysed in standard conditions (μ=0.2 h-1) using R and Bioconductor that will serve as basis for comparison of non-stressed to stressed conditions to find optimization targets to reduce cell-to-cell variability and improved productivity. Here, the differences in subpopulations at different growth rates (μ=0.1 h-1, μ=0.2 h-1 and μ=0.7 h-1) were investigated. The second part of the thesis included the investigation of tolerance levels of P. putida to biofuels precursors, for a successful establishment of the experimental set-up of stress conditions on P. putida cultures. Flow cytometry analysis showed the existence of a two subpopulations at each growth rate: a one chromosome equivalent (C1n) and a two chromosome equivalent (C2n) subpopulation at μ=0.1 h-1 and μ=0.2 h-1 and at μ=0.7 h-1it was possible to see a subpopulation with two chromosome equivalent (C2n) and an additional subpopulation with multiple chromosome equivalents (CXn). The statistical analysis on proteomic data and the experiments on phase two showed that P. putida KT2440 is very stable metabolically and it can tolerate solvents better than other industrial host systems. Therefore it can be concluded that P. putida KT2440 could be a promising candidate for a microbial cell factory chassis for industrial processes involving solvent production or 2 phase cultivation systems.
O comportamento das células pode variar até com pequenas alterações no microambiente, podendo originar heterogeneidade celular. Este fenómeno pode converter populações bacterianas com elevada capacidade de produção em subpopulações onde a taxa de produtividade pode diminuir drasticamente ou até parar por completo. Para esclarecer a heterogeneidade a nível bacteriano é necessário utilizar técnicas sofisticadas como a combinação da seleção de células ativadas por fluorescência (FACS) e espectrometria de massa (MS) originando dados de proteómica a nível das subpopulações bacterianas, e não apenas ao nível da população. O proteoma das subpopulações de Pseudomonas putida KT2440 foi analisado em condições padrão (μ=0.2 h-1) usando o R e o Bioconductor que servirá como base para a comparação dos resultados das condições padrão e as condições de stresse para encontrar novas metas de otimização para reduzir a variabilidade entre subpopulações e melhorar a produtividade a nível industrial. Desta forma, diferentes taxas de crescimento foram testadas (μ=0.1 h-1, μ=0.2 h-1 and μ=0.7 h-1) nas diferentes subpopulações. A segunda parte da tese inclui a investigação de níveis de tolerância de P. putida a precursores para a produção de biocombustíveis, para ajudar a estabelecer as condições de stresse. A análise da citometria de fluxo mostrou a existência de duas subpopulações em cada taxa de crescimento testada: subpopulação com um cromossoma equivalente (C1n) e uma subpopulação com dois cromossomas equivalente (C2n) foram encontradas nas taxas de crescimento de μ=0.1 h-1 e μ=0.2 h-1. Na taxa de crescimento de μ=0.7 h-1 foi possível ver uma subpopulação com dois cromossomas equivalente (C2n) e uma subpopulação adicional com vários cromossomos equivalente (CXn). A análise estatística dos dados de proteómica bem como os resultados da fase dois mostraram que P. putida KT2440 é muito estável metabolicamente e pode tolerar solventes melhor que outras bactérias. Portanto, pode concluir-se que P. putida KT2440 pode ser um candidato promissor para processos industriais que envolvem a produção de solventes.