Culturas de células primárias diferem de acordo com as condições ambientais nas quais se encontra o doador. Recentemente demonstramos que o ciclo claro/escuro impõe um programa molecular hereditário em cultura celular. Com o intuito de investigar os mecanismos moleculares da memória celular, no presente trabalho isolamos células progenitoras CD133+ de explante de músculo cremaster e investigamos se a expressão de microRNAs (miRNAs), resulta em fenótipos diferentes de acordo com o ciclo claro/escuro. O sequenciamento global de miRNAs utilizando a plataforma SOLiD 4 e analisado pelos programas EdgeR, TargetScan e Metacore resultou na identificação de 541 miRNAs maduros, os quais apresentam dois perfis de expressão distintos de acordo com a hora de obtenção das culturas. miR-1249 e miR-129-2-3p são mais expressos em células obtidas durante o dia e favorecem a manutenção da pluri/multipotência celular. Já células obtidas à noite expressam maior conteúdo dos miR-182, miR-96-5p, miR-223-3p, miR-146a-3p e miR-146a-5p resultando na inibição da resposta inflamatória e no favorecimento da maturação celular quando comparadas às células obtidas de dia. A análise funcional da inibição da resposta inflamatória em células obtidas à noite foi confirmada por PCR array que revelou na menor expressão de genes relacionados à via de sinalização TLR/NF-κB, incluindo Traf6, um alvo do miR-146a. Além disso, a translocação nuclear de NF-κB é reduzida à noite e é inversamente proporcional ao nível de melatonina plasmática. Demonstramos ainda que a melatonina in vitro favorece o estado de pluripotência celular por aumentar a expressão de CD133, miR-1249 e miR-129-2-3p. No entanto, esse efeito depende do contexto celular visto que a expressão de receptores de melatonina também varia de acordo com a hora de obtenção da cultura. Em conjunto, nossos dados sugerem que o ciclo claro/escuro interfere no perfil de expressão de miRNAs e impõe uma variação no fenótipo de células progenitoras CD133+ / The phenotype of primary cells in culture varies according to the donor environmental condition. We have recently shown that the light/dark cycle impose a molecular program that is hereditable in culture. In order to evaluate the molecular mechanisms of cellular memory, here we isolated CD133+ progenitor cells from cremaster muscle explants and investigated whether the expression of microRNAs (miRNAs), could result in different phenotypes according the phase of ligh/dark cycle when cells were obtained. The global miRNA sequencing using SOLiD4 Platform, and analyzed by EdgeR, TargetScan and MetaCore, revealed the expression of a total of 541 mature miRNAs, and two distinct miRNAs signatures according to the hour when cells were obtained. miR-1249 and miR-129-2-3p are more expressed during daytime and favor the maintenance of cellular pluri/multipotency. Nighttime cells express higher amounts of miR-182, miR96-5p, miR-223-3p, miR-146a-3p and miR-146a-5p that inhibit the inflammatory response and favor the cellular maturation when compared to daytime cells. The functional analysis of the inflammatory response inhibition during nighttime was confirmed by PCR array and revealed lower expression level of genes related to TLR/NF-κB pathway, including Traf6, a putative target mRNA of miR-146a. Additionally, the nuclear translocation of NF-κB is reduced in nighttime cells and it is inversely correlated to the nocturnal the plasma level of melatonin. We also showed that melatonin in vitro favors the cellular pluri/multipotency, increasing CD133, miR-1249 and miR-129-2-3p expression. However, this effect depends on cellular context, as the expression of melatonin receptors also shows a daily variation. Altogether, our data suggest that the light/dark cycle interferes on miRNAs expression profile and imposes a rhythmic phenotype variation in CD133+ cells

Culturas de células primárias diferem de acordo com as condições ambientais nas quais se encontra o doador. Recentemente demonstramos que o ciclo claro/escuro impõe um programa molecular hereditário em cultura celular. Com o intuito de investigar os mecanismos moleculares da memória celular, no presente trabalho isolamos células progenitoras CD133+ de explante de músculo cremaster e investigamos se a expressão de microRNAs (miRNAs), resulta em fenótipos diferentes de acordo com o ciclo claro/escuro. O sequenciamento global de miRNAs utilizando a plataforma SOLiD 4 e analisado pelos programas EdgeR, TargetScan e Metacore resultou na identificação de 541 miRNAs maduros, os quais apresentam dois perfis de expressão distintos de acordo com a hora de obtenção das culturas. miR-1249 e miR-129-2-3p são mais expressos em células obtidas durante o dia e favorecem a manutenção da pluri/multipotência celular. Já células obtidas à noite expressam maior conteúdo dos miR-182, miR-96-5p, miR-223-3p, miR-146a-3p e miR-146a-5p resultando na inibição da resposta inflamatória e no favorecimento da maturação celular quando comparadas às células obtidas de dia. A análise funcional da inibição da resposta inflamatória em células obtidas à noite foi confirmada por PCR array que revelou na menor expressão de genes relacionados à via de sinalização TLR/NF-κB, incluindo Traf6, um alvo do miR-146a. Além disso, a translocação nuclear de NF-κB é reduzida à noite e é inversamente proporcional ao nível de melatonina plasmática. Demonstramos ainda que a melatonina in vitro favorece o estado de pluripotência celular por aumentar a expressão de CD133, miR-1249 e miR-129-2-3p. No entanto, esse efeito depende do contexto celular visto que a expressão de receptores de melatonina também varia de acordo com a hora de obtenção da cultura. Em conjunto, nossos dados sugerem que o ciclo claro/escuro interfere no perfil de expressão de miRNAs e impõe uma variação no fenótipo de células progenitoras CD133+ / The phenotype of primary cells in culture varies according to the donor environmental condition. We have recently shown that the light/dark cycle impose a molecular program that is hereditable in culture. In order to evaluate the molecular mechanisms of cellular memory, here we isolated CD133+ progenitor cells from cremaster muscle explants and investigated whether the expression of microRNAs (miRNAs), could result in different phenotypes according the phase of ligh/dark cycle when cells were obtained. The global miRNA sequencing using SOLiD4 Platform, and analyzed by EdgeR, TargetScan and MetaCore, revealed the expression of a total of 541 mature miRNAs, and two distinct miRNAs signatures according to the hour when cells were obtained. miR-1249 and miR-129-2-3p are more expressed during daytime and favor the maintenance of cellular pluri/multipotency. Nighttime cells express higher amounts of miR-182, miR96-5p, miR-223-3p, miR-146a-3p and miR-146a-5p that inhibit the inflammatory response and favor the cellular maturation when compared to daytime cells. The functional analysis of the inflammatory response inhibition during nighttime was confirmed by PCR array and revealed lower expression level of genes related to TLR/NF-κB pathway, including Traf6, a putative target mRNA of miR-146a. Additionally, the nuclear translocation of NF-κB is reduced in nighttime cells and it is inversely correlated to the nocturnal the plasma level of melatonin. We also showed that melatonin in vitro favors the cellular pluri/multipotency, increasing CD133, miR-1249 and miR-129-2-3p expression. However, this effect depends on cellular context, as the expression of melatonin receptors also shows a daily variation. Altogether, our data suggest that the light/dark cycle interferes on miRNAs expression profile and imposes a rhythmic phenotype variation in CD133+ cells

The cancer stem cell (CSC) theory proposes that a minor population in tumor cells with specific features, such as self-renewal and reproducible tumor phenotype could contribute to tumor relapse and chemotherapy resistance. Several studies have convincingly documented the existence of ovarian CSC, but questions related to the biologic behavior and specific biomarkers of ovarian CSC remain to be clarified. In the present study, we firstly established a tumor cell line with capability of regenerating tumors through serial transplantation of ovarian tumor tissue in non-obese/severe combined immunodeficient (SCID) mice. After separation of CD133+ cells with magnetic beads, we compared the phenotype and biologic behavior of CD133+ versus CD133-cells. It was found that the CD133+ cells were much more potent to produce colonies in semi-solid agar culture than CD133-cells. The proportion of the cells in G0/1 cell cycle is much higher in CD133+ cells than in CD133-cells. Furthermore, in vivo experiments demonstrated that the CD133+ cells were capable of repeatedly regenerate tumors in NOD/SCID mice, while the CD133-cells were not. Compared with CD133-cells, the CD133+ cells expressed much higher levels of the stem cell markers Oct4, Sox2, Nanog and Mcl-1. Clinically, among a total of 290 ovarian epithelial cancers, increased level of CD133 expression was positively correlated with a high cancer stage and had a worse 5-year survival rate. Taken together, the results suggest that the CD133+ cells from human ovarian cancer have the characteristics of CSC, which may contribute to ovarian cancer relapse and anti-apoptotic activity. The method of ovarian CSC enrichment we established provides a feasible and practical way of ovarian cancer research in a molecular level. In addition, CD133 may be used as a prognostic marker for ovarian epithelial cancer, which may have a role for future therapeutic effect.

Pre-clinical studies suggest that granulocyte-colony stimulating factor (GCSF) holds promise for the treatment of ischaemic heart disease (IHD). However, its safety and efficacy in this setting, and in particular in patients with chronic refractory 'no-option' IHD, is unclear. Therefore, a clinical study was initiated in 20 such 'no-option' patients, with the aim of assessing the safety and efficacy of both G-CSF administration, and also, that of an intracoronary infusion of G-CSF mobilised CD133+ cells. The study involved initial baseline cardiac ischaemia assessment (symptom based questionnaire, exercise stress test (EST), nuclear Sestamibi (MIBI) and dobutamine stress echocardiographic (DSE) imaging). Stable 'no-option' IHD patients then received open-label G-CSF commencing at 10μg/kg s/c for five days, with an EST on days four and six (to facilitate myocardial cytokine generation and stem cell trafficking). After three months, cardiac ischaemia assessment and the same regimen of G-CSF and ESTs were repeated, but in addition, leukapheresis and then a randomised double-blinded intracoronary infusion of CD133+ or unselected cells were performed. Final cardiac ischaemia assessment was three months thereafter. Eighteen male and two female subjects (mean age 62.4) were enrolled. Eight events occurred that fulfilled pre-specified 'adverse event' criteria: four ischaemic (troponin positive) episodes, two episodes of transient thrombocytopaenia (one profound), one episode of gout and one unscheduled hospitalisation for exhaustion. Troponin was positive on 17 further occasions (all CK-MB negative), however, at these instances angina severity was identical to baseline. Importantly, no adverse event(s) resulted in any detectable long-term adverse sequelae for any subject. From baseline to final follow-up, the administration of two cycles of G-CSF was associated with statistically significant improvements in a range of subjective outcomes, including anginal symptoms, quality of life and EST performance (all p < 0.005). However, the objective MIBI and DSE scans showed only trends towards improvement (all p > 0.1). Compared to unselected cells, an intracoronary infusion of CD133+ cells did not improve either subjective or objective outcomes. In conclusion, administering G-CSF to patients with refractory 'no-option' IHD warrants careful monitoring, but may be performed with safety. A larger, randomised double-blind placebo-controlled trial of G-CSF in these patients appears warranted.

The AC133 epitope of the pentaspan transmembrane glycoprotein CD133 has been used as a cell-surface marker for normal and cancer stem cells from a broad range of tissue types. Despite the utility of CD133 as a marker, little is known regarding its regulation and biological function. To study these poorly understood aspects of CD133, I took two main experimental approaches: RNA interference (RNAi) screening and affinity purification coupled with mass spectrometry (AP-MS) to identify CD133 regulatory genes and CD133 protein-protein interactions (PPIs), respectively. Both of these experimental approaches relied on a human embryonic kidney (HEK) 293 cell line that exogenously expresses affinity tagged CD133 (HEK293/AC133). This cell line allowed me to perform a large-scale RNAi screen to interrogate 11,248 genes for their involvement in cell-surface AC133 recognition. This resulted in the identification of the N-glycosylation pathway as a direct contributor to CD133 plasma membrane localization and cell-surface AC133 detection. I used the same RNAi screening approach on the colon adenocarcinoma cell line Caco-2, which express CD133 from its native promoter, to identify factors that regulate endogenous CD133 transcription. I was able to demonstrate that AF4 promotes CD133 transcription in a number of cancer cell lines. Furthermore, I showed that CD133 expression in an acute lymphoblastic leukemia (ALL) cell line SEM, which is dependent on the mixed-lineage leukemia (MLL)-AF4 gene fusion, is critical for the viability of these cells. To gain further insight into the function of CD133, I performed AP-MS using HEK293/AC133 cells to identify CD133 PPIs. I identified histone deacetylase 6 (HDAC6) as a CD133 protein interaction partner. I found that HDAC6 negatively regulates CD133 trafficking into the endosomal-lysosomal degradation pathway. CD133 binds HDAC6 to prevent inhibition of HDAC6 deacetylase activity by phosphorylation. Protection of HDAC6 from phosphorylation promotes HDAC6 deacetylation of β-catenin, which results in β-catenin dependent signalling and the suppression of cancer cell differentiation. My thesis provide functional roles for CD133 as a pro-proliferative protein and as a key signalling protein in certain cancer cell lines.

Récemment, des spécialistes en cancérologie ont identifié au sein des tumeurs une sous-population cellulaire réfractaire aux traitements de chimio et de radiothérapie. Les caractéristiques cellulaires propres à cette population avoisinent celles des cellules souches. Il semblerait qu'aussi peu que 100 de ces cellules souches retrouvées dans les tumeurs soient capables de réinitier un cancer in vivo. Plusieurs arguments supportent un modèle de cellules souches cancéreuses (CSC) responsable de l'initiation tumorale. Dans les cancers cérébraux, ces CSC expriment le marqueur membranaire de cellules souches neuronales CD133. Les traitements ciblant les tumeurs cérébrales demeurent peu efficaces en partie à cause de la résistance des CSC CD133(+) face à ces traitements. Le ciblage de ces CSC serait donc porteur d'espoir. Le marqueur CD133 permet l'isolation et l'enrichissement de la population de CSC retrouvée au sein des lignées cellulaires ou des tumeurs primaires cérébrales. À l'aide du marqueur CD133, les caractéristiques propres aux CSC peuvent être mieux définies permettant un traitement ciblé. Les tumeurs cérébrales ayant des niveaux d'expression élevés de CD133 sont hautement malignes et un des joueurs clés de l'invasion tissulaire est la métalloprotéinase membranaire de type 1 (MT1-MMP). La protéine MT1-MMP est une protéase capable de dégrader la matrice extracellulaire et d'activer d'autres protéases. Une autre protéine qui est surexprimée dans les gliomes hautement malins est la cyclooxygénase de type 2 (COX-2). L'enzyme COX-2 joue des rôles clés dans la biosynthèse de prostaglandines impliquées entre autres dans des conditions pathologiques en encourageant l'inflammation, la sudation, la douleur et la fièvre. Cependant, une activité constitutive de COX-2 est associée au maintien de la prolifération cellulaire et à la résistance à l'apoptose dans les tumeurs. Nous avons étudié l'expression des protéines MT1-MMP et COX-2 dans les CSC CD133(+) issues de tumeurs cérébrales. Les résultats obtenus montrent que les protéines COX-2 et MT1-MMP sont surexprimées dans les cellules CD133(+) enrichies d'une lignée cellulaire de tumeur cérébrale. La surexpression de ces deux protéines semble être régulée par un axe MT1-MMP/COX-2 dans les CSC CD133(+). En effet, MT1-MMP induit la surexpression de COX-2 dans les CSC CD133(+). Ce rôle de MT1-MMP dans les cascades signalétiques cellulaires nécessite une signalisation initiée via son domaine cytoplasmique. Nous avons aussi étudié la voie de signalisation qui régule l'axe MT1-MMP/COX-2 et avons découvert un rôle critique pour les facteurs de transcription de la famille de NF-кB. Ce nouvel axe pourrait être exploité dans l'optique d'une thérapie anti-cancer afin de diminuer le potentiel invasif des CSC CD133(+) et leur résistance aux traitements actuels. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Cellules souches cancéreuses, CD133, COX-2, MT1-MMP, Glioblastome.

The primary treatment for colorectal cancer is surgery. Radiotherapy and chemotherapy, sometimes combined, are also frequently used to diminish recurrence risk. In response to radiation exposure, several cellular signaling cascades are activated to repair DNA breaks, prevent apoptosis and to keep the cells proliferating. Several proteins in the radiation response and cell survival pathways are potential targets to enhance the effects of radiation. The epidermal growth factor receptor (EGFR), which is frequently upregulated in colorectal cancer and exhibits a radiation protective function, is an attractive target for treatment. EGFR is activated by radiation which in turn activates numerous signaling pathways such as the PI3 kinase/AKT cascade, the RAS/RAF/ERK pathway and STAT leading to tumor cell proliferation. EGFR is also believed to interact with proteins in the DNA repair process, such as DNA-PKcs and MRE11. The cytotoxic effect of an affibody molecule (ZEGFR:1907)2, with high affinity to EGFR,  in combination with radiation produced a small, but significant, reduction in survival in a KRAS mutated cell line. However, not in the BRAF mutated cell line. The next step was therefore to target proteins downstream of EGFR such as AKT. There was an interaction between AKT and the DNA repair proteins DNA-PKcs and MRE11 and both AKT1 and AKT2 were involved in the radiation response. The knockout of both AKT isoforms impaired the DNA double strand break rejoining after radiation and suppression of DNA-PKcs increased the radiations sensitivity and decreased the DNA repair further. The AKT isoforms also affected the expression of cancer stem cell markers CD133 and CD44 which are associated with the formation of metastasis as well as radiation and drug resistance. The CD133 expression was associated with AKT1 but not AKT2, whereas the CD44 expression was influenced by the presence of either AKT1 or AKT2. AKT was also involved in cell migration, cell-adhesion and metabolism. Overall, these results illustrate the complexity in response to radiation and drugs in cells with different mutations and the need for combining inhibitors against several targets such as EGFR, AKT, DNA-PKcs, CD133 or CD44.

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.

The AC133 epitope of the pentaspan transmembrane glycoprotein CD133 has been used as a cell-surface marker for normal and cancer stem cells from a broad range of tissue types. Despite the utility of CD133 as a marker, little is known regarding its regulation and biological function. To study these poorly understood aspects of CD133, I took two main experimental approaches: RNA interference (RNAi) screening and affinity purification coupled with mass spectrometry (AP-MS) to identify CD133 regulatory genes and CD133 protein-protein interactions (PPIs), respectively. Both of these experimental approaches relied on a human embryonic kidney (HEK) 293 cell line that exogenously expresses affinity tagged CD133 (HEK293/AC133). This cell line allowed me to perform a large-scale RNAi screen to interrogate 11,248 genes for their involvement in cell-surface AC133 recognition. This resulted in the identification of the N-glycosylation pathway as a direct contributor to CD133 plasma membrane localization and cell-surface AC133 detection. I used the same RNAi screening approach on the colon adenocarcinoma cell line Caco-2, which express CD133 from its native promoter, to identify factors that regulate endogenous CD133 transcription. I was able to demonstrate that AF4 promotes CD133 transcription in a number of cancer cell lines. Furthermore, I showed that CD133 expression in an acute lymphoblastic leukemia (ALL) cell line SEM, which is dependent on the mixed-lineage leukemia (MLL)-AF4 gene fusion, is critical for the viability of these cells. To gain further insight into the function of CD133, I performed AP-MS using HEK293/AC133 cells to identify CD133 PPIs. I identified histone deacetylase 6 (HDAC6) as a CD133 protein interaction partner. I found that HDAC6 negatively regulates CD133 trafficking into the endosomal-lysosomal degradation pathway. CD133 binds HDAC6 to prevent inhibition of HDAC6 deacetylase activity by phosphorylation. Protection of HDAC6 from phosphorylation promotes HDAC6 deacetylation of β-catenin, which results in β-catenin dependent signalling and the suppression of cancer cell differentiation. My thesis provide functional roles for CD133 as a pro-proliferative protein and as a key signalling protein in certain cancer cell lines.

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.