Cancer cells require survival strategies to respond to microenviromental changes and out-compete their neighbours. They activate stress response mechanisms under extreme microenvironmental conditions, some of which are controlled by the amino acid-sensitive kinase complex, mechanistic Target of Rapamycin Complex 1 (mTORC1). Exosomes are secreted nanovesicles made inside intracellular endosomal compartments that mediate a specialised and complex form of intercellular signalling that can reprogramme target cells via the action of multiple active cargos. I investigated whether mTORC1 activity might modulate the type of exosome secreted in response to microenvironmental changes. Here I identify a new form of mTORC1-regulated exosome biogenesis and signalling involving recycling multivesicular endosomes (rMVEs), a previously unrecognised site for exosome biogenesis. Reduced activity of a specific form of glutamine-sensitive mTORC1 in HCT116 colorectal cancer cells results in an ‘exosome switch’ in which exosomes are preferentially released from these compartments instead of late endosomes. Importantly, RAB11a is found in association with at least a proportion of rMVEs that generate these alternative exosomes and is loaded on to some of their ILVs, providing a RAB signature of compartmental origin. I provide evidence that this exosome switch is conserved in other cancer cell types. My study also presents a proteomics analysis of extracellular vesicle (EV) preparations from normal and mTORC1-inhibited cells. I demonstrate that EV preparations isolated following exosome switching have enhanced pro-angiogenic properties and novel tumour growth-promoting activities. Activation of the receptor tyrosine kinase c-MET and its downstream mitogen-activated protein kinase (MAPK) ERK via phosphorylation is stimulated by these EVs, providing a potential explanation for their growth-promoting effects. Subsequent studies in the lab have demonstrated that several of these pro-tumorigenic activities are mediated by exosomes. I conclude that stress-induced mTORC1 inhibition allows tumour cells to initiate a novel exosome secretion pathway that potentially mediates a cancer cell survival plan that reverses microenvironmental change and supports tumour adaptation. In the future, blocking this response could improve patient outcome following treatment with mTORC1-inhibitory or anti-angiogenic drugs that have currently met with limited success in the clinic.

Les cellules somatiques peuvent être reprogrammées en cellules pluripotent en sur-exprimant 4 facteurs de transcriptions: OCT4, SOX2, KLF4 et c-MYC. Ce processus nécessite en théorie un remodelage des organelles et un changement drastique du métabolisme. De plus, la reprogrammation cellulaire possède une composante stochastique qui est peu comprise et conduit à une faible efficacité. Nous avons fait l'hypothèse que cette variabilité est en partie due aux variations de la régulation de l'homéostasie protéique. Nous nous attendons à ce que la première phase de reprogrammation active les voies de stress qui régulent l'homéostasie protéique, ce qui impacterait l'efficacité de reprogrammation. Notre attention s'est dirigée vers le rôle de la réponse aux protéines dépliées du réticulum endoplasmique. Nous avons découvert que cette voie est active pendant la reprogrammation cellulaire et que son activation peut augmenter l'efficacité de ce processus. Par ailleurs le niveau d'activation de cette voie peut prédire l'efficacité de reprogrammation. Ces résultats suggèrent que la faible efficacité de reprogrammation cellulaire est en partie due à l'incapacité des cellules à activer cette voie de stress afin de pouvoir correctement répondre à la nouvelle charge de protéines synthétisées qui changera l'état de cette cellule. / Somatic cells can be reprogrammed into a pluripotent stem cells state and is achieved by the forced expression of 4 transcription factors: OCT4, SOX2, KLF4 and c-MYC. This process theoretically requires a global remodeling of the organelles and a drastic change in metabolism. Furthermore, reprogramming has an inherent property of stochastic variation that is limiting and largely unknown. We hypothesize that this variation is due, in part, by variable regulation of the protein homeostasis network. We therefore postulated that the early steps of reprogramming would result in the activation of a variety of stress pathways that regulate the protein homeostasis network, which might in turn impact the efficiency of reprogramming. We focused in particular on the endoplasmic reticulum unfolded protein response (UPRER). We find that the UPRER is activated during reprogramming and that its activation can increase the efficiency of this process. We find that stochastic activation of the UPRER can predict reprogramming efficiency. These results suggest that the low efficiency of cellular reprogramming is partly the result of the cell’s inability to initiate a proper stress response to cope with the newly expressed load of proteins that will eventually change the fate of this cell.

En 2006 et 2007, les équipes de Yamanaka et Thomson réalisent la reprogrammation de cellules somatiques murines et humaines en cellules souches pluripotentes à partir de deux cocktails de gènes : OCT4, SOX2, KLF4, cMYC (OSKM) et OCT4, NANOG, SOX2, LIN28 (ONSL). Les cellules souches à pluripotence induite générées (iPS) partagent les propriétés fondamentales des cellules souches embryonnaires : l’auto-renouvèlement, le maintien de la pluripotence et la capacité de différenciation. Ces cellules laissent entrevoir des applications considérables tant en recherche fondamentale (compréhension des mécanismes de développement et de pathologies, développement de modèles) qu’en recherche appliquée (médecine régénérative, toxicologie prédictive, criblage de médicaments). L’avantage majeur de l’utilisation des iPS réside dans leur origine non embryonnaire. Les contraintes d’ordre éthique sont écartées et une grande diversité de types cellulaires à partir de n’importe quel donneur a priori est disponible pour une reprogrammation. L’établissement d’une banque d’hiPS issus de donneurs sains ou de patients, serait d’une grande utilité pour la communauté scientifique se consacrant à l’étude des mécanismes physiopathologiques ou de développement et une source considérable pour la dérivation à des fins de thérapie cellulaire. Dans le but de mettre en place une telle banque, nous avons développé avec la société Vectalys des rétrovirus de reprogrammation contenant les cassettes polycistroniques ONSL et OSKM. Dans un premier temps, nous avons établi un protocole de reprogrammation robuste à l’aide des rétrovirus RV-ONSL. Nous avons ensuite mis en évidence la synergie entre les facteurs ONSL et OSKM, la combinaison équimolaire de RV-ONSL et RV-OSKM permettant d’atteindre 2% d’efficacité de reprogrammation. Nous avons également entrepris la reprogrammation propre par transfections d’ARNm polycistroniques ONSL et OKM mettant à profit cette incroyable synergie. / In 2006 and 2007, Yamanaka and Thomson teams achieved the reprogramming of mouse and human somatic cells into pluripotent stem cells through the transfection of two cocktails of genes: OCT4, SOX2, KLF4, cMYC (OSKM) and OCT4, NANOG, SOX2, LIN28 (ONSL). The generated cells, called induced Pluripotent Stem Cells (iPSC) share the same fundamental properties of ESC : self-renewing, pluripotency maintenance and capacity of differentiation into the three germ layers and suggest the same application potential in basic research (developmental and epigenetic biology) as well as in therapy (regenerative medicine, disease modeling for drug development). One of the major advantages of iPSC lies in their non-embryonic origin. Indeed, the use of iPSC resolves the ethical constraints and offers the possibility to work with extensive cell types directly from the patient to treat. Stéphane Viville’s research team aims to develop a hiPSC bank from patient suffering from genetic or other diseases which will be available for the scientific community. We are experienced in human primary fibroblasts reprogramming especially with the use of two polycistronic cassettes: ONSL encoding Thomson’s cocktail and OSKM encoding Yamanaka’s cocktail separated with 2A peptides. Thanks to the combination of RV-ONSL and RV-OSKM retroviral vectors (developed with Vectalys) we are yielding more than 2% of reprogramming efficiency in a highly reproducible way. Indeed, we demonstrated the reprogramming synergy of ONSL and OSKM combination. We are now focusing our effort on non-integrative strategies (ie mRNA) which are more appropriate for clinical usage.

Estudos recentes relataram oncogenes induzindo a reprogramação metabólica no câncer. Essa reprogramação é fundamental para que as células cancerosas tenham nutrientes e biomoléculas suficiente para manter sua alta taxa proliferativa. A mitocôndria tem um papel central no metabolismo energético da célula e alterações no seu genoma, tanto em relação a mutações como em número de cópias, já foram bastante observados em vários tipos tumorais. Além disso, deficiência no fator de transcrição mitocondrial A (TFAM), fundamental para a transcrição e estabilidade do mtDNA, já foi associada com o crescimento tumoral. Diante disso, nosso estudo teve como objetivo avaliar o papel da instabilidade do genoma mitocondrial no metabolismo energético e crescimento do melanoma. Para isso, nós medimos a instabilidade do mtDNA utilizando como parâmetros: o acúmulo de mutações no mtDNA, alterações no mtDNAcn e a expressão do TFAM. O impacto da instabilidade do mtDNA foi avaliado em três modelos diferentes de melanoma: um modelo in vitro de linhagens celulares, dados de expressão gênica de tumores de melanoma metastático proveniente do TCGA e um modelo murino induzível de melanoma (BrafV600E/Ptennull), adicionado a um background alternativo de deficiência para o TFAM/mtDNAcn. Esse modelo murino também nos permitiu avaliar a deficiência do TFAM limitada a células tumorais (Tfamflox) e tanto em células tumorais, como no seu microambiente (Tfam+/-). Nas análises in vitro, nós observamos correlações positivas entre o mtDNAcn e a expressão do TFAM com a taxa de consumo de glicose e produção de ATP, indicando um impacto desses parâmetros na bioenergética celular. Análises de expressão gênica, utilizando tanto as linhagens de melanoma como tumores de melanoma metastático, nos sugeriram que o TFAM regula genes indutores de angiogênese, a resposta imunológica humoral e vias metabólicas de aminoácidos. Nas análises in vivo, nós observamos um aumento dos tumores em camundongos Tfam+/-, indicando que a deficiência de TFAM/mtDNAcn em células tumorais e no seu microambiente induz a tumorigênese, o que confirma os dados de expressão gênica encontrados com linhagens e tecido de melanoma. Além disso, análises de metabolômica e transcriptômica combinadas nos sugeriram que as células de melanoma com deficiência no TFAM/mtDNAcn são mais dependentes do metabolismo de glutamina. Diante disso, nós concluímos que a deficiência do TFAM/mtDNAcn tem um papel importante no crescimento do melanoma, induzindo a expressão de genes pro-tumorigênicos e aumentando o consumo da glutamina para suprir as necessidades proliferativas das células cancerosas. Esses dados são relevantes e podem nos ajudar a entender melhor o papel da mitocondrial na progressão do melanoma. / Recent studies have shown many oncogenes triggering metabolic reprogramming in cancer. The metabolic switch in cancer cells is necessary to supply the high demand for nutrients and biomolecules for proliferative cells. In this context, mitochondria play a central role in the energetic metabolism of the cell and changes in its genome, such as an increased load of mutations and alterations in mtDNA content, have been reported in several cancers. In addition, deficiency in the Mitochondrial Transcription Factor A (TFAM), responsible for transcription and maintenance of mtDNA stability, was previously associated with tumor growth. Based on that, our goal was to evaluate the impact of the mitochondrial genome instability in the energetic metabolism and melanoma growth. mtDNA instability was inferred measuring mtDNA mutations load and content, as well as TFAM expression. Its impact was evaluated in three different melanoma models: an in vitro model using melanoma cell lines, gene expression data from metastatic melanoma tumors, publicly available at TCGA, and an inducible murine model of melanoma (BRAFV600E/PTENnull), crossed onto different TFAMdeficient backgrounds. The murine model also provides us a tractable model to examine the consequences of mtDNA instability limited to cancer cells (Tfamflox) and in both cancer cells and tumor microenvironment (Tfam+/-). In vitro analysis showed us a positive correlation between mtDNA copy number (mtDNAcn) and TFAM expression with glucose consumption and ATP production, pointing an impact of these parameters in cellular bioenergetics. Further gene expression analysis, using both cell lines and metastatic melanoma data, suggested that TFAM could regulate the expression of angiogenesis genes, humoral immunity and amino acid metabolism. In vivo analysis confirmed the gene expression data, and revealed a higher melanoma growth in Tfam+/-. Also, combined metabolomics and transcriptomics data suggested that TFAM/mtDNAcn deficient melanoma cells rely mostly on glutamine metabolism to supply their energetic requirements. In conclusion, these data indicate that TFAM/mtDNAcn influences melanoma growth by triggering pro-tumorigenic signals and inducing metabolic reprogramming towards glutamine metabolism. These results are relevant and might help us understand how mitochondria affect melanoma progression.

Técnicas de reprodução assistida (TRAs) são utilizadas tanto na medicina humana quanto na medicina veterinária com o objetivo principal de corrigir infertilidades adquiridas ou herdadas. A transferência nuclear de célula somática (TNCS) ocupa um lugar de destaque na veterinária pela possibilidade de geração de indivíduos geneticamente idênticos, permitindo a produção de rebanhos homogêneos de alto mérito genético e servindo como modelo de estudo para técnicas de reprogramação. Porém, a utilização de TRAs, e em especial da TNCS, é considerada responsável pelo aumento na geração de conceptos portadores de alterações durante e após o desenvolvimento embrionário e fetal. A provável causa principal é a alteração na regulação da reprogramação epigenética devido à manipulação de gametas e embriões no período inicial do desenvolvimento, levando a alterações na regulação epigenética de genes imprinted. O presente estudo teve como objetivo principal avaliar marcas epigenéticas e expressão de genes imprinted no desenvolvimento de conceptos bovinos produzidos por TNCS ou inseminação artificial (IA). Para tal, foram coletadas amostras de tecido muscular e membranas corioalantoideana e amniótica de animais na fase pré natal (fetal) e tecidos muscular, nervoso e hepático na fase pós natal (animais nascidos saudáveis adultos ou não) de animais derivados de IA ou TNCS. Foi analisada a expressão dos genes imprinted H19, IGF2, IGF2R e Airn quando possível, assim como a metilação do DNA no locus H19/IGF2 na fase pós natal. Foi observado que na fase pré natal não foi detectada expressão do IGF2, enquanto que a expressão de H19 é aumentada em relação ao IGF2R, porém, sem diferenças entre os grupos nos tecidos estudados. Na fase pós natal, o padrão de expressão dos genes IGF2, H19 e IGF2R indica diminuição da expressão gênica relativa no fígado de animais TNCS e no aumento da expressão gênica do H19 na musculatura de animais adultos (saudáveis) bovinos produzidos por TNCS, apesar de o padrão de metilação dos genes imprinted IGF2/H19 não ser diferente entre organismos considerados saudáveis e não saudáveis. Os resultados deste projeto contribuem para o entendimento dos mecanismos epigenéticos relacionados ao desenvolvimento embrionário e fetal, em especial aqueles relacionados à dinâmica das alterações epigenéticas envolvidas no imprinting genômico / Assisted reproductive technologies (ARTs) are usually used in both human and veterinary medicine aiming the correction of heritable or acquired infertilities. The somatic cell nuclear transfer technique (SCNT) is of particular importance in veterinary as it enables the generation of genetically identical organisms, allowing the production of homogeneous genetically improved herds, and also serving as a model for reprogramming studies. However, the use of TRAs, SCNT in special, may be responsible for the increase of developmental-related abnormalities in the conceptuses. Such phenotypes are probably caused by a disruption during the epigenetic reprogramming due to the manipulation of gametes and embryos during the early development period, and therefore leading to disturbances in the epigenetic regulation of imprinted genes. The present study aimed to evaluate epigenetic marks and expression of imprinted genes in different developmental periods of cattle generated by SCNT or artificial insemination (AI). For that, corionic/alantoic and amniotic membranes from fetuses and muscular, nervous and hepatic tissues from born animals, healthy (adult) or not, produced by SCNT or AI were collected. The expression of the imprinted genes H19, IGF2, IGF2R and Airn was analyzed as well as the DNA methylation at locus H19/IGF2 in post-natal period. It was observed that IGF2 was not detected during pre-natal period, whereas H19 expression is increased when compared to IGF2R in the groups studied herein. At post-natal period the IGF2, H19 and IGF2R expression patterns infers the decrease of relative gene expression in the liver and the increase of H19 expression in the muscle of SCNT adult animals. The methylation pattern of IGF2/H19 locus, however, did not differ between healthy or not animals. The results described herein may contribute to the understanding of the epigenetic mechanisms related to embryonic and fetal development, and in special, to those related to the epigenetic dynamics during genomic imprinting

A geração de células-tronco pluripotentes induzidas (iPS) a partir de células somáticas demonstrou que células adultas de mamíferos podem ser reprogramadas a um estágio de pluripotência através da inserção de fatores de transcrição embrionários. Esta descoberta tem levantado questões fundamentais sobre os mecanismos, que através destes fatores de transcrição, influenciam epigeneticamente as células e seus potenciais de diferenciação após a reprogramação e um normal desenvolvimento. Componentes lipídicos e lipoprotéicos afetam vários aspectos no comportamento celular durante sua manutenção e diferenciação, podendo afetar diretamente fatores essenciais em processos de reprogramação celular, manutenção da pluripotência e perfil epigenético das células. Nesse sentido, esta tese propôs o estudo da composição lipídica com diferentes abordagens entre células iPS, células-tronco embrionárias (H1) e células fibroblastos (BJ). Foram produzidas três linhagens de células pluripotentes induzidas no modelo humano que foram caracterizadas quanto 1a sua pluripotência e utilizadas, juntamente às linhagens H1 e BJ como modelos para o estudo da composição lipídica proposto. Foram identificadas e estudadas um total de 44 espécies lipídicas das classes PC, PE, PI, SM e PS, e discutidas frente a reprogramação celular e manutenção da pluripotência. Foi identificado um padrão de composição fosfolipídica distinta entre células pluripotentes e não pluripotentes, e especulamos que a presença dessas espécies parecem ter um envolvimento fundamental para a manutenção da pluripotência. Este padrão, mostrou pela análise de componente principal, que durante o processo de reprogramação, alterações na composição lipídica ocorrem de forma com que a pluripotência surge durante a reprogramação, evidenciando alterações lipídicas particulares do estádio da pluripotência, sugerindo uma ligação entre estas alterações na composição lipídica com as alterações metabólicas da própria reprogramação celular. O estudo da quantificação de fosfolipídios entre linhagens celulares pluripotentes e não pluripotentes evidenciaram que existe uma diferença fosfolipídica entre estas linhagens, observamos que as linhagens iPS e H1, do ponto de vista das classes observadas e os fosfolipídios quantificados, são similares entre si e diferentes de células não pluripotentes. É evidente que estas moléculas lipídicas, individualmente, não são capazes de modular processos como a reprogramação celular, entretanto, é de extrema importância o entendimento das mesmas dentro da reprogramação celular e manutenção da pluripotência. Nossos dados sugerem que a composição lipídica de células pluripotentes tem importante papel para o desenvolvimento e evolução do processo de reprogramação celular e o entendimento da manutenção da pluripotência / The generation of induced pluripotent stem cells (iPS) from adult somatic cells has shown that mammalian cells can be reprogrammed to a pluripotent state by the insertion of embryonic transcription factors. This finding has raised questions about the fundamental mechanisms through which these transcription factors epigenetically influence cells, their potential of differentiation after reprogramming and normal development. Lipid and lipoprotein components affect numerous aspects of cell behavior during its maintenance and differentiation, which can directly affect main factors in cell reprogramming processes, maintenance of pluripotency and epigenetic profile of the cells. Thus, this thesis proposed to study, with different approaches, the lipid composition of iPS cells, embryonic stem cells (H1) and fibroblast cells (BJ). Three induced pluripotent cell lines were produced in the human model. They were characterized regarding their pluripotency and used along with H1 and BJ cell lines, as models for the proposed lipid composition study. A total of 44 species of lipid from the classes PC, PE, PI, PS and SM have been identified, studied and discussed regarding cellular reprogramming and maintenance of pluripotency. A different phospholipid composition pattern was observed between pluripotent and non-pluripotent cells, and it is speculated that the presence of these species appears to have a major involvement on the maintenance of pluripotency. This array showed, by the principal component analysis, that during the reprogramming process changes in the lipid composition occur, so that pluripotency takes place during reprogramming, highlighting lipid changes particular of the pluripotency state, suggesting a connection between these changes in lipid composition and the metabolic changes of cell reprogramming. The study of the quantitation of phospholipids from pluripotent and non-pluripotent cell lines indicated a phospholipid difference between these cell lines when considering the observed classes and quantified phospholipid. It was eminent that iPS lines and H1 are similar and differ from non-pluripotent cells. It is clear that these lipid molecules are not individually capable of modulating processes such as cell reprogramming, however, it is extremely important to understand them within cellular reprogramming and maintenance of pluripotency. Our data suggests that the lipid composition of pluripotent cells has important role in the development and evolution of cellular reprogramming process and the understanding the maintenance of pluripotency

Apolipoprotéines L est une famille nouvellement caractérisée en humain sans une fonction patho- physiologique définitive. Ces protéines sont classiquement considérées être impliquées dans le transport et métabolisme des lipides, principalement due à l'association de son premier membre de la famille sécrétée l’apolipoprotéine L1 aux particules des lipoprotéines de haute densité. Néanmoins, le reste des membres sont des protéines intracellulaires (absence de domaine de peptide signal). Apolipoprotéine L1 a été initialement identifiée comme l'élément clé du facteur trypanolytique dans le sérum humain. L'exploration de la séquence des différents apolipoprotéines L a révélé un domaine distinct «B cell lymphoma-2 homology domain 3» ayant des similitudes structurelles et fonctionnelles avec le domaine B cell lymphoma-2 homology domain 3 des protéines de la famille B cell lymphoma-2. Ainsi la découverte de ce domaine peut contribuer à la compréhension de la fonction et rôle des apoLs dans différents mécanismes et processus tels que la mort cellulaire programmée, la prolifération cellulaire, le métabolisme cellulaire .Notre étude visait à caractériser les fonctions de patho- physiologique du premier membre de la famille «apolipoprotéine L1 ». L’expression de l’apolipoprotéine L1 ARNm, à partir de 48 carcinomes papillaires de la thyroïde, a été évaluée par des études à haut débit et normalisée à un pool de tissus normal de la thyroïde. Une confirmation de PCR en temps réel valide ainsi la surexpression d’apoL1 dans 91,67 % des cas testés. Le niveau élevé de l’apolipoprotéine L1 ARNm est en corrélation avec une expression protéique élevée dans les échantillons histologiques (70%), et détermine que les cellules folliculaires de la thyroïde dans la zone de la tumeur sont les cellules principales responsables de l’expression spécifique de l’apolipoprotéine L1. Nous avons étudié l'expression apolipoprotéine L1 dans le modèle de cancer pour approfondir notre compréhension des relations reliant cette expression distincte dans le cancer papillaire de la thyroïde et son rôle et fonction concernant le métabolisme du cancer (de reprogrammation métabolique :effet Warburg).7En outre, la localisation de l’apolipoprotéine L1 dans la mitochondrie des cellules cancéreuses de la thyroïde ainsi que dans la mitochondrie de levure, a été le point de départ de la recherche dans ce nouveau modèle, il nous a permis de révéler et d'introduire de nouvelles hypothèses pour expliquer l'effet inhibiteur de l’apolipoprotéine L1 en fonction des conditions métabolique variantes et l’effet pléotropiques de l’apolipoprotéine L1 sur la levure (dommages des mitochondries et vacuoles). Dans ce manuscrit, nous avons décrit nos efforts à mettre en évidence la spécificité d'expression de l’apolipoprotéine L1 dans le cancer papillaire thyroïdien notamment au niveau de la transcription ainsi que la localisation mitochondriale et l'interférence probable avec les voies métaboliques. / Option Biologie moléculaire du Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Background and objectives: In 2006 Shinya Yamanaka successfully reprogrammed mouse fibroblasts back to an embryonic stem cell-like state (called induced pluripotent cells, iPS cells) using retrovirus to introduce four genes that encode critical transcription factor proteins (Oct4, Sox2, KLF4, and c-Myc). This ability to reprogram has promising future applications in clinical and biomedical research for study of diseases, development of candidate drugs and to support therapeutic treatments in regenerative medicine. However, the clinical applications have to meet GMP requirements without the risk of insertional mutagenesis associated with retrovirus. Chromatin modifying agents are widely used in many protocols to generate iPS cells and culture of blood CD34+ cells with chromatin-modifying agents can lead to an increase in marrow repopulating cells and in the case of valproic acid increased erythroid cell colony formation. We undertook research to help understand what effects these reagents have on mobilised peripheral blood (mPB) CD34+ cells and optimised the expansion medium protocol to facilitate reprogramming work. This project aims to utilize peripheral blood mononuclear cells (MNC), one of the most easily accessible tissues to generate iPS cells using an efficient non-viral, feeder cell free methodology, with the ultimate goal of moving this methodology towards clinical use. Materials and Methods: G-CSF mobilised peripheral blood, buffy coat, cord blood and fetal liver were obtained from patients and donors under informed consent and ethics committee approval. Haematopoietic stem/progenitor cells CD34+ or CD133+) isolated by magnetic separation were flow cytometry sorted into CD34+/CD133+, CD34+/CD133-, and CD34-/CD133+ sub-populations and their lineage potential were assessed in colony forming unit assays. The effect of epigenetic modifiers valproic acid and 5-aza-2-deoxycytidine used singly or in combination with each other and with IL3 on phenotype and lineage potential of cultured CD34+ cells from mobilised peripheral blood were assessed by flow cytometry and colony-forming unit assays. Prior to reprogramming mononuclear cells from peripheral blood or CD34+ cells from blood were expanded in culture medium supplemented with stem cell factor (SCF), Fms-related tyrosine kinase 3 ligand (Flt3L) and Interleukin- 3 (IL-3) for several days. Actively proliferating cells were reprogrammed by electroporation using episomal vectors with an oriP/EBNA-1 backbone to deliver five reprogramming genes, Oct4, Sox2, Lin28, L-Myc, and Klf4. Electroporated cells were seeded onto matrigel coated plates immediately after transfection or were reseeded after three days’ culture. Subsequently, cells were cultured in specific medium on different days. When iPS colonies appeared, they were picked and cultured as for ES cells. Once established, iPS cell lines were immunophenotyped using flow cytometry and immunofluorescence and their potential to differentiate into the three germ layers was assessed in vitro. Results and Conclusion: The largest subpopulation of CD34+ cells was CD34+/CD133+ population which was essentially committed to myeloid colony production, while much smaller CD34+/CD133- subpopulation had a greater capacity to generate erythroid colonies. Optimised cytokine cocktail for expansion of CD34+ cells included IL-3, important in improving expansion and maintaining functionality of CD34+ cells. The optimised cytokine cocktail comprised 100 ng/ml SCF, 10 ng/ml Flt3L, and 20 ng/ml IL-3, which maintained CD34+ cells and MNC in an active proliferating state. In addition, valproic acid and IL3 were found to act synergistically, to increase the numbers of CD34+/CD36+ positive cells. However, we found that an apparent increase in red cell colony formation actually resulted from a decrease in white cell colonies, so no overall increase in red cell colonies was seen when equivalent numbers of CD34+ cells were plated. Proliferating MNC maintained in optimised cytokine cocktail were amenable to electroporation for the effective delivery of episomal transcription factors (Oct4, Sox2, Klf4, L-Myc, and Lin28) within a backbone of oriP/EBNA-1. We successfully developed an efficient and simple method for reprogramming MNC from fresh or frozen samples to generate induced pluripotent cells using episomal vectors in a feeder-free system without any requirement for small molecules and the highest reprogramming efficiency is 0.033% (65 colonies from 2 ◊ 105 seeding MNC). The cytokine cocktail and reprogramming methods work better in CD34+ cells from cord blood or fetal liver, and we obtained 148 iPS colonies from 105 seeding cells (0.148%) at most. In addition, fibroblasts from adult and fetal liver can be successfully reprogrammed using the same reprogramming method. The use of episomal vectors with an oriP/EBNA-1 backbone to deliver reprogramming genes, and efficient electroporation were the most important factors in efficiency of the reprogramming process. In addition, it is pivotal to initiate transfection when cells are actively proliferating. The iPS cell lines we generated maintained the successful expression of ES markers including Oct4, Nanog, SSEA3. SSEA4, TRA-1-60 and TRA-1-81, and had the capacity to successfully differentiate into cell types of ectoderm, mesoderm and endoderm layers in vitro.

La réplication de l'ADN, qui doit assurer à chaque cycle cellulaire une copie fidèle du génome pour que les cellules filles héritent du même génome, est un processus hautement régulé, faisant intervenir son organisation en chromatine mais aussi sa dynamique au sein de l'architecture nucléaire. Le vieillissement cellulaire, qu'il soit physiologique, pathologique ou induit in vitro par des conditions de culture sub-optimales, est accompagné de modifications de l'organisation du génome en chromatine, susceptibles de modifier la régulation spatiotemporelle du programme de réplication. Dans quelle mesure ces modifications sont réversibles et s'accompagnent d'une restauration du programme de réplication sont des questions que nous avons abordées. Notre étude a donc consisté dans un premier temps à analyser les modifications du programme de la réplication, dans différentes situations de vieillissement cellulaire, afin de vérifier notre hypothèse. Nous avons analysé sur l'ensemble du génome l'organisation spatiale (le long du génome) et temporelle des domaines de réplication, le timing, de cellules prolifératives ou approchant de la sénescence réplicative, de donneurs jeunes, âgés ou encore atteints de vieillissement accéléré ou progéria. Nous avons pu observer que certains domaines de timing permettent de distinguer des cellules jeunes de cellules âgées, ou des cellules prolifératives de pré-sénescentes. Afin d'explorer la réversibilité de ces processus, nous avons utilisé la reprogrammation en cellules souches pluripotentes induites ou iPS, suivie d'une redifférenciation fibroblastique. Nous avons pu démontrer que les iPS produites présentaient toutes les mêmes profils de timing, correspondant à celui d'une cellule pluripotente, indiquant que les modifications liées à l'âge ou à la sénescence pouvaient être reprogrammées. Ceci a ensuite été confirmé par une redifférenciation de ces iPS en cellules fibroblastiques dont les profils de timing de réplication ont pu être associés à ceux de fibroblastes jeunes. Cette étude nous a permis de mettre en évidence l'extrême plasticité de l'organisation spatio-temporelle de la réplication, révélant la possibilité de restaurer une dynamique de réplication altérée avec le vieillissement et l'entrée en sénescence, en manipulant le destin cellulaire vers un état indifférencié. Cette étude de la dynamique des domaines de réplication qui accompagne les modifications épigénétiques de la vie cellulaire a été complétée par l'étude à l'échelle moléculaire du rôle d'une histone déméthylase, Jarid1C/KDM5C, dans la réplication au sein des clusters d'origines. Ensemble, ces résultats apportent de nouveaux éléments sur l'interdépendance des dynamiques chromatiniennes et de réplication au cours de la vie cellulaire. / DNA replication allows at each cell cycle the exact copy of the genome that will be transmitted to daughter cells. Thus, the replication process is highly regulated in concert with its chromatin organization but also its dynamics in the nuclear architecture. Cellular ageing, be it physiologic, pathologic or induced in vitro by sub-optimal culture conditions, is accompanied by modifications of the chromatin organization of the genome. This could lead to spatio-temporal modifications of the replication program. We studied to what extent these modifications are reversible and could lead to the recovery of the replication program. In a first step, we analyzed modifications of the replication program upon several ageing situations to test our hypothesis. We analyzed the whole genome spatio-temporal organization of replication domains, the timing, of proliferating or near-senescent cells, of young, old or progeria (a premature ageing disease)-affected donors. We observed that young cells could be distinguished from old cells, and proliferative from near-senescent, by looking at some particular timing domains. To explore the reversibility of these processes, we used reprogramming to induce pluripotent stem cells (iPS cells) followed by fibroblastic re-differentiation. We were able to demonstrate that the derived iPS cells have similar timing profiles corresponding to pluripotent cells profiles: ageing- and senescence-related modifications of the replication timing could be reprogrammed. It was confirmed by re-differentiating these iPS into fibroblastic cells which timing profiles could be associated to young fibroblasts ones. By manipulating cell fate toward an undifferentiated state, this study shows the extreme plasticity of the DNA replication spatio-temporal organization and highlights a chance to restore the replication dynamics when altered by ageing and senescence. This study of the replication dynamics linked to the epigenetic modifications of cells life was completed by a study at the molecular scale of the Jarid1C/KDM5C histone demethylase influence on replication within origin clusters. Together, these results bring new insights into the interdependency of chromatin and replication dynamics during cell fate modifications.

Le rein est un organe considéré comme statique, montrant une capacité régénérative très limitée. Les cellules épithéliales du glomérule, appelées podocytes, sont des cellules hautement différenciées qui possèdent des extensions cytoplasmiques indispensables à leur fonction de filtration du sang. Ces cellules sont particulièrement impactées dans les pathologies rénales chroniques, et il apparaît primordial de développer des stratégies thérapeutiques permettant de restaurer leur fonction. Une des approches thérapeutiques qui semble des plus prometteuses consiste en le remplacement des cellules lésées par des cellules fonctionnelles. Dans cette approche de médecine régénérative, les capacités endogènes de régénération des organes sont exploitées et stimulées afin de permettre un rétablissement des tissus constituant les organes. Bien que les podocytes montrent un potentiel de prolifération et de régénération limité, un moyen unique de stimuler ces cellules consiste en la surexpression de la sous-unité protéique TERT de la télomérase. En effet, la surexpression transitoire de TERT dans le rein adulte induit la dédifférenciation et la prolifération des podocytes, suivi par la régénération de ces cellules. L’objectif de mon travail de thèse était d’identifier les voies de signalisation moléculaires ciblées par TERT lors de la reprogrammation des podocytes en cellules dédifférenciées et prolifératives. Le travail réalisé a permis de mettre en évidence les facteurs moléculaires impliqués dans l’initiation de ce processus ainsi que les effecteurs de la reprogrammation ciblés par TERT. De plus, l’analyse des voies de signalisation dérégulées par TERT montre que l’interaction et le remodelage de la matrice extracellulaire représentent des événements très précoces lors de la reprogrammation. Un autre objectif de ma thèse consistait en l’élucidation des mécanismes cellulaires mis en œuvre lors de la régénération des podocytes suite à la surexpression transitoire de TERT. Aussi, les résultats obtenus grâce à l’emploie d’une approche non biaisée de traçage cellulaire a révélé la présence de cellules progénitrices dans le néphron du rein adulte capables de s’amplifier de manière clonale afin de régénérer les podocytes de manière efficace et rapide. Ces résultats présentent un mécanisme cellulaire encore jamais appréhendé, menant à la régénération efficace des podocytes dans le rein des mammifères adultes. Ces données représentent une véritable percée des connaissances au regard de l’existence et de la fonction des progénitures rénaux, ouvrant la voie à des stratégies thérapeutiques permettant d’améliorer la régénération cellulaire de patients souffrant de maladies rénales chroniques. / In mammals, the kidney is considered a static organ with a limited regenerative capacity. Glomerular epithelial cells, named podocytes, are highly differentiated cells harboring cytoplasmic extensions essential for their function of blood filtration. These cells appear to be the weak link in chronic kidney diseases, rising up the necessity to develop therapeutic strategies to restore their function. One promising therapeutic approach consist in the replacement of impaired cells with fully functional cells. The aim of this regenerative medicine approach is to stimulate the endogenous regenerative capacity to reestablish the functionality of tissues within the organ. Although podocytes display a limited regenerative capacity, transient overexpression of the telomerase protein component TERT appears to be an efficient way to stimulate this capacity in vivo. Indeed, TERT exhibits potent effects on kidney podocytes in steady state conditions resulting in acute cell cycle entry and loss of differentiation. Such reprogramming of kidney podocytes is followed by replenishment of those cells by functional podocytes upon TERT withdrawal. TERT effects on kidney podocytes are independent of its role in telomere synthesis, and rather rely on its ability to modulate signaling pathways. My thesis objective was to identify the molecular mechanisms targeted by TERT non-canonical activity upon initiation and progression of podocyte reprogramming. Analysis of the molecular signaling modulated by TERT show that interaction and remodeling of the extracellular matrix represent early events of the reprogramming process. Those results highlighting TERTtarget genes and pathways upon in vivo cellular change of fate provide precious knowledge for unprecedented therapeutic strategies that aim to target TERT non-canonical activity in kidney cancers and other epithelial cancers more broadly. The second objective of my thesis was to elucidate the cellular mechanisms that support podocytes regeneration upon transient overexpression of TERT. Using podocyte lineage tracing approaches, we found that renewed podocytes observed following a TERT pulse are not derived from initially present podocytes. Using an unbiased lineage tracing approach, we further found that clonal amplification of progenitor cells is the source of podocyte replenishment in this system. Those results unveil a cellular mechanism that have never been apprehended previously, which activation lead to efficient podocyte regeneration in the adult mammalian kidney. Those data represent a real breakthrough in knowledge regarding kidney progenitor cells existence and function, and have profound implications for the development of therapeutic strategies that aim to maintain/enhance regeneration in patients with kidney diseases and in the elderly.