Les effets biologiques de l'hypoxie sont très étudiés aujourd'hui, principalement en raison du rôle crucial que jouent les conditions d'oxygénation dans le développement des cancers.Depuis plusieurs années, une littérature foisonnante tente ainsi de décrire les multiples aspects de la réponse moléculaire, cellulaire et physiologique à l'hypoxie. La complexité des voies de signalisation impliquées et la diversité de leurs effets cellulaires rendent la tâche délicate. Cet état de fait se reflète dans la pluralité des méthodes utilisées, depuis les simulations numériques jusqu'aux approches expérimentales.Dans cette thèse, j'ai abordé ce sujet sur la base de deux outils: la modélisation mathématique et une démarche expérimentale utilisant les cellules HeLa-FUCCI. Cette lignée cellulaire récemment développée est en effet un instrument de choix encore peu exploité. Par une construction génétique liant des protéines du cycle cellulaire à un fluorophore, elle rend possible l'étude, en continue, de la dynamique du cycle en microscopie de fluorescence. Nous avons ainsi pu analyser plusieurs aspects de la réponse cellulaire à l'hypoxie, dans un contexte tumoral.Dans un premier temps, nous avons cherché à caractériser mathématiquement les liens tissés entre le cycle cellulaire et les voies de signalisation de l'hypoxie, centrées sur le facteur de transcription HiF-1. Ce modèle propose un explication simple à l'arrêt du cycle observé notamment dans les cellules tumorales en conditions hypoxiques. Nous avons ainsi montré que l'induction de chimiorésistance pouvait se concevoir comme une entrée facilitée en quiescence des cellules cancéreuses. Dans le but de valider ces observations, nous avons ensuite cherché à quantifier expérimentalement la dynamique de la prolifération cellulaire en utilisant les cellules HeLa-FUCCI. Comme il est apparu que les fluorophores qu'elles portent sont sensibles au manque d'oxygène, nous avons testé différentes molécules couramment utilisées pour induire HiF-1 et mimer l'hypoxie (DFO et CoCl2). De cette étude ont émergé des résultats originaux quant à la dynamique de blocage du cycle des cellules HeLa en présence de chélateurs du fer.Si les conditions hypoxiques ne sont pas favorables à l'utilisation des cellules FUCCI, nous avons pu en revanche montrer qu'elles étaient tout à fait adaptées à l'étude de la dynamique du cycle cellulaire en condition de réoxygénation. De manière intéressante, nous avons alors pu observer un ralentissement significatif de la phase S après retour à la normoxie. Afin d'apporter un éclairage théorique à cette observation, nous avons proposé un modèle mathématique de la dynamique de régulation de HiF-1 en conditions d'oxygène fluctuantes, basé sur le couple HiF-1/pVHL, dont les relations sont pensées dans un cadre compartimenté (noyau/cytoplasme). Ce modèle simple reproduit fidèlement les caractéristiques principales de la réponse cellulaire à l'hypoxie. En outre, en simulant les conséquences d'une réoxygénation brutale, nous avons observé la genèse de fortes instabilités du niveau intracellulaire de HiF-1. Enfin, nous avons mené une étude expérimentale de la compartimentation de HiF-1. L'outil FUCCI permet en effet d'observer simultanément l'avancement du cycle (en microscopie de fluorescence), et la localisation intra-cellulaire de HiF-1(par immunomarquage). Nous avons pu montrer que la variabilité de la localisation de HiF-1α n'était pas due à la progression dans le cycle. Elle est donc certainement liée soit à des différences génétiques inter-cellulaire, soit à une stochasticité de la régulation de HiF-1. / The biological effects of hypoxia are intensively studied today, mainly because of the crucial role played by oxygenation conditions during the development of cancers.For several years, a huge literature aims at describing the multiple aspects of the molecular, cellular and physiological responses to hypoxia. The complexity of the pathways which are involved and the diversity of their cellular effects make this task difficult.This situation is reflected in the plurality of the methods used, from the numerical simulations to the experimental approaches.In this thesis, I studied this subject using two tools: mathematical modeling and experimental approaches using HeLa-FUCCI cells.This recently developed cell line is an interesting tool not yetmuch exploited. By a genetic construction linking cell cycle proteins to a fluorophore, it makes possible the study of cell cycle dynamics using fluorescent microscopy.We could analyze various aspects of the cellular response to hypoxia, in a tumoral context. In a first time,we tried to mathematically characterize the links existing between cell cycle and the hypoxia pathways,driven by HiF-1.This model proposed a simple explanation to the cell cycle arrest notably observed in the tumor cells in hypoxicconditions.We then showed that the induction of chemoresistances could be considered as an entry into quiescence of tumor cells.In order to validate these observations we then tried to experimentally quantify the dynamics of cell proliferation using HeLa-FUCCI cells. As it appeared that the fluorophores were sensitive tothe lack of oxygen, we tested different molecules currently used to induceHiF-1 and mimic hypoxia (DFO and COCl2).From this study have emerged original results about the dynamics of cell cyclearrest of HeLa cells in presence of iron-chelators.If hypoxic conditions are not favorable to the use of HeLa-FUCCI cells, we could show that they were totally adapted to the study of cell cycle dynamics during reoxygenation.Interestingly, we then could observe a significant slowing down of the S-phase after the return to normoxia. In order to bring theoretical elements to this observation, we proposed a mathematical model of the dynamics of HiF-1 regulation in fluctuating oxygen conditions, based on thepVHL/HiF-1 couple, in the frame of a nucleo-cytoplasmic compartmentalization of HiF-1.This simple model well reproduce the main characteristics of the cell response to hypoxia.Besides, by simulating the consequences of a sudden reoxygenation, we observed the genesis of strong instabilities of HiF-1 intracellular level.Finally, we propose an experimental study of HiF-1 compartmentalization.Indeed, the FUCCI cells allow to simultaneously observe cell cycle progression (using fluorescent microscopy),and HiF-1 intra-cellular localization (with immunomarkage). We then could show that the variability of HiF-1 localization was not due to the progression into the cell cycle. Then, it is certainly linked to inter-cellular genetic differences, or to a stochasticity of HiF-1 regulation.

Cellular checkpoints are typically considered to both facilitate the ordered execution of the cell cycle and to act as a barrier to oncogene driven cell cycles and the transmission of unresolved genetic lesions from one phase to the next. Furthermore, these mechanisms are also believed to underpin the responses of cells, both in normal and cancerous tissues, to those therapies that either directly or indirectly generate DNA damage. In recent studies however, it has become clear these checkpoints permit the passage of significant genomic aberrations into subsequent cell cycle phases and even descendant cells, and that heterogeneous responses are apparent amongst genetically identical cells. The consequences of this checkpoint ‘negligence’ remain relatively uncharacterised despite the importance of checkpoints in current models for how genomic instability is avoided in the face of ubiquitous DNA damage. Unresolved DNA damage is presumably inherited by subsequent cell cycle phases and descendant cells yet characterisation of the consequences of this has been relatively limited to date. I therefore utilised microscopy-based lineage tracing of cells expressing genetically encoded fluorescent sensors, particularly the Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) probes (Sakaue-Sawano et al., 2008), with semi-automated image analysis to characterise the response of single cells and their descendants to DNA lesions across multiple cell cycle generations. This approach, complemented by generational tracing by flow cytometry, permitted me to characterise the timing of cell fate determination in treated and descendant cells, the non-genetic heterogeneity in checkpoint responses and overall lineage behaviour, correlations between cells (similarly to Sandler et al., 2015) and cell cycle timing dependencies in the response to DNA damaging agents. With these single cell analytical approaches I show that the consequences of DNA damage on descendant cell fate is dramatic, suggesting checkpoint mechanisms may have consequences and even cooperate across phases and generations. U2OS cell lineages traced for three generations following the induction of DNA damage in the form of strand breaks showed greatly induced cell death in the daughters and granddaughters of DNA damaged cells, termed delayed death. Furthermore, lineage behaviour was characterised as highly heterogeneous in when and whether cell death occurred. Complementary flow cytometric approaches validated the findings in U2OS cells and suggested HeLa cells may show similar behaviour. These findings indicate that checkpoint models need to incorporate multigenerational behaviour in order to better describe the response of cells to DNA damage. Understanding the processes governing cell fate determination in descendant cells will impact upon our understanding of the development of genomic instability during carcinogenesis and how DNA-damaging chemotherapeutics drive cells to ‘quit’ the cell cycle.

Adult mammalian <a></a><a>cardiomyocytes </a>(CMs, or heart muscle cells) have little, if any, ability to proliferate in response to injury, and after myocardial infarction this defect underlies the poor regenerative ability of human hearts. In contrast, early stage of CMs (such as fetal CMs) still have some ability to proliferate, and we seek to identify novel gene regulators as potential therapeutic targets for heart regeneration. Here we use human pluripotent stem cells (hPSCs) as an in vitro human model to investigate the roles of emerging long non-coding RNAs (lncRNAs), with the lengths of over 200 nucleotides are able to be transcribed but not translated into protein, for heart regeneration. With public available RNA-sequencing data, we identified several human genes, including lncRNAs, that are highly enriched in fetal CMs. We generated targeted gene knockout hPSC lines using CRISPR/Cas9-mediated genome editing and will use them to study the roles of selected genes in regulating CM proliferation. To identify more therapeutic targets, we also generated a fluorescence ubiquitination cell cycle indicator (FUCCI) reporter cell line that express either green (indicating dividing cells) or red fluorescence (indicating non-dividing cells), on which we’ll perform unbiased genome-wide screening to identity genes that regulate CM proliferation. High-throughput chemical screening will also be performed on FUCCI reporter lines to identify potential therapeutic drugs for heart regeneration.

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