京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22412号 / 工博第4673号 / 新制||工||1729(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 浜地 格, 教授 森 泰生, 教授 生越 友樹 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

La voie de signalisation Ras/MAPK (Ras/mitogen-activated protein kinase) régule une variété de protéines intracellulaires qui jouent un rôle important dans la croissance et la prolifération cellulaire. La régulation inappropriée de cette voie de signalisation conduit au développement de nombreux cancers comme le mélanome, qui est caractérisé par des mutations activatrices au niveau des gènes NRAS et BRAF. La protéine kinase RSK (p90 ribosomal S6 kinase) est un composant central de la voie Ras/MAPK, mais son rôle dans la croissance et la prolifération cellulaire n’est pas bien compris. RSK a été montrée pour participer à la résistance des mélanomes aux chimiothérapies, mais le mécanisme moléculaire reste encore à élucider. Nous montrons à l’aide d’un anticorps phospho-spécifique que MDM2 est phosphorylée en réponse à des agonistes et des mutations oncogéniques activant spécifiquement la voie Ras/MAPK. En utilisant des méthodes in vitro et in vivo, nous avons constaté que RSK phosphoryle directement MDM2 sur les Sérines 166 et 186, ce qui suggère que MDM2 est un substrat de RSK. La mutagénèse dirigée envers ces sites nous indique que ces résidus régulent l’ubiquitination de MDM2, suggérant que RSK régule la stabilité de MDM2 et de p53. De plus, nous avons observé que l’inhibition de RSK conduit à une augmentation du niveau protéique de p53 après un dommage à l’ADN dans les cellules de mélanomes. En conclusion, nos travaux suggèrent un rôle important de la protéine kinase RSK dans la régulation de MDM2 et de sa cible, p53. L’étude de ces mécanismes moléculaires aidera à mieux définir le rôle de RSK dans la croissance tumorale, mais également dans la résistance aux agents chimiothérapeutiques. / The Ras/mitogen-activated protein kinase (Ras/MAPK) signaling cascade regulates various intracellular targets involved in growth and proliferation. Inappropriate regulation of this pathway leads to many types of cancer, including melanomas, which are characterized by activating mutations in NRAS and BRAF. The protein kinase RSK (p90 ribosomal S6 kinase) is a central component of the Ras/MAPK pathway, but its role in cell growth and proliferation is not well understood. RSK has also been shown to participate in the resistance of melanoma cells to chemotherapy, but the mechanisms involved remain elusive. We show that MDM2 becomes phosphorylated in response to agonists and oncogenes of the Ras/MAPK pathway. Using in vitro and in vivo approaches, we found that RSK directly phosphorylates MDM2 at Ser166 and Ser186, suggesting that MDM2 is a bona fide RSK substrate. Site-directed mutagenesis indicated that these residues regulate MDM2 ubiquitination, suggesting that RSK regulates p53 function in an MDM2-dependent manner. Overexpression of active and inactive mutants of RSK revealed that this kinase regulates p53 stability, suggesting a role for RSK in the DNA damage response. Taken together, our results suggest an important role for RSK in the regulation of MDM2 and its target p53. In view of the role of p53 in the response to DNA-damaging agents, our results provide a potential mechanism involved in melanoma chemoresistance.

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Almost all organisms have an endogenously generated and self-sustained time-keeping system that oscillates with a periodicity of about 24 h, namely the circadian clock, that help them adapt to daily environmental changes. Mammalian circadian rhythms are generated and maintained by transcription-translation feedback loops (TTFLs) and include post-translational modifications to help fine-tune the oscillation. Circadian rhythms control a broad range of cellular signaling pathways including those mechanisms involved in cell division and DNA damage response (DDR). We have previously established that the core clock component PERIOD2 (PER2) binds to the tumor suppressor protein p53, a key regulatory checkpoint component that modulates cell cycle progression and the cellular response to genotoxic stress. PER2 binding to p53 modulates p53's stability, cellular localization, and transcriptional activity. As described in Chapter 2, we now identified PER2 as a previously uncharacterized substrate for the ubiquitin E3 ligase mouse double minute 2 homolog (MDM2), an oncoprotein and negative regulator of p53. Our findings showed that the association between PER2 and MDM2 is independent of the presence of p53. In addition, MDM2 targets PER2 for ubiquitylation and degradation in a phosphorylation-independent fashion. Lastly, our studies showed that MDM2 collaborates with β-transducin repeat-containing proteins (β-TrCPs), an E3 ligase that targets PER2 for ubiquitylation in a phosphorylation-dependent manner, to control PER2 degradation and thus the length of circadian period. Because the p53:MDM2 pathway plays a critical role in the cellular response to genotoxic stress, the project described in Chapter 3 is based on the hypothesis that DNA damage caused by radiation shifts the circadian clock phase via the p53:PER2:MDM2 complex. Firstly, we generated Trp53KO (Trp53 gene encodes mouse p53) cell lines in NIH 3T3 Per2:dLuc reporter cells expressing luciferase driven by the Per2 promoter. Phase-response curves (PRCs) for Trp53WT and Trp53KO reporter cells were obtained in response to ionizing radiation (IR) treatments. Results indicated that Trp53 knockout did not affect radiation-induced circadian phase shifts, whereas increased p53 levels induced by transient inhibitor treatments prevented phase shifts when IR was performed at the trough of PER2 abundance. Additional mechanisms were unveiled that kinases ATM (Ataxia Telangiectasia Mutated), ATR (ATM- and Rad3-related) and CHK2 (Checkpoint Kinase 2) regulate radiation-induced phase shifts. Lastly, we found that CLOCK (Circadian Locomotor Output Cycles Kaput) and CRY1 (CRYPTOCHROME 1) were phosphorylated in response to radiation. Taken together, these results indicate that radiation-induced clock phase shifts involve the activity of kinases ATM, ATR and CHK2, and the modification in CLOCK and CRY1. Chapter 4 is a review of current findings about the interaction between circadian rhythms and the cell division cycle regulation pathway. The article highlights a multidisciplinary approach that combines mathematical modeling and experimental data to reveal how p53:PER2:MDM2 acts as a node controlling timely cell cycle progression. In summary, our work provided evidence that MDM2 targets PER2 for ubiquitylation and degradation in a phosphorylation-independent manner, and this influences circadian oscillation. Furthermore, the exploration of p53:PER2:MDM2 association shed light on how radiation-induced DNA damage shifts clock phase. These findings expose a crosstalk mechanism that senses DNA damage and shifts the clock system. / Doctor of Philosophy / Mammals have a time-keeping system that oscillates with a periodicity of about 24 h, namely the circadian clock, that allows physiological and behavioral adaptation to environmental changes. The circadian clock controls and coordinates processes as diverse as sleep/wake cycle, feeding cycle, daily changes in body temperature, blood pressure and hormone secretion. At the cellular level, the circadian clock exists in almost all cells and controls a broad range of cellular signaling pathways including mechanisms involved in cell division and DNA damage response (DDR) pathway. Circadian disruption, for example, by night shift work, results in accumulation of DNA damage in cells and increases risk of cancer. In my thesis, we found that MDM2, a protein that is involved in the DDR signaling pathway and has the potential to cause cancer, controls the degradation of the core clock protein PERIOD2 (PER2), and thus regulates the length of circadian period. Further work exposed the mechanism for how DNA damage shifts the circadian clock. Our findings will have significant impacts on health and biomedical science, especially shedding light on optimizing the time in a day to give chemo- and radiation therapies to cancer patients.

Intrinsically disordered proteins (IDPs) are an abundant class of proteins and protein regions which rapidly change between multiple structures without an equilibrium position. IDPs exist as a series of conformational ensembles of semi-stable conformations that can be adopted based on a hilly landscape of shallow free energy minima. Disordered sequences share characteristic features differentiating them from globular proteins, including low sequence complexity, low occurrence of hydrophobic residues, high polar and charged residue content, and high flexibility. IDPs are commonly involved in regulation in the cell, and frequently function as, or interact with, hub proteins in protein-protein interaction networks, making them an important class of macromolecules for understanding regulatory and other processes. Given their functional importance, these proteins are widely studied. Many analytical techniques are used, though rapid conformational sampling by IDPs makes it difficult to detect many states with NMR or other techniques. Computational approaches such as molecular dynamics are increasingly used to probe the binding and conformational sampling of these proteins, allowing for observation of factors that cannot be observed with traditional analytical methods such as NMR, such as differing conformational ensembles and the dipoles of individual residues. Here, we studied the role of electrostatic interactions in IDP protein-protein interaction using molecular dynamics simulations performed with the Drude-2019 force field (FF), a polarizable model that allows for more accurate representation of electrostatics, an important factor for highly charged systems like IDPs. For this project, a prototypical protein with disordered regions, p53, was simulated with two protein partners, the nuclear coactivator domain of the CREB binding protein (CBP), and the E3 ubiquitin-protein ligase mouse double minute 2 (MDM2). p53 is widely studied, and the p53 transactivation domain (TAD) is disordered and binds to many structurally diverse partners, making this protein domain a useful model for probing the role of electrostatic interactions formed by IDPs at protein-protein binding interfaces. We found that the Drude-2019 FF allows for simulation of the p53 TAD with Cα chemical shifts comparable to those observed with NMR, supporting that the Drude-2019 FF performs well in simulating IDPs. We observed large relative change in sidechain dipole moments when comparing the p53 TAD alone and when bound to either CBP or MDM2. We observed that aliphatic and aromatic amino acids experienced the largest relative change in sidechain dipole moments, and that there is sensitivity to binding shown in this dipole response. The largest percent changes in sidechain dipole moment were found to localize at and around the binding interface. Understanding the binding interactions of IDPs at a fundamental level, including the role of electrostatic interactions, may help with targeting IDPs or their partners for drug design. / Master of Science in Life Sciences / Many proteins adopt one main structure, and these proteins are called ordered proteins. Intrinsically disordered proteins (IDPs) are an abundant category of proteins which adopt multiple structures, and transition between these different structures is based on factors such as the environment around them, modifications, or interactions with other macromolecules. The flexible structures of IDPs allow them to bind to multiple different partners and to regulate processes in the cell. Since IDPs often regulate processes important to cell function, when these proteins are mutated, misfolded, or otherwise mis-regulated the resulting issues are associated with disease states. IDPs are widely studied with analytical techniques, but because IDPs frequently change shape it can be difficult to observe certain behaviors or certain factors with these techniques. Computational approaches, such as molecular dynamics (MD). MD is the study of molecular motion and interaction, and can allow observation of factors that would be difficult or impossible to observe otherwise, such as the varying structures of IDPs or the dipole moments of specific amino acids within the proteins. For this project we wanted to probe the role of dipole moments, which are charge-based interactions, in the binding of IDPs to protein partners, to better understand how IDPs bind to different partners. We used the p53 protein as an example of IDP binding and simulated it alone and bound to two other proteins, the CREB binding protein (CBP), and the E3 ubiquitin-protein ligase mouse double minute 2 (MDM2). We observed that our simulations were comparable to experiments done with nuclear magnetic resonance spectroscopy, which served to validate that our simulations were realistic. We observed that the dipole moments of the proteins change when simulating the proteins alone and in complex, and that the largest relative changes in dipole are observed for regions of the proteins involved in binding. Probing the role of charge-based interactions in protein-protein binding interactions for IDPs can help us to greater understand these interactions at a more fundamental level and could help with targeting IDPs or their partners for drug design or other problems.

Le terme d’« hypertension artérielle pulmonaire » (HTAP) décrit une maladie vasculaire pulmonaire caractérisée par une augmentation progressive des pressions artérielles pulmonaires (PAP), définie par une PAP moyenne supérieure ou égale à 25 mmHg au repos et dont le principal symptôme est un essoufflement à l’effort. Un remodelage artériel pulmonaire intense conduisant à une obstruction des petits vaisseaux pulmonaires est responsable de la maladie. C’est une maladie rare mais néanmoins grave car pouvant aboutir à une insuffisance ventriculaire droite et entraîner le décès du patient.Le cadre général de notre étude est l’amélioration de la compréhension des mécanismes physiopathologiques de l’HTAP afin d’identifier de nouvelles cibles thérapeutiques potentielles. Nous nous sommes intéressés plus particulièrement au phénotype « pseudo-tumoral » des cellules musculaires lisses des artères pulmonaires (CML-AP) des patients atteints d’HTAP qui jouent un rôle primordial dans le remodelage vasculaire pulmonaire de l’HTAP et qui présentent des caractéristiques communes avec les cellules cancéreuses, notamment une hyper-prolifération, une résistance à l’apoptose, des désordres métaboliques et une instabilité génomique. Etant donné que la protéine p53, un des plus importants suppresseurs de tumeur, est largement décrite comme inactivée dans la plupart des cancers, nous avons émis l’hypothèse qu’elle pourrait également jouer un rôle important dans le développement de l’HTAP. Les résultats des études in vitro menées sur des CML-AP de patients atteints d'HTAP idiopathiques (HTAPi) versus des sujets contrôles semblent indiquer que la protéine p53 n’est pas altérée dans les CML-AP HTAPi. En effet, la séquence codante du gène TP53 ne présente pas de mutation dans les CML-AP HTAPi, les expressions génique et protéique de p53 (et de certaines de ses protéines cibles) ne semblent pas être différentes entre contrôles et HTAPi, ni à l’état basal ni en réponse à différents stress cellulaires inducteurs de p53 (étoposide et H2O2). Cependant, la régulation de p53 semble altérée puisque nous avons observé une augmentation du taux protéique de MDM2, principal régulateur de p53, dans les CML-AP HTAPi. Ce résultat peut être considéré comme une des caractéristiques « pseudo-tumorales » des CML-AP HTAPi mais également être un élément déterminant du mécanisme d’action de la Nutlin-3a, qui a montré des effets anti-prolifératifs accrus dans les CML-AP HTAPi.Dans des études in vivo menées chez le rat, la protéine p53 semble jouer un rôle dans l’initiation de la pathogénèse d’une HTAP. En effet, les taux protéiques pulmonaires de p53, de sa cible p21 et de son régulateur (mais également cible transcriptionnelle) MDM2 sont diminués lors de la première semaine dans un modèle d’induction d’HTAP par mono-injection de monocrotaline (MCT) chez le rat, au cours duquel la pathologie se développe à partir de la 2ème semaine. De plus, l’administration quotidienne à des rats d’un inhibiteur de l’activité transcriptionnelle de p53, le pifithrin-α (PFT), conduit au développement d’une HTAP en 14 jours, au même titre qu’une mono-injection de MCT, et aggrave l’HTAP induite par la MCT. Des effets pro-prolifératifs et anti-apoptotiques du PFT révélés sur des CML-AP indiquent que l’inhibition de l’activité transcriptionnelle de p53 est à l'origine d'une prolifération exagéree et une résistance à l'apoptose, deux composantes clés dans le remaniement vasculaire pulmonaire et le développement de l'HTAP.En conclusion, ces résultats mettent en évidence l’implication de l’inactivation de la voie de p53 lors de la phase initiatrice du développement de l’HTAP, alors qu’aux stades tardifs et sévères de la maladie, il semble il y avoir une normalisation de p53. En revanche, l’augmentation de l’expression de son principal régulateur MDM2 observée dans les CML-AP de patients HTAP semble être une cible thérapeutique potentiellement intéressante. / Pulmonary artery hypertension (PAH) is a severe pulmonary vascular disease characterized by a progressive increase of the pulmonary arterial pressure (PAP), defined by a mean PAP greater than or equal to 25 mmHg at rest. The main symptom is a shortness of breath. An intense pulmonary arterial remodeling that leads to an obstruction of the small pulmonary vessels is responsible of the disease. PAH is a rare but severe disease that develops into right ventricular cardiac failure leading to the patient's death.The general framework of our study was to improve the understanding of the pathophysiology of PAH in order to identify new potential therapeutic targets and improve the clinical management of patients. In particular, we were interested in the “cancer-like phenotype” of PAH patient pulmonary arterial smooth muscle cells (PA-SMCs). PA-SMCs play a key role in the pulmonary vascular remodeling of PAH. These cells share characteristics with cancerous cells, such as: exaggerated proliferation, apoptosis resistance, metabolic disorders and genomic instability. Owing to the growth-suppressive and pro-apoptotic functions of p53 protein and its inactivation largely described in cancer, we hypothesized that the p53 pathway could also be altered during PAH development in PA-SMCs.The results of in vitro studies on PA-SMCs of late stage patients with idiopathic PAH (iPAH) versus control patients suggest that the p53 protein nor pathway is not altered in iPAH PA-SMCs. Indeed, the coding sequence of the TP53 gene presented no mutations in iPAH PA-SMCs. Analysis of mRNA and protein levels of p53 and its target proteins showed no difference between controls and iPAH PA-SMCs, neither in a basal state or in response to various cellular stresses such as etoposide and H2O2. However, regulation of p53 may be altered in iPAH PA-SMCs as we observed an increase of the MDM2 (the main p53 regulator) protein level compared to control. This last result may be considered as a “cancer-like” characteristic of iPAH PA-SMCs and also be a determining factor in the mechanism of action of Nutlin-3a, which had more important anti-proliferative effects in iPAH PA-SMCs than in control cells.In vivo studies in rats revealed, however, that the p53 pathway may play a role in the initiation stage of PAH pathogenesis. Indeed, kinetics evaluation of p53 lung expression in the PAH model, induced by a single injection of monocrotaline (MCT), revealed a decrease in the p53 protein level during the first week, followed by a normalization by the second week. PAH symptoms are developed in MCT rats after two weeks. Similarly, the protein levels of p21, a p53 target, and MDM2, the major p53 regulator, and also a transcriptional target of p53, decreased during the first week in the MCT-PAH model. In addition, daily treatment in rats with an inhibitor of p53 transcriptional activity, pifithrin-α (PFT), led to the development of PAH in 14 days, similarly to MCT, and worsened the PAH induced by MCT. Pro-apoptotic and anti-proliferative effects of PFT on PA-SMCs indicate that inhibition of p53 transcriptional activity causes an excessive proliferation and an apoptosis resistance, which are two key components of the pulmonary vascular remodeling and development of human and experimental PAH.In conclusion, these results demonstrate the involvement of the p53 pathway inactivation in the initiation stage of PAH development, whereas in late and severe stages of disease, its role seems to be less implicated. In contrast, the increased expression of MDM2 observed in PA-SMCs of PAH patients may be a potential therapeutic target.

Dissertation (Ph.D.)--University of South Florida, 2007. / Title from PDF of title page. Document formatted into pages; contains 131 pages. Includes vita. Includes bibliographical references.