Thesis (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2006. / Not embargoed. Vita. Bibliography: 97-109.

Nous nous proposons d'étudier la gestion du bruit stochastique d'expression génique. On s'intéresse plus particulièrement à la dynamique du bruit lors de la réponse cellulaire. Comment évolue le bruit? Quels sont les mécanismes en jeux? Quelle est l'importance du bruit dans le fonctionnement cellulaire? Pour répondre à ces questions, nous nous appuyons sur le réseau de régulation génétique qui gère la réponse au stress nutritionnel chez E. Coli. L'étude du comportement dynamique de ce réseau, au niveau d'une population de bactéries, a été initiée et est portée par la forte collaboration de deux équipes de la région : une de bio-informaticiens (l'équipe de Hidde de Jong de l'INRIA Rhône-Alpes) et la deuxième de biologistes (l'équipe de Hans Geiselmann, Laboratoire d'Adaptation et Pathogénie des Micro-organismes). En profitant donc de l'expérience et de la compréhension acquise par ces équipes, nous étudions les réponses individuelles de chaque bactérie lors de la transition entre état de stress nutritionnel, et état de croissance exponentielle. Le bruit d'expression génique est quantifié dans des nœuds clés du réseau de régulation. Pour ce faire, les bactéries sont suivies individuellement par microscopie de fluorescence sur plusieurs générations. Les données de fluorescence collectées sur cellules uniques permettent d'étudier la variabilité inter-cellulaire. Cette variabilité est quantifiée tout le long de la réponse: à chaque instant, on connaît la distribution des densités de fluorescence cellulaire dans la population de cellules. Et le suivi des lignées individuelles permet de travailler sur une population de cellules saines: les individus malades ou morts qui ne se divisent pas, sont écartés. En réduisant ainsi les phénomènes cellulaires en jeux, on réduit le nombre de paramètres. Les sources de bruit sont moins nombreuses, et il est plus facile de comprendre les mécanismes en jeux. Les informations de lignage cellulaire permettent aussi d'étudier la variabilité introduite par la phase du cycle cellulaire: les événements de division cellulaire peut être artificiellement synchronisés. Le bruit est alors étudié sur une population en phase lors de la division. Cette étude montre que le bruit sondé n'est pas dominé par les différences dans la phase du cycle cellulaire. On peut donc modéliser nos cellules sans tenir compte des différences introduites par le cycle cellulaire. Le modèle testé est simplifié aux étapes de transcription-traduction-maturation. Les paramètres du modèle sont inférés de nos données expérimentales, et le modèle est testé à travers des simulations. / We aim to investigate the management of the stochastic noise in gene expression and more precisely the study of noise in dynamical cellular responses. How the noise varies following a perturbation? What mechanisms are at play? How important is noise in the cellular function? To answer these questions, we are interested in the genetic regulatory network that handles the nutritional stress response in E. Coli. The noise of gene expression is quantified in a key node of the network control. For that bacteria are followed individually by fluorescence and phase contrast microscopy over several generations. This variability between cells is quantified throughout the response to the nutritional perturbation: at every moment, we know the density distribution of cellular fluorescence in the cell population. And monitoring of individual lines allows us to take into account only the population of healthy cells: individuals that do not divide neither grow, are discarded. Thereby reducing other sources of variability (e.g. cellular phenomena) we reduce the number of parameters. Noise sources are less numerous, and it is easier to understand the mechanisms at play. Also the information on cell lineage allow to study the variability introduced by the phase of the cell cycle: the events of cell division can be artificially synchronized. This study shows that the noise sounded is not dominated by differences in the phase of the cell cycle. We can therefore model our cells regardless of the differences introduced by the cell cycle. The tested model is simplified to the steps of transcription-translation-maturation. The model parameters are inferred from our experimental data and the model is tested through simulations.

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Erythropoiesis maintains stable tissue oxygenation in the basal state, while accelerating red cell production in anemia, blood loss or high altitude. The principal regulator of erythropoiesis is the hormone erythropoietin (Epo). In response to hypoxic stress, Epo can increase a 1000-fold, driving erythropoietic rate by up to 10-fold. It’s been suggested that survival pathways activated by the Epo receptor (EpoR) underlie its regulation of erythropoietic rate. A number of apparently redundant EpoR survival pathways were identified in vitro, raising the possibility of their functional specialization in vivo. Here I assessed the roles of three survival pathways activated by EpoR in erythroblasts in-vivo: the suppression of cell-surface Fas and FasL, the suppression of the pro-apoptotic regulator Bim, and the induction of the anti-apoptotic regulator Bcl-xL. I used the novel CD71/Ter119 flow-cytometric method of identifying erythroblast maturation stages in vivo to measure these apoptotic pathways in fetal liver and adult erythropoietic tissues. I found that these pathways differ markedly in their regulation of erythropoietic rate. Using mouse genetic models, I found that apoptosis mediated by interaction between erythroblasts that co-express cell-surface Fas and FasL plays a key autoregulatory role in stabilizing the size of the erythroblast pool in the basal state. Further, mice mutant for Fas or FasL showed a delayed erythropoietic response to hypoxia or high Epo. This suggests that Fas and FasL accelerate the stress response by providing an apoptotic ‘cell reserve’ that can be rescued by Epo in stress. I also examined the in-vivo behavior of two cell-intrinsic apoptotic regulators, Bcl-xL and Bim, previously unexamined in stress. The induction of Bcl-xL was rapid but transient, whilst the suppression of Bim was slower but persistent. My data suggest that Bcl-xL is a key mediator of EpoR’s anti-apoptotic signal very early in the stress response, before Bim and Fas are suppressed. Bcl-xL adaptation to high Epo occurs through inhibition of Stat5 activation, and resets it for the next acute stress. My findings suggest that in vivo, Epo regulates erythropoietic rate through erythroblast apoptosis, and that various apoptotic regulators play distinct and unique roles in this process. My work provides new molecular insights into erythropoiesis that are relevant to cytokine biology and to clinical approaches of disease treatment.

Beclin 1 is a haplo-insufficient tumor suppressor that is decreased in many human tumors. The function of Beclin 1 in cancer has been attributed primarily to its role in the degradative process of autophagy. However, the role of autophagy itself in tumorigenesis is context-dependent and can be both preventive and promoting. Due to its dual function in cancer a better understanding of this process is necessary to develop potential novel cancer therapies. To gain insight into the role of autophagy in breast carcinoma, I analyzed the autophagydependency of different subtypes of breast cancer. My results implicate that triple-negative breast carcinoma cells are more dependent on autophagy than luminal breast carcinoma cells. Chemical inhibition of autophagy decreased the tumorigenicity of triple-negative breast carcinoma cells with regard to proliferation and anchorage-independent growth. However, RNAi-mediated suppression of two autophagy genes, ATG5 and Beclin 1, revealed different outcomes. While suppression of ATG5 decreased glycolysis, Beclin 1 depletion did not affect the glycolytic rates. These results suggest autophagy-independent pro-tumorigenic effects of loss of Beclin 1 in cancer. Beclin 1 is a core component of the Vps34/Class III PI3K (PI3KC3) and Vps15/p150 complex that regulates multiple membrane trafficking events. I describe a novel mechanism of action for Beclin 1 in breast cancer involving its control of growth factor receptor signaling. I identify a specific stage of early endosome maturation that is regulated by Beclin 1, the transition of APPL1- containing phosphatidyIinositol 3-phosphate-negative (PI3P-) endosomes to PI3P+ endosomes. Beclin 1 regulates PI3P production in response to growth factor stimulation to control the residency time of growth factor receptors in the PI3P-/APPL+ signaling competent compartment. As a result, suppression of BECN1 sustains growth factor stimulated AKT and ERK activation resulting in increased breast carcinoma cell invasion. In human breast tumors, Beclin 1 expression is inversely correlated with AKT and ERK phosphorylation. Taken together my data identify a novel role for Beclin 1 in regulating growth factor signaling and reveal a mechanism by which loss of Beclin 1 expression would enhance breast cancer progression independent of its impact on autophagy.

Indiana University-Purdue University Indianapolis (IUPUI) / Monomers like triethylene glycol dimethacrylate (TEGDMA) leach from dental composites and adhesives due to incomplete polymerization or polymer degradation. The release of these monomers causes a variety of reactions that can lead to cell death. This death can be either necrotic, which is characterized mainly by inflammation and injury to the surrounding tissues, or apoptotic, which elicits little inflammatory responses, if any at all. TEGDMA-induced apoptosis in human pulp has been reported recently. However, the molecular mechanisms and the apoptotic (pro and anti) proteins involved in this process remain unclear. The objective of this study was to determine the apoptotic proteins expressed or suppressed during TEGDMA-induced apoptosis. Human pulp fibroblasts (HPFs) were incubated for 24 hours with different TEGDMA concentrations (0.125-1.0 mM). Cytotoxicity was determined using the cytotoxicity Detection KitPLUS (Roche Applied Science, Mannheim, Germany). TEGDMA was shown to cause cell cytotoxicity at concentrations of 0.50 mM and up. The highest concentration with no significant cytotoxicity was used. Cells were incubated with or without 0.25 mM TEGDMA for 6 h and 24 h. Cell lysates were then prepared and the protein concentrations determined using the Bradford protein assay. A Human Apoptosis Array kit (Bio-Rad Hercules, CA ) was utilized to detect the relative levels of 43 apoptotic proteins. The results of this study showed statistically significant increases of multiple examined pro-apoptotic proteins. The anti-apoptotic proteins were also altered. Pro-apoptotic proteins involved in the intrinsic and extrinsic apoptotic pathways were increased significantly. The results indicated that TEGDMA has effects on both the extrinsic and intrinsic apoptotic pathways.

Hepatocellular carcinoma (HCC) is the third commonest cancer worldwide. However HCC is considered to be highly resistant to chemotherapy. Gene therapies aimed to regulate Bd-2 proteins may sensitize HCC cells to chemotherapy. Studies have demonstrated that Bid/tBid are crucial in hepatocyte apoptosis. Bid also plays important roles in the development and chemotherapeutic sensitivity of HCC. The objective of this study is to test effect of Ad/AFPtBid and chemotherapeutic agents in combination on an orthotopic HCC model. / In conclusion, (1) Ad/AFPtBid can specifically target and effectively suppress the AFP-producing HCC. (2) Ad/AFPtBid can significantly sensitize HCC to 5-FU, their combination can significantly increase the anti-tumor effectiveness. (3) Ad/AFPtBid shows little toxicity in vivo. (4) The complementary effect of tBid and 5-FU on different phases of the cell cycle may explain the better therapeutic result if both are used to treat HCC. (5) The elucidation of phase specific effect of tBid points to a possible therapeutic option that combines tBid with different phase specific agents to treat HCC. / It is well established that many apoptosis inducers act in a cell cycle-specific fashion. This leads us to hypothesize that tBid might have phase specific effect. So, we tested the susceptibility of Hep3B cells at 00/01, S or G2/M phases to tBid. The results revealed that tBid significantly reduced Hep3B cells in G0/G1 phase, increased cells in G2/M phase. On the contrary, 5-FU arrested Hep3B cells in G0/G1 phase, and significantly reduced cells in G2/M phase. The levels of cell cycle-related proteins were altered in line with the result of the cell cycle. This suggests Hep3B cells in G0/G1 phase may be more susceptible to tBid. The complementary effects tBid and 5-FU on different phases of the cell cycle may explain the better therapeutic result if both are used to treat HCC. / The mice bearing orthotopic HCC tumors were treated with Ad/AFPtBid alone or in combination with 5-FU/Dox. Serum AFP levels were measured to mornitor tumor progression. The mice were killed four weeks after treatment. Liver tissues were subjected to immunohistochemical staining of proliferation cell nuclear antigen (PCNA) and TUNEL staining. Another batch of mice was observed for survival rate over a six month period. In addition, possible side effects of Ad/AFPtBid were tested in BALB/c mice. Results demonstrated that Ad/AFPtBid significantly inhibited Hep3B tumor growth. The combination of Ad/AFPtBid with 5-FU was more effective in tumor regression than either agent alone. However, the combination of Ad/AFPtBid with Dox treatment failed to demonstrated better effect than Dox treatment alone because the mice that received Dox exhibited serious weight loss. Tumor tissues from Ad/AFPtBid alone or combination treatment groups showed a decrease in cells positive for PCNA, and an increase in apoptosis by TUNEL staining, indicating that Ad/AFPtBid induced tumor regression through its pro-apoptotic effect. Inflammatory cell infiltration was also increased. Furthermore, Ad/AFPtBid did not suppress the hepatic tumor formed by non-AFP producing SK-HEP-1 or DLD-1. Finally, Ad/AFPtBid and 5-FU in combination results in better survival rate. No acute toxic effect of Ad/AFPtBid was observed. / Ma, Shihong. / "December 2009." / Adviser: CHEN Gong George. / Source: Dissertation Abstracts International, Volume: 72-01, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 114-138). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.