In the presence of a non-fermentable carbon source, nitrogen-starved diploid cells of the yeast Saccharomyces cerevisiae undergo a meiotic program called sporulation to form gametes called spores. While four spores are produced under standard laboratory sporulation conditions, spore number is known to be regulated by carbon availability: under carbon-depleted conditions, yeast cells package a portion of the four haploid meiotic nuclei into spores. Our lab has demonstrated that these unpackaged meiotic products undergo programmed nuclear destruction (PND) that is associated with apoptotic-like DNA fragmentation. Nevertheless, the mechanism that mediates PND remained to be elucidated. Here, I describe the execution of PND through an unusual form of autophagy that has not been documented previously in yeast. This form of autophagy is most similar to megaautophagy in plants and lysosomal membrane permeabilization in mammals. My results demonstrate further diversity in cell death programs in unicellular microbes that is potentially conserved across eukaryotes.

Autophagy is an evolutionarily conserved degradative eukaryotic cell pathway that plays a role in multiple cellular processes. One important function is as a key component of the cellular immune response to invading microbes. Autophagy has been found to directly target and degrade multiple intracellular bacterial species. In this thesis, I identify and characterize two distinct regulatory mechanisms for this pathway involving the second messengers: diacylglycerol and cyclic adenosine monophosphate (cAMP). Salmonella enteric serovar Typhimurium (S. Typhimurium) is a Gram-negative bacterial species that has been shown to be intracellularly targeted for degradation by autophagy. While targeting of this species has been previously shown to involve ubiquitination, this pathway accounts for only half of targeted bacteria. Here I show that ubiquitin-independent autophagy of S. Typhimurium requires the lipid second messenger diacylglycerol. Diacylglycerol localization to the bacteria precedes autophagy and functions as a signal to recruit the delta isoform of protein kinase C (PKC) in order to promote the specific autophagy of tagged bacteria. Furthermore, I have found that the role of diacylglycerol and PKC delta is not limited to antibacterial autophagy but also functions in rapamycin-induced autophagy indicating a general role for these components in this process. Multiple bacterial species have been found to be targeted by autophagy and while some have developed strategies that allow them to avoid targeting, no bacterial factor has yet been identified that is able to inhibit the initiation of this process. Here I show that two bacterial species, Bacillus anthracis and Vibrio cholera inhibit autophagy through the elevation of intracellular cAMP and activation of protein kinase A. Using two different bacterial cAMP-elevating toxins, I show that multiple types of autophagy are inhibited in the presence of these toxins. This is indicative of a general inhibitory function for these toxins and identifies a novel bacterial defence strategy. This work characterizes both a novel regulatory signal for the induction of autophagy and identifies a novel bacterial tactic to inhibit this process. Together the data presented in this thesis provide novel insight into the regulation of autophagy and offer potential targets for modulation of this process.

Autophagy is an evolutionarily conserved degradative eukaryotic cell pathway that plays a role in multiple cellular processes. One important function is as a key component of the cellular immune response to invading microbes. Autophagy has been found to directly target and degrade multiple intracellular bacterial species. In this thesis, I identify and characterize two distinct regulatory mechanisms for this pathway involving the second messengers: diacylglycerol and cyclic adenosine monophosphate (cAMP). Salmonella enteric serovar Typhimurium (S. Typhimurium) is a Gram-negative bacterial species that has been shown to be intracellularly targeted for degradation by autophagy. While targeting of this species has been previously shown to involve ubiquitination, this pathway accounts for only half of targeted bacteria. Here I show that ubiquitin-independent autophagy of S. Typhimurium requires the lipid second messenger diacylglycerol. Diacylglycerol localization to the bacteria precedes autophagy and functions as a signal to recruit the delta isoform of protein kinase C (PKC) in order to promote the specific autophagy of tagged bacteria. Furthermore, I have found that the role of diacylglycerol and PKC delta is not limited to antibacterial autophagy but also functions in rapamycin-induced autophagy indicating a general role for these components in this process. Multiple bacterial species have been found to be targeted by autophagy and while some have developed strategies that allow them to avoid targeting, no bacterial factor has yet been identified that is able to inhibit the initiation of this process. Here I show that two bacterial species, Bacillus anthracis and Vibrio cholera inhibit autophagy through the elevation of intracellular cAMP and activation of protein kinase A. Using two different bacterial cAMP-elevating toxins, I show that multiple types of autophagy are inhibited in the presence of these toxins. This is indicative of a general inhibitory function for these toxins and identifies a novel bacterial defence strategy. This work characterizes both a novel regulatory signal for the induction of autophagy and identifies a novel bacterial tactic to inhibit this process. Together the data presented in this thesis provide novel insight into the regulation of autophagy and offer potential targets for modulation of this process.

Medulloblastoma cells do not contain detectable amounts of the bZIP protein Zhangfei. However, previous work has shown that expression of this protein in cells of the ONS-76 line, derived from a human medulloblastoma, causes the cells to stop growing and develop processes that resemble neuritis (a characteristic of differentiated neurons). Zhangfei-expressing cells eventually die. My objective was to determine the molecular mechanisms by which Zhangfei influences ONS-76 cells. My strategy was to infect ONS-76 cells with adenovirus vectors expressing either Zhangfei or the control E. coli protein â-galactosidase (LacZ) and then to compare the following parameters in Zhangfei and LacZ-expressing cells: a) markers of apoptosis, autophagy and macropinocytosis (the three main pathways of cell death); b) transcripts for genes involved in neurogenesis and apoptosis; c) phosphorylation of peptide targets of selected cellular protein kinases; and d) active transcription factors. Zhangfei-expressing cells appeared to succumb to apoptosis as determined by the expression of phosphatidylserine on the cell surface and intensity of nuclear staining with the DNA dye Hoechst. Increased staining for autophagic vesicles and upregulated expression of autophagy response genes in these cells indicated that they were undergoing autophagy, possibly associated with apoptosis. My analysis of steady-state transcripts for genes involved in apoptosis and neurogenesis and functional protein kinases in Zhangfei-expressing cells indicated that the mitogen-activated protein kinase (MAPK) pathway was active in these cells. In addition, I found that the transcription factor Brn3a as well as factors implicated in differentiation were also active. These observations led me to hypothesize that Zhangfei enhances the expression of Brn3a, a known inducer of TrkA, the high-affinity receptor for nerve growth factor (NGF). TrkA then binds in an autocrine manner to NGF, triggering the MAPK pathway and leading to differentiation of ONS-76 cells into neuron and glia-like cells, eventually bringing about cell death by apoptosis and autophagy. I tested this hypothesis by showing that Zhangfei could enhance transcription from the isolated Brn3a promoter, that ONS-76 cells produce NGF as detected in a bioassay, and that antibodies against NGF and inhibitors of TrkA and selected components of the MAPK pathway could partially restore the growth of Zhangfei-expressing ONS-76 cells. My work supports previous work highlighting the importance of NGF-TrkA signaling in the outcome of medulloblastomas and shows how Zhangfei is able to trigger this pathway.

Deregulation of autophagy plays an important role in the pathogenesis of diseases such as cancer, neuronal degenerative or cardiovascular disease. Autophagy is a process to engulf the cytoplasmic contents into autophagosome and deliver them for lysosomal degradation. Its major function is to clear unfolded protein or damage organelles for maintaining proper metabolic homeostasis and normal cell physiological activities. Autophagy and multivesicular bodies, MVBs, cooperate to regulate the turnover of intracellular macromolecule, defective organelles and signaling receptor. Endosomal sorting complex required for transport, ESCRT, is important for the formation of MVBs, which regulates membrane receptor recycling, protein sorting and vesicular trafficking. Tumor Susceptibility Gene 101(TSG101) is a member of ESCRT-I that plays an important role on MVBs formation and maintaining ESCRT function. Previous report indicated that autophagosome accumulation upon deprivation of TSG101, implying possible role of TSG101 during autophagic process. In this study, we observed the increase of TSG101 and autophagic marker proteins, such as LC3-II and ATG upon nutrient starvation. Furthermore, knockdown TSG101 in cervical carcinoma HeLa cell resulted in the elevation of LC3-II, ATG3 and ubiquitinated protein aggregates marker protein p62, which is congruous to other reports. However, in neuroblastoma SH-SY5Y cell, transfection of siRNA led to the decrease of LC-II and ubiquitinated protein level. These results indicated that TSG101 might be critical for autophagy and the maintenance of steady-state level of cellular ubiquitinated proteins. Ectopic upregulatory expression of HA-TSG101 led to the increase of LC3-II in both cell type. The elevation of ATG3 level is also observed in HeLa cell. Therefore, we speculated that TSG101 might be important for the formation of autophagosome, but our data did not exclude the possible role of TSG101 in regulation of the fusion of autophagosome and lysosome, because the increase of ATG3 indicated ectopic HA-TSG101 might facilitate the execution of autophagic flow. In addition, we have established GFP-LC3 expression cell lines. Our imaging data showed the colocalization of TSG101 and GFP-LC3 in both cytoplasm and nucleus that might be an interesting research topic for investigation the role of TSG101 in autophagic pathway.

Melanoma manifests itself from the malignant transformation of melanocytes and represents the deadliest form of skin cancer, being responsible for the disproportionate majority of all skin cancer deaths. The 2002 discovery that 50% of all melanoma patients possess activating BRAF mutations ignited a significant paradigm shift in the way the melanoma field approached research and how patients were treated [1]. The era of targeted therapy had begun and with it came successful targeted BRAF inhibitor therapy regimens, which have accomplished improved clinical benefit (response rate, progression free survival, and overall survival) compared with treatment with chemotherapy in three phase III clinical trials [2]. Although there has been much success in the subgroup of patients whose melanomas harbor activating BRAF mutations, approximately 50% of all melanoma patients do not harbor BRAF mutations. This subgroup of melanoma is composed of ~15-20% of all patients with NRAS mutations and another ~25-30% of patients with neither BRAF nor NRAS mutations. Successful targeted treatment strategies are currently lacking for this subgroup of BRAF-wild type melanomas and therefore novel targeted therapeutic modalities are urgently needed. The work described in this dissertation sheds light on potential approaches for the treatment of BRAF wild type melanoma and will be split into three separate strategies. The first will focus upon the treatment of melanomas without BRAF or NRAS mutations (BRAF/NRAS wild type melanoma) and will expand upon a clinical observation where two melanoma patients were treated with an experimental combination of carboplatin and paclitaxel, with the addition of the AKT inhibitor MK-2206. We demonstrate that the inhibition of AKT significantly enhances the efficacy of chemotherapy in a reactive oxygen species (ROS) mediated fashion, and an induction of autophagy plays a cyto-protective role. The second story focuses upon the treatment of NRAS mutant melanomas by investigating resistance mechanisms to MEK inhibitor treatment. We discovered a MEKi-mediated induction of receptor tyrosine kinase (RTK) signaling to serve as a significant mechanism of escape for NRAS mutant melanomas treated chronically with the MEK inhibitor AZD6244, as well as the recently U.S. Food and Drug Administration (FDA) approved MEK inhibitor trametinib. Novel targeted therapy combinations were then added to overcome the escape from MEK inhibitor therapy. Co-targeting of the receptor tyrosine kinases AXL, PDGFR-β and c-MET with a pan-RTK inhibitor, as well as the mitogen-activated protein kinase (MAPK) pathway with a MEK inhibitor greatly enhanced treatment-induced apoptosis and inhibition of proliferation. The final strategy builds upon the observation that single agent MEK-inhibition is largely ineffective in the treatment of NRAS mutant melanomas. A recovery of MAPK pathway activity in response to MEK inhibition was established to play a significant role in escape of NRAS mutant cells from cell cycle arrest and apoptosis. The combination of a MEK inhibitor with the novel ERK inhibitor VTX-11e prevents the onset of resistant clones and enhances cytotoxicity of the NRAS mutant melanoma cells. This body of work establishes original targeted therapy combinations for the treatment of both NRAS mutant melanomas and BRAF/NRAS wild type melanomas. We propose future clinical investigation with these strategies in the treatment of BRAF wild type melanoma patients in hopes to further extend overall survival.

Autophagy is a catabolic pathway utilized by cells to maintain homeostasis. Dysregulation of this pathway often leads to various diseases, such as cancers and neurodegeneration. Therefore, autophagy must be tightly regulated by the extracellular environment or signaling pathways. The class III PI3 kinase complex, a lipid kinase complex functioning in converting phosphatidylinositol to phosphatidylinositol-3-phosphate, is a key regulator of autophagy that functions as a signaling hub where multiple regulatory signals converge. Here, we demonstrate that the class III PI3 kinase complex is negatively regulated by cyclin-dependent kinases (Cdks). The catalytic subunit of the kinase complex, Vps34, is phosphorylated by Cdk1 in mitotic cells and by Cdk5 in postmitotic cells. Phosphorylation on Vps34 results in its dissociation from a regulatory subunit Beclin 1, leading to decreased lipid kinase activity. As a result, autophagy is inhibited in dividing cells and postmitotic neuronal cells with elevated Cdk5 activity. Since dysfunction of autophagy has been shown to be implicated in cancers and neurodegeneration, which are characterized by abnormal activity of Cdk1 and Cdk5, respectively, our study provides a mechanism by which autophagy is modulated in those diseases. To further discover the regulatory mechanisms of autophagy, we used a novel autophagy inhibitor, spautin-1, identified in a small molecule screening. Spautin-1 inhibits autophagy by inhibiting Usp10/Usp13, which deubiquitinate and stabilize the class III PI3 kinase complex. Interestingly, Usp10/Usp13 are also stabilized by the class III PI3 kinase complex, suggesting that they are reciprocally regulated. These results led us to the observation that p53, a substrate of Usp10 is regulated by the class III PI3 kinase complex and spautin-1. We also report that A70, a more potent derivative of spautin-1, leads to the degradation of mutant p53 through the chaperone-mediated autophagy, whereas the wild-type p53 is degraded by the ubiquitin-proteasome system. Our study demonstrates an important regulatory interaction between the class III PI3 kinase complex and p53, suggesting a novel tumor suppressive function of the class III PI3 kinase complex.

Head and neck cancer is one of the most common cancers worldwide. The current standard of care for head and neck cancer includes surgical resection of the tumor followed by chemoradiation. This targeted head and neck radiation causes dysfunction of the salivary glands, which leads to xerostomia, mucositis, dysphagia, dental caries, and malnutrition. These side effects greatly decrease patient quality of life and increase their financial responsibility. Current therapies available to ameliorate these negative side effects are expensive, only provide short-term relief, and many of them have negative side effects of their own. Therefore, another therapy is needed to prevent salivary gland dysfunction or restore its function following targeted head and neck radiation. Autophagy is a homeostatic cellular mechanism that could be targeted as a therapeutic mechanism in the salivary glands following targeted head and neck radiation. Autophagy is a catabolic process necessary to maintain cellular homeostasis. It has been shown to play a beneficial role in a variety of disease states including diabetes mellitus, obesity, and cancer. The role of autophagy in the response of cancerous tissue to radiation has been vastly studied. However, the role autophagy plays in normal tissue response to radiation remains poorly understood and much more research in this area is needed.Atg5^(f/f);Aqp5-Cre mice have a conditional knockout of Atg5, a gene necessary for autophagy, in the salivary glands. These mice have unchanged baseline levels of apoptosis, proliferation, and stimulated salivary flow rates when compared to wild-type mice. Therefore, they are a useful model to investigate the role of autophagy in the response of the salivary glands to targeted head and neck radiation. These Atg5^(f/f);Aqp5-Cre autophagy-deficient mice display increased radiosensitivity following targeted head and neck radiation. Furthermore, post-therapy use of CCI-779, a rapalogue and inducer of autophagy, allowed for restoration of salivary gland function following targeted head and neck radiation. Taken together, these results implicate autophagy as playing a beneficial role in normal salivary function following radiation. Therefore, autophagy could be utilized by normal salivary gland tissue following targeted head and neck radiation to maintain salivary gland function.

Autophagie ist ein Degradationsprozess der streng reguliert ist und in welchem eine eukaryotische Zelle zelleigene Organellen und Proteine bei Nährstoffmangel abbaut. Außerdem konnte gezeigt werden, dass dieser Prozess auch in verschiedene Entwicklungsprozesse involviert ist. Die molekulare Entschlüsselung der Autophagie wurde hauptsächlich in der Bäckerhefe S. cerevisiae vorgenommen. Allerdings ist Beteiligung der Autophagie an Entwicklungsprozessen in multizellulären filamentösen Ascomyceten weitestgehend unbekannt. Die Fruchtkörperentwicklung von Pilzen ist ein komplex gestalteter Differenzierungsprozess der von einem zwei-dimensionalem Pilzgeflecht ausgeht das sich zu einem dreidimensionalem Perithezium entwickelt. Die Fruchtkörperentwicklung erfordert spezifische Umgebungsbedingungen und wird durch viele entwicklungsassoziierten Genen reguliert. In dieser Studie diente der Modellorganismus Sordaria macrospora zur Untersuchung des Einflusses der Autophagie auf die Fruchtkörperentwicklung. Der coprophytische filamentöse Ascomycet S. macrospora pflanzt sich lediglich sexuell fort, was ihn ideal für die Fragestellung dieser Arbeit macht. Für diese Arbeit wurden eine Reihe konservierter Autophagie bezogener Gene auserwählt. Folgende Gene die homolog zu denen anderer Ascomyceten sind wurden isoliert: Smvps34, Smvps15, Smatg8, Smatg4, und Smjlb1. Durch die Deletion dieser Gene sollte geklärt werden wie Autophagie in die Fruchtkörperentwicklung involviert ist. Die Deletion des Phospolipidkinase Gens Smvps34 und des Proteinkinase Gens Smvps15 führte zur Lethalität von S. macrospora was durch eine Auskeimungsuntersuchung belegt wurde. Die Deletion des Gens Smatg8, welches eine autophagosomale Strukturkomponente kodiert und des Gens Smatg4, das eine Cystein-Protease kodiert, die SmATG8 prozessiert, beeinträchtigte ebenfalls die Fruchtkörperentwicklung und das vegetative Wachstum. Durch Fluoreszenzmikroskopie konnte gezeigt werden, daß SmATG8 in Autophagosomen lokalisiert und SmATG4 vorwiegend im Zytoplasma lokalisiert ist. Die Prozessierung von SmATG8 durch SmATG4 wurde ebenfalls durch Fluoreszenzmikroskopie und Western-blot Analyse bestätigt. Die heterologe Expression von Smatg8 und Smatg4 in S. cerevisiae und der Ape1 Reifungsuntersuchung zeigte, das die cDNA von Smatg8 und Smatg4 den Deletionsphenotyp der jeweiligen Hefedeletionsmutanten aufheben konnte. Somit konnte die Konservierung dieser beiden Gene innerhalb der Ascomyceten gezeigt werden. Die Blockade der Fruchtköperentwicklung wurde durch die Deletion des bZIP Transkriptionsfaktor Gens Smjlb1 verursacht genauso wie die Beeinträchtigung des vegetativen Wachstums. SmJLB1 ist im Kern lokalisiert und durch qRT-PCR Experimente wurde gezeigt, dass die Autophagiegene Smatg8 und Smatg4 durch Smjlb1 reguliert werden. Dies läßt vermuten, dass Smjlb1 in den Prozess der Autophagie involviert ist. Die Ergebnisse dieser Arbeit weisen darauf hin, dass Autophagie und Fruchtkörperentwicklung des filamentösen Pilzes S. macrospora streng miteinander verknüpft sind.

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