Cancer continues to be a leading cause death in the United States despite improved treatments. Cancerous lesions form after acquiring oncogenic driver mutations or losing tumor suppressor function in normal cells. Traditional therapies have included use of genotoxic substances that take advantage of the increased growth rate and loss of tumor suppressor function to cause cell death. One such drug is the anthracycline antibiotic doxorubicin (DOX). DOX interchelates into DNA and disrupts transcriptional machinery while also poisoning topoisomerase II. This results in single and double stranded DNA breaks, which if severe enough leads to either necrotic or apoptotic cell death. DOX has been very effective at treating several different cancers and is still widely used today however its clinical use is limited due to cumulative dose dependent cardiotoxicity. Therefore, combination therapy targeting survival pathways is utilized to minimize the cumulative dose of DOX without ameliorating its anti-tumor effects. We investigated the potential anti-cancer effects of combining the dual PI3K/mTOR inhibitor, BEZ235 (BEZ), with DOX in pancreatic, breast and other cancer cells lines as well as its associated effects on the heart. Our results showed that co-treatment of BEZ with DOX increased apoptosis in a manner that was dependent on inhibition of the AKT survival pathway. Moreover, BEZ co-treatment with DOX had additive effects towards cell viability while it significantly enhanced necrotic cell death compared to either drug alone. Furthermore, we observed that physiological concentrations of BEZ inhibited ABCB1 efflux resulting in increased intracellular accumulation of DOX, which led to increased DNA damage. In addition, BEZ in combination with gemcitabine (Gem) reduced cell proliferation but did not enhance necrosis or apoptosis. Treatment with BEZ and DOX in mice bearing tumor xenographs reduced tumor growth as compared to BEZ, DOX or Gem. Moreover, BEZ reduced DOX toxicity in rat myoblast cells and did not potentiate the effects of DOX in tumor-bearing mice. We propose that combining BEZ with DOX could be a novel therapeutic approach for the treatment of patients with cancer in the hope of improving the prognosis of this deadly disease.

The American Cancer Society predicts there will be 110,070 new cases and 32,120 deaths due to gynecological malignancies in 2018. A major contributing factor to the high mortality associated with gynecological cancers is the recurrence of treatment-resistant tumors. Ovarian cancer (OC) remains the most lethal gynecological malignancy, yet the mechanisms responsible for regulating tumor resistance and vulnerability are largely unknown or undruggable. Therefore, the goal of this research is to identify mechanisms responsible for therapeutic resistance in gynecological cancers and discover innovative approaches to circumvent these molecular alterations. Our efforts began in OC where secondary analysis of gene expression data from OC studies revealed that Sab, an outer mitochondrial membrane (OMM) scaffold protein, was down-regulated in OC tumors compared to normal tissue controls. Our previous studies demonstrate that Sab-mediated OMM signaling induces cell death in cervical cancer. In the current study, we found that Sab concentrations corresponded to chemoresponsiveness in a panel of OC cells; wherein, OC cells with low Sab levels were chemo resistant. Dynamic BH3 profiling revealed that cells with high Sab expression were primed for apoptosis. Furthermore, over-expression of Sab in chemo resistant cells enhanced apoptotic priming and restored cellular vulnerability to cisplatin/paclitaxel treatment. Additionally, an examination of treatment-resistant metastatic uterine cancer (UC) cells were found to have low Sab concentrations compared to vulnerable primary site-derived UC cells. Ectopic expression of Sab in chemo resistant UC cells enhanced the susceptibility towards megestrol acetate and BH3-mimetic ABT-737. To exploit the relationship between Sab concentrations and chemo-responsiveness in gynecological cancer cells, we developed a high-throughput screening assay to detect Sab levels in chemo-resistant OC cells. In collaboration with the Torrey Pines Institute for molecular studies, we have identified compounds that can increase Sab levels in resistant OC cells. The identified compounds improved the effectiveness of cisplatin/paclitaxel therapy. We propose that Sab may be a prognostic marker to discern personalized treatments for gynecological cancer patients. Furthermore, pharmacologically enhancing Sab-mediated signaling may increase the efficacy of chemotherapeutic agents, which would mean lower doses that would limit toxic side-effects.

For structure-based drug discovery, structural information of a target protein is necessary. NMR, or X-ray crystallography can provide necessary information on active site configuration that can lead a successful virtual screening campaign into identifying binders that may then be optimized into potent inhibitors. However, many challenges exist in the structure-based drug discovery cycle. For instance, structure determination of a protein of interest can many times be a daunting task. In addition, complex structure determination, which can allow essential characterization of protein-ligand interactions, is also challenging and many times impossible. Virtual screening heavily relies on such structural information, but hit-to-lead optimization schemes do as well. Furthermore, inherent protein characteristics such as conformational flexibility only add to the complexities in using structural information to identifying and optimizing inhibitors. In the scope of the work presented here, a structure-based drug discovery approach against three different protein targets is described. Each is presented with it's own set of challenges, but each has successfully led to the identification of new ligands. The drug discovery project against CXCL12 will first be described. CXCL12 is a small chemokine (~10KDa) that binds to the CXCR4 receptor promoting chemotaxis of lymphocytes but also metastasis of cancer cells. This interaction is further supported by sulfated tyrosines on CXCR4 that bind specific sites on the CXCL12 surface. The CXCL12-CXCR4 signaling axis has been a major focus of drug discovery, but efforts are mainly focused on CXCR4, since CXCL12 is a small protein lacking surface characteristics that are thought to be druggable. Yet, through a combination of rigid, flexible, and ensemble docking in virtual screening studies, we have successfully identified compounds that bind each of the three sulfotyrosine recognition sites on CXCL12, which normally bind the sulfated tyrosines on CXCR4 (sY7, sY12, and sY21). Furthermore, we have led a hit-to-lead approach in optimizing compounds against the sY21-binding site, aided by trivial information gained through crystallographic complex structure determination of CXCL12 bound by such a compound. We aim to eventually link compounds against different sites together and greatly improve potency. Next, the drug discovery project against P. aeruginosa LpxA will be described. In Gram-negative bacteria, the first step of lipid A biosynthesis is catalyzed by UDP-N-acetylglucosamine acyltrasferase (LpxA) through the transfer of a R-3-hydroxyacyl chain from the acyl carrier protein (ACP) to the 3'-hydroxyl group of UDP-GlcNAc. Acyl chain length selectivity varies between species of bacteria, but is highly specific and conserved within certain species. In E. coli and L. interrogans for example, LpxA is highly selective for longer R-3-hydroxyacil chains (C14 and C12 respectively), while in P. aeruginosa the enzyme is highly selective for R-3-hydroxydecanoyl, a 10-hydrocarbon long acyl chain. Three P. aeruginosa LpxA crystal structures will be described here for the first time; the apo form, the complex with its substrate UDP-GlcNAc, and the complex with its product UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc. A comparison between the APO form and complexes identifies key residues that position UDP-GlcNAc appropriately for catalysis, and supports the role of His121 in generating the nucleophile by interacting with the UDP-GlcNAc 3'-hydroxyl group. Furthermore, the product-complex structure supports the role of Met169 as the "hydrocarbon ruler", providing structural information on how P. aeruginosa LpxA is granted its exceptional selectivity for the 10-hydrocarbon long acyl chain. Structural information of the active site was subsequently used in designing virtual screening experiments that led to the identification of two ligands, confirmed by X-ray crystallography screening to bind to the active site. We aim to continue application of X-ray crystallography into screening compound binding, and to also use a hit-to-lead approach in compound optimization. Finally, the drug discovery project against the Tiam1 PDZ domain will be described. Tiam1 (T-cell lymphoma invasion and metastasis gene 1) is a GEF (guanine exchange factor) protein that activates Rac1 and initiates tumor formation. Tiam1 is regulated through its PDZ domain, which binds to syndecan1. We have successfully applied a virtual screening strategy to an existing crystallographic structure of the Tiam1 PDZ domain complexed to a syndecan1 peptide and identified four ligands that bind to the PDZ domain with low affinities. These compounds provide a starting point for future hit-to-lead optimization strategies.

Although the prostate specific antigen (PSA) test is widely used in clinical settings for prostate cancer (PCa) diagnosis and post-treatment follow-up monitoring, false positive PSA test results, which contribute to over-diagnosis of PCa, and false negative results, which miss some patients with aggressive PCa, remain problems of clinical importance. Our study demonstrates that radiation therapy, which is widely used for treatment of localized PCa, generates TNF-α in tumor cells and stromal fibroblasts, redox dependently. Interestingly, TNF-α rapidly and transiently triggers the RelA-mediated NF-κB canonical pathway, but its effect on RelB expression is more robust and long lasting, which leads to sustainable suppression of PSA expression. TNF-α further amplifies endogenous reactive oxygen species (ROS) partially through NADPH oxidase activation and mediates redox-dependent downstream signaling pathways. Addition of the NADPH oxidase inhibitor or ROS scavengers such as superoxide dismutase (SOD) mimetic can abrogate TNF-α-mediated suppression of PSA expression by inhibiting the RelB-AR axis. Treatment with TNF-α suppresses PSA expression and it confers minor yet statistically significant protection to LNCap cells against irradiation, indicating that radiation-induced TNF-α may not only interfere with the PSA-based PCa diagnosis and post-treatment monitoring but may also diminish the efficacy of radiotherapy. In addition, we uncover a role for RelB in suppressing PSA expression at the advanced stage of PCa, which could be a mechanism for the low PSA level in some patients bearing aggressive PCa. Experiments with both RelB overexpression and siRNA knockdown indicate that RelB negatively regulates androgen receptor (AR) and PSA levels in human prostate cancer, LNCap, cells. RelB directly interacts with AR to form a complex on the enhancer elements of the PSA promoter. Thus, the RelB-AR axis is an important contributor to PSA suppression at the advanced stage of PCa. Overall, this study is the first to reveal a redox-mediated association among radiation-generated TNF-α, activation of the RelB-mediated alternative NF-kappaB pathway and PSA suppression. This mechanistic information provides new insights with practical and clinical implications for PSA-based PCa diagnosis and post-treatment monitoring as well as redox intervention in radiation therapy.

Recent Genome Wide Association Studies (GWAS) have identified a series of single nucleotide polymorphism (SNP)s that are associated with Alzheimer’s disease (AD). One of the SNPs, rs3851179 (G/A), is near the gene phosphatidylinositol-binding clathrin assembly protein (PICALM). To evaluate whether this SNP is associated with PICALM expression, we quantified PICALM mRNA in 56 brain cDNA samples. Using linear regression analysis, we analyzed PICALM expression relative to rs3851179, AD status, and cell type specific markers. An association was detected between rs3851179 and PICALM, microvessel mRNA, glial fibrillary acidic protein (GFAP) mRNA, and synaptophysin (SYN) mRNA. To gain clarity into other possible SNP mechanisms, we searched brain cDNA for PICALM splice variants. We identified several PICALM splice variants involving exons 13-19. To identify and gain an estimation of relative abundance of splice variants, we PCR-amplified across exons 13-20 in cDNA from six individuals, three rs3851179 GG individuals and three rs3851179 AA individuals. Sequencing the cloned isoforms we found that PICALM lacking exon 13 (delta 13) is the most abundant isoform. Other isoforms detected included deletion of exon 18-19. We targeted the latter part of the gene, exon 17-20, to investigate unequal allelic expression using next generation sequencing. Individuals heterozygous for rs76719109 (n= 35), located in exon 17, were used to study the abundance of G/T allele in cDNA and genomic DNA. When we analyzed the T:G allelic ratio, the variant lacking exons 18 and 19 showed unequal allelic expression (p-value < 0.001) in a subset of individuals. One individual was an outlier, showing overall unequal allelic expression, which maybe be harboring a rare mutation capable of modifying PICALM expression. The PICALM intronic SNP rs588076 was associated with delta 18-19 isoform splicing (p-value < 0.001). In conclusion, this study gained a greater insight into the role of AD genetics in PICALM expression and splicing.

Electronic cigarette usage is becoming increasingly prevalent among school age children and young adults. A known bactericidal agent, propylene glycol, is often used as a carrier for nicotine, flavoring, and additional constituents of electronic cigarette juice. This study examined the relationship between propylene glycol and virulence gene expression in Streptococcus pyogenes, a respiratory tract pathogen commonly found in school-age individuals. A variety of virulence genes controlled by the three stand alone regulators mga, RofA, and Rgg/RopB were sampled in an effort to understand the pathway by which virulence is affected. The genes chosen encode C5a peptidase, fibronectin binding protein, hyaluronate lyase, NAD glycohydrolase, Streptococcal pyrogenic exotoxin A and B, streptodornase, streptokinase, Streptolysin O, and Streptolysin S. No significant change in gene expression was observed, but a novel method to test the effects of aerosols on cells was developed. This method can be used in the future to observe the effect of aerosols, including commercial electronic cigarette juice, on both bacterial and mammalian cells.

<p>Huntington’s disease (HD) is a progressive, neurodegenerative disorder that leads to the selective loss of neurons in the striatum and the cerebral cortex. HD is caused by a CAG trinucleotide repeat expansion beyond the normal length in the <em>IT15 </em>(<em>Htt</em>) gene. The CAG stretch codes for an elongated polyglutamine tract within the amino‐terminus of the huntingtin protein. Polyglutamine tracts with lengths exceeding 37 repeats cause HD whereas repeat lengths below do not. This phenomenon has plagued the HD community since the discovery of the gene in 1993. In this thesis, we sought to elucidate the molecular mechanism by which huntingtin becomes toxic at polyglutamine lengths above 37. Using Förster resonance energy transfer (FRET) techniques, we describe an intramolecular proximity between the first 17 residues (N17) and the proline-rich regions, which flank the polyglutamine tract of huntingtin. We report that we can precisely measure differences between the conformations adopted by the huntingtin protein with polyglutamine tracts below and above the pathogenic repeat threshold of 37 repeats. Our data supports the hypothesis that polyglutamine tracts below the pathogenic threshold can act as a flexible hinge allowing the N17 domain to freely fold back upon huntingtin and come into close 3D proximity with the polyproline region. This flexibility is lost in polyglutamine tracts with >37 repeats resulting in a diminished spatial proximity between N17 and the polyproline domain.</p> / Doctor of Philosophy (PhD)

Sulfiredoxin (Srx) is an antioxidant enzyme that can be induced by oxidative stress. It promotes oncogenic phenotypes of cell proliferation, colony formation, migration, and metastasis in lung, skin and colon cancers. Srx reduces the overoxidation of 2-cysteine peroxiredoxins in cells, in addition to its role of removing glutathione modification from several proteins. In this study, I explored additional physiological functions of Srx in lung cancer through studying its interacting proteins. Protein disulfide isomerase (PDI) family members, thioredoxin domain containing protein 5 (TXNDC5) and protein disulfide isomerase family A member 6 (PDIA6), were detected to interact with Srx. Therefore, I proposed that TXNDC5 and PDIA6 are important for the oncogenic phenotypes of Srx in lung cancer. In chapter one, I presented background information about the role of Srx as an antioxidant enzyme in cancer. I also explained the functional significance of PDIs as oxidoreductase and chaperones in cells. In chapter two, I verified the Srx-TXNDC5/PDIA6 interaction in HEK293T and A549 cells by co-immunoprecipitation and other assays. In TXNDC5 and PDIA6, the N-terminal thioredoxin-like domain (D1) is determined to be the main platform for interaction with Srx. The Srx-TXNDC5 interaction was enhanced by H2O2 treatment in A549 cells. Srx was determined to localize in the endoplasmic reticulum (ER) of A549 cells along with TXNDC5 and PDIA6. This localization was confirmed by both subcellular fractionation and immunofluorescence imaging experiments. In chapter three I focused on studying the physiological function of Srx interacting proteins in the ER. A549 subcellular fractionation results showed that TXNDC5 facilitates Srx retention in the ER. Moreover, TXNDC5 and Srx were found to participate in chaperone activities in lung cancer. Both proteins contributed in the refolding of heat-shock induced protein aggregates. In addition, TXNDC5 and PDIA6 were found to enhance the protein refolding in response to H2O2 treatment. Conversely, Srx appeared to have an inhibitory effect on protein folding under same treatment conditions. Downregulation of Srx, TXNDC5, or PDIA6 significantly reduced cell viability in response to tunicamycin treatment. TXNDC5 knockdown decreased the time required for the splicing of X-box binding protein-1 (XBP-1). In either knockdown Srx or TXNDC5 cells, there was an observable decrease in the expression of GRP78 and the splicing of spliced XBP-1. These results suggest a possible role of Srx in unfolded protein response signaling. TXNDC5 and PDIA6, similar to Srx, contribute to the proliferation, anchorage independent colony formation and migration of lung cancer cells. In this dissertation I concluded that Srx TXNDC5, and PDIA6 proteins participate in oxidative protein folding in lung cancer. Srx and TXNDC5 can modulate unfolded protein response (UPR) sensor activation and growth inhibition. Furthermore, TXNDC5 and PDIA6 can promote tumorigenesis of lung cancer cells. Therefore, the molecular interaction of Srx with TXNDC5/PDIA6 has the potential to be used as novel therapeutic targets for lung cancer treatment.

Maintaining balance in the human immune system is critical for the body’s ability to discriminate between foreign and self-antigens. This balance is achieved, in part, by a subpopulation of T cells known as induced regulatory T cells (iTregs). Dysregulation of this population may contribute to the onset and progression of cancer, chronic inflammation and autoimmune diseases. Therefore, manipulation of iTreg development holds promising therapeutic potential; however, studying this vital population has proven difficult due to low numbers, heterogeneous cell populations, substantial phenotypic differences between mouse and human cells, and the high plasticity seen in iTregs. These current limitations have prevented a full understanding of the molecular signaling events that govern their development and function. Our lab has established a novel cell culture system that mimics in vivo human iTreg development. This system allows for the discrimination and comparison of naïve, memory and iTreg T cell populations simultaneously within a single donor. These iTregs exhibit high levels of CD25, FoxP3, CTLA4, GITR, low levels of CD127 and display strong suppressor activity. Using this innovative system, we have demonstrated a rewiring of T cell receptor (TCR) signaling in iTregs compared to conventional T cells. We found that the voltage gated K+ ion channel-Kv1.3 is not active in response to TCR engagement in iTregs, even though Ca2+ influx remains intact. Kv1.3 and the linked Src-family kinase Lck were redistributed to the highly active IL2-Receptor (IL2-R) complex. Additionally, we have shown that there is increased AKT protein expression in iTregs versus conventional T cell populations that does not correlate with the TCR-induced increase in its active (phosphorylated) form. This blockage appears to be due to an imbalance of kinase to phosphatase activity in iTregs with a specific TCR-induced inhibition of mTOR activity. We have also demonstrated that AKT accumulation in iTregs leads to its physical association with SMAD3, suggesting a novel, non-enzymatic function of AKT through transcription factor inhibition. This study sheds light on the reciprocal cross talk between the IL-2R and TCR signaling pathways and uncovers the mechanism of AKT blockade in primary human iTregs, thus opening novel avenues for therapeutic manipulation

Glioblastoma multiforme (GBM) is the most common primary brain tumor. Studies have shown that targeting the DNA damage response can sensitize cancer cells to DNA damaging agents. Ataxia telangiectasia mutated (ATM) is involved in signaling DNA double strand breaks. Our group has previously shown that ATM inhibitors (ATMi) sensitize GBM cells and tumors to ionizing radiation. This effect is greater when the tumor suppressor p53 is mutated. The goals of this work include validation of a new ATM inhibitor, AZ32, and elucidation of how ATMi and p53 status interact to promote cell death after radiation. We propose that ATMi and radiation induce mitotic catastrophe in p53 mutants by overriding cell cycle arrest. We tested this hypothesis in human colon carcinoma and glioma cells that differ only in p53 status. We found that AZ32 effectively inhibits phosphorylation of ATM targets. In addition, AZ32 significantly sensitizes glioma cells to ionizing radiation. While HCT116 colon carcinoma cells fail to arrest the cell cycle after radiation, their response to ATMi differs from that in gliomas. Indeed, wild type HCT116 cells were more sensitive than p53 mutants to ionizing radiation in the presence of ATMi. In contrast, ATMi significantly radiosensitized glioma cells in which p53 is knocked down. Live cell imaging confirmed that radiation and ATMi preferentially induce mitotic catastrophe in p53-deficient cells. We conclude that p53-deficient cells rely on ATM signaling for G2/M cell cycle arrest. We propose a model of G2/M arrest whereby ATM and p53-dependent signaling pathways converge to ultimately inhibit Cdc25 phosphatases.