Digital Commons Network^™

Dna Polymerase Ε: Replication Error Prevention And Consequences Of A Cancer-Associated Mutation, Chelsea R. Bulock

Theses & Dissertations

Genome integrity is necessary to prevent mutations and disease. During eukaryotic DNA replication, DNA polymerases ε (Polε) and δ (Polδ) synthesize the leading and lagging strand, respectively. Polε and Polδ also have exonuclease activity that acts in series with post-replicative mismatch repair (MMR) to remove replication errors. Defects in proofreading and MMR lead to an increase in mutations and cause cancer in humans. This dissertation focuses on several unresolved issues involving the relationship between Polε and Polδ in replication error avoidance. First, despite an abundance of data supporting the one-strand-one-polymerase replication fork model, defects in the fidelity of Polε have …

Investigation Of Proliferation Suppressors In Genetic Fitness Screens, Walter Frank Lenoir Iv

Dissertations & Theses (Open Access)

Innovation of CRISPR gene-editing technology has provided scientists genome manipulation tools that allowed rapid advancement of scientific capabilities and thus improved our ability to systematically study mammalian genetic functional profiles. Genome-wide CRISPR knockout screens conducted in collections of human cell lines can knock out genes at multiple loci, and have provided new insights into functional roles for independent genes. This method has launched massive efforts in looking across genetic backgrounds for context specific genetic vulnerabilities within cancer. Much of the research effort thus far has been spent on optimizing phenotype distinctions between essential, genes required for cell fitness, and non-essential, …

Hpv Mediated Antagonism Of The Il-18 Proinflammatory Pathway In Head And Neck Cancer, Wyatt W. Anderson

Electronic Thesis and Dissertation Repository

In this thesis, I examined the effect of human papillomavirus (HPV) on the proinflammatory IL-18 cytokine pathway in head and neck cancers. I investigated the expression and methylation of genes associated with this pathway using The Cancer Genome Atlas (TCGA) data. In HPV+ cancers, IL18, CASP1, and AIM2 were downregulated, while IL18BP was upregulated compared to HPV- cancers and adjacent non-cancerous tissues, and IL18’s promoter was significantly more methylated. I compared HPV+ and HPV- head and neck cancer cell lines for expression of RNA and protein levels of IL-18 and IL-18BP by qPCR, western blot, and ELISA. IL-18 …

Inducing Dna-Mismatch Repair Deficiency In Tumours: A Strategy To Enhance Anti-Tumour Immunity, Mikal El-Hajjar

Electronic Thesis and Dissertation Repository

Immunotherapy has improved patient outcomes in advanced or metastatic settings across a number of cancers. Patients with tumours deficient in the DNA mismatch repair (DNA-MMR) pathway often show high response rates to immune checkpoint inhibitors (ICIs) with a rise in immune surveillance. However, little is known about the immune sensitization effects of inducing DNA- MMR-deficiency in low tumour mutational burden (TMB) cancers, such as ICI refractory neuroblastoma. In addition, the dynamic T-cell profile that results from such a DNA-MMR inactivation, and whether this may confer a therapeutic benefit, is poorly understood. Here we used CRISPR/CAS9 genome editing technology to knock …

Exploiting The Immunomodulatory Potentials Of Inkt Cells In Sepsis And Cancer., Joshua Choi

Electronic Thesis and Dissertation Repository

Invariant natural killer T (iNKT) cells are a unique unconventional T cell subset that recognize glycolipids presented by CD1d expressing cells. The prototypical glycolipid agonist of iNKT cells, α-Galactosylceramide (α-GalCer), can induce the rapid release of an arsenal of cytotoxic effector molecules and enormous amounts of immunomodulatory cytokines as early as two hours after activation. In addition to α-GalCer, various glycolipid agonists are available that allow for specific, in vivo targeting of iNKT cells, and can exert divergent T-helper (T_H)1 and/or T_H2 immune responses. Therefore, the type of response instigated by iNKT cells can profoundly influence …

Mechanisms Of Cross-Presentation By Cdc1s, Derek James Theisen

Arts & Sciences Electronic Theses and Dissertations

Classical dendritic cells (cDCs) are specialized antigen presenting cells that can be divided into distinct subsets based on the types of pathogens they respond to and the type of immune response they generate. The cDC1 subset is specialized in priming CD8 T cell responses through the process of cross-presentation. During cross-presentation, exogenous protein antigens are taken up by cDC1 and presented on MHCI molecules, allowing for the priming of CD8 T cells during conditions when DCs themselves are not directly infected. The ability to cross-present in vivo is unique to cDC1, and is essential for anti-viral responses and rejection of …

Genomic And Transcriptomic Alterations In Metabolic Regulators And Implications For Anti-Tumoral Immune Response, Ryan J. King

Theses & Dissertations

Metabolic and immune alterations are ubiquitous hallmarks of cancer that are established during the foundational mutations and are further selected upon to generate highly aggressive tumors. Recent evidence suggests that cancer cells employ an altered metabolism to induce immune evasion. To further discover the relationship between metabolism and immunity in cancer, this thesis aimed to discover potential candidates of interest by first examining the mucin family for differences, as they exert a wide range of activities in cancer, including altered metabolism and immune alterations. Unique differences lead to further profiling in pancreatic and esophageal cancer. In pancreatic cancer, CD73 was …

From Development To Therapy: A Panoramic Approach To Further Our Understanding Of Cancer, Brittany Poelaert

Theses & Dissertations

Solid tumors, such as pancreatic cancer, often result in dismally low survival outcomes for patients due to insufficient understanding of disease development and progression. Pancreatic cancer is the fourth leading cause of cancer-related deaths in the United States and although oncogenic drivers (such as KRAS mutation or loss of tumor suppressor p53) and stages of disease development have been studied, further understanding of pancreatic cancer development is greatly needed. Studies from our laboratory have identified novel and varied functions of amyloid precursor-like protein 2 (APLP2) in the development and progression of pancreatic cancer. These functions include promoting cancer cell migration, …

Formulation And Evaluation Of Gemcitabine Plus Romidepsin + Cisplatin Combination For Controlling Tumors, Pawat Pattarawat

Doctoral Dissertations

Cancer is a deadly malignant disease that is costly to treat and still impossible to cure. Cancer treatments often come with side effects that impact the overall health of patients. Breast cancer is the most common type of cancer in the United State and bladder cancer mortality and recurrence rates are still high among cancer patients. Thus, safe and effective regimens are needed to combat these diseases.

In this study, the safe and efficacious combination of gemcitabine, cisplatin, and romidepsin (Gem plus Rom+Cis) to treat two types of cancer: bladder and breast cancer, was formulated. In vitro data from this …

Statistical Methods For Resolving Intratumor Heterogeneity With Single-Cell Dna Sequencing, Alexander Davis

Dissertations & Theses (Open Access)

Tumor cells have heterogeneous genotypes, which drives progression and treatment resistance. Such genetic intratumor heterogeneity plays a role in the process of clonal evolution that underlies tumor progression and treatment resistance. Single-cell DNA sequencing is a promising experimental method for studying intratumor heterogeneity, but brings unique statistical challenges in interpreting the resulting data. Researchers lack methods to determine whether sufficiently many cells have been sampled from a tumor. In addition, there are no proven computational methods for determining the ploidy of a cell, a necessary step in the determination of copy number. In this work, software for calculating probabilities from …

Genetic Analysis Of Pi3k And Mtor Inhibition In U87mg Glioblastoma Cell Line, Carl G. Litif

Theses and Dissertations

NVP-BEZ235 is a Glioblastoma Multiform chemotherapeutic dual PI3K/mTOR pathway inhibitor created in 2008 and has since been proven experimentally to induce pluripotentcy in oncological cell populations. The inhibition of PI3K and mTOR has shown to coerce phenotypes associated with stem cell markers, most notably OCT4. It is necessary to understand the genetic composure of how PI3K/mTOR inhibited tumor cells are bypassing the canonical pathway for proliferation and growth and utilizing other parallel sources for tumor invasion into other neural regions. Taking a genetic approach with RNA-sequencing allowed us to gain insight into how glioblastoma interact with cytoskeleton factors MAPK4 and …

Elucidating Mechanisms Of Metastasis With Implantable Biomaterial Niches, Ryan Adam Carpenter

Doctoral Dissertations

Metastasis is the leading cause of cancer related deaths, yet it remains the most poorly understood aspect of tumor biology. This can be attributed to the lack of relevant experimental models that can recapitulate the complex and lengthy progression of metastatic relapse observed in patients. Mouse models have been widely used to study cancer, however they are critically limited to study metastasis. Most models generate aggressive metastases in the lung without the use of unique cell lines or specialized injection techniques. This limits the ability to study disseminated tumor cells (DTCs) in other relevant metastasis prone tissues. Prolonged observation of …

Survival-Related Clustering Of Cancer Patients By Integrating Clinical And Biological Datasets, Xinming Wei

Master's Theses (2009 -)

Subtype-based treatments and drug therapies are essential aspects to be considered in cancer patients' clinical trials to provide appropriate personalized therapies. With the advancement of the next-generation sequencing technology, several computational models, integrating genomic and transcriptomic datasets (i.e., multi-omics) in the prediction of subtype-based classification in cancer patients, were emerged. However, integration of the prognostic features from the clinical data, related to survival risks with the multi-omics datasets in the prediction of different subtypes, is limited and an important research area to be explored. In this study, we proposed a data integration pipeline with the prognostic features from the clinical …

B Cell Acute Lymphoblastic Leukemia Is Driven By Activating Janus Kinase Mutations Cooperating With Spi1 And Spib Deletions In A Murine Model, Michelle Lim

Electronic Thesis and Dissertation Repository

B cell acute lymphoblastic leukemia (B-ALL) is caused by genetic lesions in developing B cells that function as drivers for accumulation of additional mutations in an evolutionary selection process. We investigated secondary drivers of leukemogenesis and their mechanism(s) of arising in a mouse model of B-ALL driven by PU.1/Spi-B deletion (Mb1-CreDPB). Whole exome sequencing revealed recurrent mutations in Jak3 (encoding Janus Kinase 3) and Jak1. Mutations with high variant allele frequency (VAF) were dominated by C->T transition mutations that were compatible with AID, whereas the majority of mutations, with low VAF, were dominated by C->A transversions associated with …

Effects Of Aurora Kinase C Expression On Retina Pigmented Epithelial Cell Migration, Proliferation, And Anchorage Independent Growth, Justin Bejar

Seton Hall University Dissertations and Theses (ETDs)

Cancer is a common and deadly disease in the United States with 1,806,590 new cancer cases in 2019 and 606,520 cancer deaths projected in 2020. These deaths are primarily due to the uncontrolled cell proliferation and migratory nature of the disease. Many cancer cells express genes normally restricted to meiotic cells. For example, Aurora Kinase C (AURKC) is known to regulate chromosome segregation in meiotic cells yet it is expressed in many different types of cancer, such as breast, prostate, colorectal, liver, cervical, thyroid, and testicular cancers. As a means to study the function of AURKC, an …

Multi-Omics Integration For Gene Fusion Discovery And Somatic Mutation Haplotyping In Cancer, Steven Mason Foltz

Arts & Sciences Electronic Theses and Dissertations

Cancer is a disease caused by changes to the genome and dysregulation of gene expression. Among many types of mutations, including point mutations, small insertions and deletions, large scale structural variants, and copy number changes, gene fusions are another category of genomic and transcriptomic alteration that can lead to cancer and which can serve as therapeutic targets. We studied gene fusion events using data from The Cancer Genome Atlas, including over 9,000 patients from 33 cancer types, finding patterns of gene fusion events and dysregulation of gene expression within and across cancer types. With data from the CoMMpass study (Multiple …

Glucose Metabolism Of Breast Cancer Sub-Clones That Preferentially Metastasize To The Lungs And Bone, Anna G. Skubiz

Honors Theses

Malignant breast cancers exhibit preferential metastasis to bone and lung (1). While changes in gene expression in lung-specific (LM) and bone-specific metastasis (BoM) lines derived from the MDA-MB-231 breast cancer line have been identified, few metabolic genes are differentially expressed; thus it is unknown if tissue-specific metabolic reprogramming occurs. Two hallmarks of cancer cells are an altered metabolic phenotype characterized by enhanced conversion of glucose to lactate in spite of adequate oxygen availability for complete mitochondrial oxidation of this substrate (referred to as aerobic glycolysis or the Warburg effect) and a greater dependence on glutamine. These changes in primary tumor …

The Role Of The Cxcr3 Signaling Axes In Pancreatic Ductal Adenocarcinoma, Andrew C. Cannon

Theses & Dissertations

Numerous cytokines promote pancreatic ductal adenocarcinoma (PDAC) progression and suppress anti-tumor immune response leading to poor prognosis in PDAC patients. Despite this, many cytokines, have not been investigated in PDAC. Bioinformatic analyses of PDAC microarray and RNA-Seq datasets were used to identify cytokines overexpressed in PDAC, confirm the expression of cognate receptors, determine the association of cytokines with patient survival and define key underlying molecular associations. Bioinformatic findings were validated using immunohistochemical (IHC) staining, comparative cytokine qPCR-array in Kras^LSL-G12D:TP53^LSL-R172H:Pdx1-Cre (KPC) and Kras^LSL-G12D:Pdx1-Cre (KC) PDAC models and multicolor immunofluorescence staining. Tail-vein injections of PDAC cells …

Defining The Let-7 Microrna-Mediated Molecular Mechanisms Regulating T Cell Differentiation, Constance C. Angelou

Doctoral Dissertations

CD4⁺ and CD8⁺ T cells are lymphocytes of the adaptive immune system that play essential roles in immunity. Both T cell subsets recognize their cognate antigen through the T cell receptor (TCR), which induces the proliferation and differentiation of these antigen-specific cells into effector T cells. CD4⁺ T cells have the potential to differentiate into one of multiple lineages of helper T (Th) cells and participate indirectly in antigen clearance by orchestrating the function of other cells. CD8⁺ T cells differentiate into cytotoxic T lymphocytes (CTL), which directly contributes to the resolution of an infection by …

Investigating The Localization Of Foxo Transcription Factors In Glioblastoma, Leetoria Hinojosa

Theses and Dissertations

The Phosphatidylinositol 3 Kinase (PI3K) pathway is an essential intracellular signaling pathway that regulates cellular growth, survival, and fate. Canonically, the activation of this pathway removes forkhead box subfamily O transcription factors (FOXO -1, -3, and -4) from the nucleus. However, in cancer cells such as glioblastoma multiforme, FOXO factors are at least in part nuclear despite the activation of the PI3K pathway. Previous research indicated that FOXO3 localization was not affected when the pathway was inhibited in breast cancer cells, which challenged the conventional paradigms for FOXO factor regulation. Therefore, we were interested in investigating the nuclear localization of …

The Role Of Protein Degradation In Cancer Cachexia In Female Tumor Bearing Mice, Noah Thomas

Graduate Theses and Dissertations

Background: Cancer is a leading cause of death in the world in which half of the people affected by this disease die from its effects. Cancer-cachexia is a syndrome associated with the significant loss of skeletal muscle mass and function, which cannot be fully reversed by nutritional intervention alone and in turn, impairs the host. Cancer-cachexia affects 50-80% of cancer patients and is a primary cause of death accounting for 20-40% of cancer related deaths. Efforts to reverse the effects of cancer-related cachexia have been largely unsuccessful and have primarily focused on the late stages of CC. Methods: Lewis Lung …

Novel Cyanoximates As An Alternative In Cancer Chemotherapy, Kafayat Aderonke Yusuf

MSU Graduate Theses

Chemotherapy is one of the most effective treatment plans for several cancer types. The recurrent side effects derived from chemotherapy agents have warranted the search for novel chemical compounds with better efficacy and minimal side effects. In line with this idea, I investigated effects of a group of newly synthesized metal based chemical compounds called cyanoximates on HeLa human cancer cells. Cyanoximates used were Pt(DECO)₂, Pt(MCO)₂, and Pd(DECO)₂ along with the chemotherapy drug cisplatin as a positive control. I found that the metal cyanoximates reduced cell viability via apoptosis, and that Pt(DECO)₂ was most …

Vestigial-Like 1 Is A Shared Targetable Cancer-Placenta Antigen Expressed By Pancreatic And Basal-Like Breast Cancers, Sherille Denae Bradley

Dissertations & Theses (Open Access)

Cytotoxic T lymphocyte (CTL)-based cancer immunotherapies have shown great promise for inducing clinical regression by targeting tumor-associated antigens (TAA). To expand the TAA landscape of pancreatic ductal adenocarcinoma (PDAC), we performed tandem mass spectrometry analysis of HLA class I-bound peptides from tumors of PDAC patients. This led to the identification of a shared HLA-A*0101 restricted peptide derived from co-transcriptional activator Vestigial-like 1 (VGLL1), a novel putative TAA demonstrating overexpression in multiple tumor types and low or absent transcript expression in normal tissues with the exception of placenta. VGLL1-specific CTL isolated and expanded from the blood of a male PDAC patient …

Synthesis Of An Arylidene Pyrazolone And Its Effects On Glioblastoma Cancer Cells, Joanna Deonarine

Honors Theses

The purpose of this research is to develop a new technique to synthesize a heterocyclic arylidene compound using fruit puree catalysis and investigate its anti-cancer activity on glioblastoma cancer cells. Recently, there has been interest in heterocycles due to their anticancer properties and they have been used in almost two-thirds of the novel molecular anticancer agents. Varying fruit purees were used to synthesize a novel hybrid arylidene pyrazolone from 3-methyl-1-phenyl-5-pyrazolone and 4-dimethylaminobenzaldehyde by modifying methodology developed by Dr. Murray. This arylidene pyrazolone was then tested for its anticancer activity on glioblastoma brain cancer cells using Dr. Smith’s 12-well cell viability …

Synthesized Tripodal Amine As Potential Anti-Cancer Therapeutic, Abigail G. Mcnamee

Honors College Theses

Cancer remains a prevalent disease today. This disease may manifest itself in many different ways and affect a variety of tissues with everything from the brain to the blood. With this wide diversity of cancer types, treatment can be complicated since there is not a “one size fits all” treatment for the disease. Surgery, radiation, and chemotherapy are all options that must be weighed with their benefits and side effects. Ultimately though, there are not enough effective treatment options available for every type of cancer. This leaves many with the grim prognosis of never being cured. With this clear need …

Investigating The Toxicology Of Intramuscular Injected Cnt-Ab In Mice Followed By Microwave Hyperthermia., Conner Clark

Honors College Theses

The advent of carbon nanotubes (CNTs) has led to a wide range of research in various fields including cancer therapy for targeting specific localized and site-specific treatment. Carbon nanotubes bound to tumor specific antibodies (Ab) offers specific treatment for cancer cells without affecting surrounding tissue. This treatment makes use of infrared absorptive properties of nanotubes to incinerate both the nanotube and its associated tumor in vivo. We seek to affirm the initial results of CNT in cancer therapy by investigating the toxicological effect in mice injected with CNT-Ab followed by microwave hypothermia. After 1-week post-injection, mice were sacrificed followed …

Assay Development For Isolation And Characterization Of Anticancer Properties Of Marine Fungi, Kyra Ricci

Honors Theses

Metabolites from fungi have potential use in the drug discovery process and have been used in the past to develop therapeutic agents for human use. Initial characterization of potential therapeutic properties of fungi is thus an important first step in identifying novel therapeutic compounds. In the present study, marine fungi were isolated from Myrtle Beach and assayed for anticancer properties using the soft agar colony formation assay in a 3D in vitro cellular environment. Many species were isolated from environmental samples, displaying unique morphologies and growth patterns. To optimize the soft agar assay in a six-well cell culture plate for …

Developing A New Water-Soluble Porphyrin As A Potential Photodynamic Cancer Therapy Agent, Catherine Shirley

Honors Theses

Photodynamic cancer therapy (PDT) is a type of treatment involving the use of light in conjunction with a photosensitive agent- a chemical or series of chemicals designed for activation when exposed to light. This research project investigated the synthesis and identification of the novel photosensitive agent, H2TPP-Pro-OH. To create the water-soluble porphyrin, (S)-(+)-prolinol was reacted with the tetra-carboxyl porphyrin, H2TPPC, to form the final H2TPP-Pro-OH product. This compound was then purified using syringe filtration and column chromatography, and subsequently characterized using infrared (IR), nuclear magnetic resonance (NMR), and Ultraviolet-visible (UV-vis) spectroscopies, as well as High Performance Liquid Chromatography (HPLC). Finally, …

Preparation And Cytotoxicity Of Novel Carbon Nano-Onion Materials, Cammie York

Honors Theses

The applications of carbon nanomaterials (CNM), including graphene and its derivatives such as carbon nanotubes (CNTs) in nanomedicine is well established. These nanomaterials have been widely used as theranostic delivery systems with the potential to deliver bioactive agents and simultaneously detect selectively diseased tissues. A rather underexplored CNM for biomedical imaging and theranostics delivery are carbon nano-onions (CNOs). CNOs are carbon-based nanomaterials that can potentially be used in cancer therapy when they are functionalized. Recent studies on cellular fate of different CNMs, including CNOs, have demonstrated that the surface composition is critical for the in vivo application of these CNM. …

Practical Applications And Future Directions Of Genetic Code Expansion: Validation Of Novel Akt1 Substrates And The Design Of A Synthetic Auxotroph Strain Of B. Subtilis, Mcshane M. Mckenna

Electronic Thesis and Dissertation Repository

In Chapter 1, site-specifically phosphorylated variants of the oncogene Akt1 were made in Escherichia coli using the orthogonal translation system that enable genetic code expansion with phosphoserine. The differentially phosphorylated variants of Akt1 were used to validate newly predicted Akt1 substrates. The predicted target sites of the peptide substrates were synthesized and subjected to in vitro kinase assays to quantify the activity of each Akt1 phosphorylated variant towards the predicted peptide. A previously uncharacterized kinase-substrate interaction between Akt1 and a peptide derived from RAB11 Family Interacting Protein 2 (RAB11FIP2) was validated in vitro. Chapter 2 describes the preliminary development of …