Life Sciences Commons^™

Identification Of Clonal Evolution Pattern And Mutation Event Associated With Relapsed/Refractory Diffuse Large B-Cell Lymphoma Using Next-Generation Sequencing, Cheng Wang

Theses & Dissertations

Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoid malignancy. About 30% of DLBCL cases respond poorly to initial treatment and eventually relapse. For these patients, the current treatment regimen is quite limited, and the prognosis is poor. Gene mutations and genetic alterations play an important role in lymphomagenesis. However, the genetic alterations or gene mutations underlying the disease resistance/relapse in DLBCL are still unknown. The clonal evolution during the process of disease progression is elusive as well. Our goal is to study the genetic alterations in DLBCL, particularly paired diagnostic and relapsed/refractory DLBCL, to better understand the mutation landscape …

Rilpivirine-Associated Aggregation-Induced Emission Enables Cell-Based Nanoparticle Tracking, Insiya Mukadam

Theses & Dissertations

Antiretroviral therapy (ART) has improved the quality and duration of life for people living with human immunodeficiency virus (HIV) infection. However, limitations in drug efficacy, the emergence of viral mutations and the paucity of cell-tissue targeting remain. We posit that to maximize ART potency and therapeutic outcomes newer drug formulations that reach HIV cellular reservoirs need to be created. In a step towards achieving this goal we discovered the aggregation-induced emission (AIE) property of the non-nucleoside reverse transcriptase inhibitor Rilpivirine (RPV) and used it as a platform for drug cell and subcellular tracking. RPV nanocrystals were created with endogenous AIE …

Mechanisms By Which Mnte-2-Pyp Suppresses Prostate Cancer Cell Growth, Yuxiang Zhu

Theses & Dissertations

Prostate cancer patients are often treated with radiotherapy. MnTE-2-PyP, is a superoxide dismutase (SOD) mimic and a known radioprotector of normal tissues. Our recent work demonstrates that MnTE-2-PyP also inhibits prostate cancer progression with radiotherapy; however, the mechanisms remain unclear. In this thesis, we identified that MnTE-2-PyP-induced intracellular H2O2 levels are critical in inhibiting growth of prostate cancer cells. We found that MnTE-2-PyP induced protein oxidations in PC3 cells and one major group of oxidized protein targets were involved in energy metabolism. The oxidative phosphorylation rates were significantly enhanced in both PC3 and LNCaP cells with MnTE-2-PyP treatment, but mitochondrial …

Targeted Therapies In Select Gastrointestinal Cancers And Cancer Cachexia, Scott Mulder

Theses & Dissertations

Hepatocellular carcinomas exhibit metabolic alterations to support their proliferative and biosynthetic needs. We identified that elevated expression of the mitochondrial oxidative carboxylase, malic enzyme 2 (ME2), correlates with poorer hepatocellular carcinoma patient survival. Hepatocellular carcinoma patient tumors with high ME2 expression exhibit transcriptomic alterations indicative of PI3K/AKT/mTOR and c-Myc signaling as well as elevated central carbon, fatty acid, and redox metabolism pathways. Depletion of ME2 in the hepatocellular carcinoma cell line PLC or in the livers of mice treated with diethylnitrosamine to chemically induce hepatocellular carcinomas, results in impaired proliferation and reduced tumor formation. Additionally, the loss of …

Multistrain Hiv-1 Elimination: A Crispr-Cas9 And Theranostics-Based Approach, Jonathan Herskovitz

Theses & Dissertations

A critical barrier to achieving a functional cure for infection by human immunodeficiency virus type one (HIV-1) rests in the presence of latent proviral DNA integrated in the nuclei of host CD4+ T cells and mononuclear phagocytes. Accordingly, HIV-1-infected patients must adhere to lifelong regimens of antiretroviral therapy (ART) to prevent viral rebound, CD4+ T cell decline, and progression to acquired immunodeficiency syndrome (AIDS). Gene editing using clustered regularly interspersed short palindromic repeat (CRISPR)-Cas9 technology stands as one means to inactivate integrated proviral DNA. We devised a mosaic gRNA CRISPR-Cas9 system- TatDE- that targets viral transcriptional regulator genes tat / …

Characterizing The Critical Role Of Metabolic And Redox Homeostasis In Colorectal Cancer, Danielle Frodyma

Theses & Dissertations

Metabolic alterations are a hallmark of cancer and the mechanism by which these adaptations sustain cancer cell growth are complex and dependent on tissue type. In colon cancer, Peroxisome Proliferator Activated Receptor γ Coactivator 1 β(PGC1��) and Estrogen-Related Receptor α (ERR��) are overexpressed and contribute to tumor growth. Previous studies have shown that PGC1�� and ERR�� regulate many metabolic processes by controlling vital gene expression. Here, we show that PGC1�� and ERR�� drive oxidative phosphorylation and glycolysis in colon cancer cell lines and we evaluated downstream effectors and processes.

A dysfunction in the reductive and oxidative capacity of the cell …

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 …

Long-Acting Nanoformulated Antivirals For The Treatment And Prevention Of Hiv-1 And Hbv Infections, Dhruvkumar M. Soni Dr.

Theses & Dissertations

While antiretroviral therapy (ART) has revolutionized treatment and prevention of human immunodeficiency virus type one (HIV-1) infection, regimen adherence, viral mutations, drug toxicities, stigma and pill fatigue are limitations. These have led to the development of long acting (LA) ART. These include, but are not limited to, implantable devices, new chemical entities, prodrug modifications and nanoformulations. To these ends, this thesis focues on the transformation of nucleoside reverse transcriptase inhibitors (NRTIs) into LA parenterals, While elusive, data from our laboratories demonstrated that modifications to the PROdrug and nucleoTide technology (ProTide) enables improvements in drug apparent half-life and tissue and cell …

The Cellular Origin And Molecular Drivers Of Claudin-Low Mammary Cancer, Patrick D. Raedler

Theses & Dissertations

Breast cancers of the claudin-low subtype make up a substantial portion of triple-negative breast cancers and have stem cell-like and mesenchymal features. Although it has been recognized for some time that this breast cancer subtype is highly aggressive and difficult to treat, the molecular drivers and cellular origin of claudin-low breast cancer have been poorly defined. The lack of suitable in vivo models has prohibited the study of tumor initiation and progression of this subtype. In this work, we report two novel mouse models that, upon expression of oncogenic RAS in the mammary epithelium, develop highly metastatic triple-negative mammary tumors …

Elucidating The Role Of Ecdysoneless In Mrna Processing, Irfana Saleem

Theses & Dissertations

The mammalian orthologue of the evolutionarily conserved Ecdysoneless (ECD) protein is required for embryogenesis, cell cycle progression and mitigation of ER stress. However, the molecular mechanisms of ECD function in mammalian cells remain unclear. Here, using mass spectrometry analysis of the mammalian ECD interactome, we identified several components of the mRNA export complexes as binding partners of ECD and then characterized the functional interaction of ECD with key mRNA export-related DEAD BOX protein helicase DDX39A and its associated partners. FISH analysis of Poly-A-tailed mRNAs revealed that ECD depletion/deletion blocks the mRNA export from the nucleus to the cytoplasm. We have …

Deciphering The Catalytic Mechanism Of Human Manganese Superoxide Dismutase, Jahaun Azadmanesh

Theses & Dissertations

The livelihood of human cells is heavily dependent on the ability to modulate the presence of highly reactive oxygen-based molecules termed reactive oxygen species (ROS). In excess, ROS facilitate oxidative damage to the macromolecules of cellular life. SODs are the major family of antioxidant proteins that prevent the buildup of overwhelming amounts of ROS within cells. Sometimes dubbed the “first line of defense” against oxidative damage, SODs defend against the harmful accumulation of ROS by eliminating superoxide. Superoxide is a ROS itself that is also a precursor to much more harmful ROS molecules. MnSOD is the manganese containing form of …

Next Generation Aryl Hydantoins As Antischistosomal Agents, Derek A. Leas

Theses & Dissertations

Schistosomiasis, also known as “snail fever,” is both an acute and chronic disease spread by trematode flukes from the tropical parasitic worm genus Schistosoma. The flukes are spread via diseased freshwater snails, which release the parasites into the water column where they find a new human host. According to the World Health Organization (WHO), 99 million people were treated for schistosomiasis in 2017. The primary treatment used to combat schistosomiasis is the drug praziquantel (PZQ), but due to high drug pressure and widespread administration, its effectiveness has eroded because of rising drug resistance. Furthermore, PZQ is active against adult but …

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 …

Comprehensive Analysis Of Chromosome 14q32 Deletions In Chronic Lymphocytic Leukemia, Rachel A. Harris

Theses & Dissertations

Chronic lymphocytic leukemia (CLL) is a genetically heterogeneous disease characterized in part by a combination of conventional cytogenetic and fluorescence in situ hybridization (FISH) analyses. Previous studies have investigated the occurrence of many cytogenetic abnormalities in CLL. However, few have focused on the frequency and variation of deletions within chromosome 14 (14q32), including genes associated with the IGH gene region and the possible related prognostic implications. We performed a comprehensive analysis and examined the frequency of abnormalities, specifically, deletions of the 14q32 region, categorized the size variation of these deletions using microarray, and assessed the effect on time-to-first-treatment (TTFT) and …

Development Of An Lc-Esi-Ms/Ms Method For Determination Of A Novel Pyrrolomycin (Mp-1) And Application To Pre-Clinical Adme Studies, Wafaa N. Aldhafiri

Theses & Dissertations

A rapid, selective, and sensitive liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) method was developed and validated for quantitation of a novel Pyrrolomycin (MP-1) in mouse plasma. MP-1 was extracted from plasma utilizing a structural analog (PL-3) as the internal standard (IS). Analyte separation was achieved using a Waters Acquity UPLC®BEH C18 column (1.7 µm, 100 x 2.1 mm) protected with Acquity UPLC C18 guard column. Mobile phase consisted of 0.1% acetic acid in water (10%) and methanol (90%) at a total flow rate of 0.25 mL/min. The mass spectrometer was operated at unit resolution in the multiple reaction …

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, …

Glycan-Dependent Adherence And Skin Colonization Of Staphylococcus Epidermidis Mediated By The Surface Protein Aap., Paroma Roy

Theses & Dissertations

Skin-dwelling coagulase-negative staphylococci (CoNS), a group of bacteria that includes Staphylococcus epidermidis, has been implicated to promote skin immunity and antimicrobial defense and prohibit colonization of skin by pathogens like S. aureus. As a skin inhabitant, S. epidermidis lives in tight association with corneocytes, the cells that constitute the uppermost layer of the skin epidermis. Yet the molecular mechanism responsible for adhesion of S. epidermidis to corneocytes remains poorly understood. Our study indicated that Accumulation-associated protein (Aap), a cell-wall anchored, fibrillar adhesin mediates bacterial-host interaction, demonstrated by significantly higher corneocyte binding by Aap-positive 1457 mutants as compared to …

Fundamental Differences In The B Cell Locus, V(D)J Repertoire, And Marburg Virus Epitope Recognition Of The Egyptian Rousette Bat That May Allow For Asymptomatic Presentation, Maggie Linn Bartlett

Theses & Dissertations

Marburg virus (MARV) causes a hemorrhagic fever in humans but is asymptomatic in a known reservoir, the Egyptian rousette bat (Rousettus aegyptiacus, ERB). Understanding the mechanisms that drive these different outcomes could potentially advance the development of therapeutics. The immunoglobulin (Ig) response to MARV infection in ERBs in known to serve a roll in protection. The Ig germline encodes Variable (VH), Diversity (DH), and Joining (JH) genes that then recombine (V(D)J) to make up the binding site of an Ig. Understanding the gene composition of the Ig germline is critical to defining the potential B cell repertoire. We …

Dimers Of Isatin Derived Spirocyclic Nf-Κb Inhibitor Exhibit Potent Anticancer Activity By Inducing Upr Mediated Apoptosis, Smit Kour

Theses & Dissertations

Activation of NFκB pathway has been implicated in several malignancies and plays a role in many key processes including tumor initiation and progression. The NFκB pathway is activated when TNFα in the tumor microenvironment binds to its receptor, eventually leading to the phosphorylation of the kinase IKKβ. Once active, IKKβ phosphorylates IκBα, a protein that functions to sequester NFκB in the cytosol of resting cells. The phosphorylation of IκBα leads to its degradation in the proteasome and allows NFκB to translocate to the nucleus where it can drive gene transcription. The sulfhydryl groups on solvent-exposed cysteine (Cys) residues of the …

Dynamic Oscillatory Interactions Between Neural Attention And Sensorimotor Systems, Alex Wiesman

Theses & Dissertations

The adaptive and flexible ability of the human brain to preference the processing of salient environmental features in the visual space is essential to normative cognitive function, and various neurologically afflicted patient groups report negative impacts on visual attention. While the brain-bases of human attentional processing have begun to be unraveled, very little is known regarding the interactions between attention systems and systems supporting sensory and motor processing. This is essential, as these interactions are dynamic; evolving rapidly in time and across a wide range of functionally defined rhythmic frequencies. Using magnetoencephalography (MEG) and a range of novel cognitive paradigms …

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 …

Flavonoid And Cannabidiol Neural Glyoxalase Pathway Enhancement Against Aging And Alzheimer’S Disease, Joel R. Frandsen

Theses & Dissertations

Alzheimer’s Disease is a neurodegenerative condition featuring neural cell death and a decline in cognitive capacity caused by elevated inflammation and production of reactive oxygen species. The glyoxalase pathway is an endogenous antioxidant system that neutralizes reactive methylglyoxal through sequential reactions. Dysfunction of the glyoxalase pathway contributes to oxidative stress and the accumulation of inflammatory metabolic byproducts. Plant-produced compounds with antioxidant activity can enhance endogenous antioxidant pathways and protect cells from elevated ROS production. We hypothesize that flavonoids and limited Cannabis Sativa-produced cannabidiol can enhance glyoxalase pathway function through regulation of antioxidant and pro-apoptotic signaling pathways to prevent methylglyoxal-mediated …

Molecular Insights Into Paf-1 Mediated Pancreatic Homeostasis, Stemness, And Cancer Progression, Saswati Karmakar

Theses & Dissertations

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease that has one of the lowest 5-year survival rates among cancers, at just 9%. This grim prognosis is primarily due to the extensive metastatic spread of tumor cells beyond the pancreas at diagnosis and the inability of current therapeutic modalities to treat this aggressive disease effectively. Given that the cancer cells in pancreatic tumors are heterogeneous, the major culprit for cancer initiation, progression, and metastasis remains elusive. Recent studies provide evidence for the existence of highly tumorigenic and drug-resistant cells that are capable of tumor initiation, known as the cancer stem cells …

The Role Of Central Ace2 And Nrf2 In Sympatho-Excitation: Responses To Central Angiotensin Ii, Anyun Ma

Theses & Dissertations

Sympatho-excitation is a key characteristic in cardiovascular diseases such as chronic heart failure (CHF) and primary Hypertension (HTN). Evidence suggests that increased sympathetic tone is closely related to activation of the Renin-Angiotensin-Aldosterone system (RAAS) in the central nervous system. An underlying mechanism for sympatho-excitation is thought to be oxidative stress resulting from Angiotensin II (AngII) type 1 receptor (AT1R) activation. Over the past several decades, pharmacological targeting of components of the RAAS have been used as standard therapy in CHF and HTN. However, additional therapeutic strategies are necessary to control these diseases. Oxidative stress is regulated, in part, by the …

The Evolving Management Of Aortic Valve Disease: Trends In The Utilization And Cost Of Savr, Tavr, And Medical Therapy, Andrew Goldsweig

Theses & Dissertations

Aortic stenosis (AS) and regurgitation (AR) may be treated with surgical aortic valve replacement (SAVR), transcatheter AVR (TAVR), or medical therapy (MT). Data are lacking regarding usage and cost of SAVR, TAVR, and MT for patients hospitalized with aortic valve disease. From the Nationwide Readmissions Database, we determined utilization and cost trends for SAVR, TAVR, and MT in patients with aortic valve disease admitted 2012-2016 for valve replacement, heart failure, unstable angina, non-ST-elevation myocardial infarction, or syncope. From 2012 through 2016, there was a 48.1% increase in the number of patients hospitalized for aortic valve disease annually. Overall, 19.9%, 6.7%, …

Mitochondrial Metabolism As A Therapeutic Target For Pancreatic Cancer, Simon Shin

Theses & Dissertations

Mitochondria are biosynthetic and bioenergetic hubs that confer cancer cells the metabolic flexibility to survive and grow in harsh tumor microenvironments. Accordingly, mitochondrial metabolism represents a promising target for pancreatic ductal adenocarcinoma (PDAC), which is frequently characterized as desmoplastic and nutrient poor. The findings presented in the first set of studies highlight the importance of mitochondria-dependent metabolic flexibility in PDAC cells upon exposure to acidic conditions. An acidic tumor microenvironment is a common feature of many solid tumors and exerts a profound influence on cancer biology. Similar to previous findings, we demonstrated that low extracellular pH induces epithelial-to-mesenchymal transition (EMT) …

Insights Into The Chlamydial Niche: The Dynamic Roles Of Inclusion Membrane (Inc) Proteins In Chlamydia Trachomatis Development, Macy G. Wood

Theses & Dissertations

Chlamydia trachomatis (Ctr) is the leading cause of bacterial sexually transmitted infections. Ctr, an obligate intracellular bacterium, develops within a membrane-bound vacuole called an inclusion. The inclusion membrane is modified by chlamydial inclusion membrane (Inc) proteins, the functions of which are poorly characterized. Bacterial two-hybrid analyses found some Incs (e.g., IncF) interacted with numerous Incs while others (e.g., IncA) did not. We hypothesize that some Incs organize the inclusion through Inc-Inc interactions whereas other Incs promote chlamydial-host interactions by binding eukaryotic proteins. To test our hypothesis, we implemented the ascorbate peroxidase proximity labeling system (APEX2), which labels proximal proteins with …

Novel Regulatory Roles Of Endocytic Membrane Trafficking Proteins In Mitochondrial Homeostasis, Trey Farmer

Theses & Dissertations

Endocytic membrane trafficking is a basic cell process that is critical for regulating the transport of lipids and proteins. Our lab focuses on the cellular functions and mechanisms of the proteins that regulate these pathways. A key family of regulatory proteins is the C-terminal Eps15 Homology Domain (EHD) protein family. The EHD family includes EHD1-4, which are ubiquitously expressed in mammalian tissues. While these isoforms do have some overlapping functions, each protein also has distinct activities in regulating the shape and fission of membranes throughout the endocytic pathways. Specifically, EHD1 uses ATP hydrolysis to induce constriction and fission of endocytic …

Molecular And Behavioral Studies In Cdkl5 Deficiency Disorder, Ethan Schroeder

Theses & Dissertations

CDKL5 Deficiency Disorder (CDD) is an X-linked neurodevelopmental disorder associated with epilepsy, developmental retardation, autism, and related phenotypes. Currently, there is no cure available for the disorder. Thus, the identification of cellular and molecular aberrations in this disorder and the generation and validation of mouse models that recapitulate core aspects of the disorder are a pressing need in the field. Our studies are aimed at filling this gap.

Mutations in the CDKL5 gene, encoding CDKL5, have been identified in this disorder. CDKL5 is a protein with homology to the serine-threonine kinases and incompletely characterized function. Mutations in CDKL5 are predominately …