Bachelor of Sciences, Ohio University, 2023, Biological Sciences

Globally, metastasis causes approximately 90% of mortality in cancer, making it a leading cause of death. In the United States, in both men and women, lung cancer is the second most prevalent cancer, with over 283,000 new cases estimated to be diagnosed in 2023. Both the tumor microenvironment (TME) and macropinocytosis have been shown to play a role in invasion, proliferation, and recurrence of cancers. Dr. Xiaozhuo Chen's lab at Ohio University studied the effects of the TME on cancer cells by performing RNA sequencing on A549. A549 are non-small cell human lung cancer (NSCLC) cells, which showed a consistent, significant upregulation of Stanniocalcin 1(STC1) gene expression when treated with extracellular ATP (eATP) and TGF-β. STC1 is a protein hormone involved in the regulation of the calcium phosphate balance, as well as ATP synthesis in mitochondria within the cell. Further studies showed that knock down of the STC1 gene led to reduced invasion and proliferation when compared to the untreated A549 cells. The aim of this project was to perform two main studies; one, to identify and assess macropinocytosis in a variety of cancer cell lines, and two, to investigate the effects of the STC1 gene on macropinocytosis. Using ATP concentration assays and IPA3 inhibition assays, macropinocytosis was examined in 11 cancer cell lines of varying cancer types. Macropinocytosis was confirmed with fluorescence microscopy by the colocalization of green fluorescent ATP and red fluorescent dextran. The impact of the knock-out of STC1 on macropinocytosis in A549 cells was investigated and quantified using ImageJ. The fluorescence microscopy study revealed that STC1 gene did play a role in macropinocytosis as predicted, which may be important for its effect on proliferation and invasion, the first step of metastasis.

Committee: Xiaozhuo Chen PhD (Advisor); Janet Duerr PhD (Advisor) Subjects: Biology; Cellular Biology; Molecular Biology

Doctor of Philosophy, The Ohio State University, 2021, Biomedical Sciences

Few therapeutic options exist for the 15-25% of melanoma patients whose disease is driven by oncogenic NRAS. NRAS is a member of the RAS family of proto-oncogenic GTPase proteins which trigger signal transduction pathways involved in cellular motility, survival, proliferation, and metabolism. Therapeutic targeting of NRAS is a decades-old challenge, hindered by the inability to develop small molecule inhibitors specific for the mutant protein. Furthermore, oncogenic NRAS can circumvent treatments targeting post-translational RAS modifications, interacting partners, and downstream signaling pathways. Current first-line therapies for NRAS-driven melanoma are immune-based. While such drugs are effective in 40-50% of individuals, many patients suffer from high-grade adverse events and only a subset of responders experience durable remissions. With NRAS-driven melanomas being the most aggressive subtype of this disease, new and effective therapeutic options are needed. Oncogenic NRAS mutations primarily affect codons 12, 13, and 61, resulting in constitutive GTP-binding, activation, and downstream signal transduction. However, each NRAS-driven malignancy shows selection bias for a different subset of NRAS mutants. For example, NRAS-driven melanomas are enriched for genetic mutations in codon 61 (>80%) while mutations in acute myeloid leukemia primarily occur in codons 12 and 13. This mutational bias remains poorly understood, especially in melanoma where the codon 61 alterations are not directly attributed to ultraviolet light. I developed a suite of conditional, Nras knock-in mouse models (LSL-Nras Q61R, -K, -L, -H, -P, -Q; G12D and G13D, -R) to test the hypothesis that NRAS mutants commonly observed in melanoma possess functional properties required for efficient melanocyte transformation. Expression of these alleles in melanocytes revealed that the melanomagenic potential of each NRAS variant parallels the frequency of that mutation in human melanoma. Specifical (open full item for complete abstract)

Committee: Christin Burd E (Advisor); Joanna Groden (Committee Chair); Michael Freitas A (Committee Member); Terence Williams M (Committee Member) Subjects: Biology; Biomedical Research; Cellular Biology; Molecular Biology; Oncology

Doctor of Philosophy, Case Western Reserve University, 2020, Biomedical Engineering

As the arsenal of therapeutic strategies in the fight against cancer grows, so too does the need for predictive biomarkers that can precisely guide their use in order to match patients with their optimal personalized treatment plan. Currently, clinicians often have little recourse but to initiate treatment and monitor a tumor for signs of response or progression, which exposes non-responsive patients to overtreatment, harmful side effects, and windows of ineffective therapy that increase a patient's risk of progression or metastasis. Thus, there is an urgent need for new sources of predictive biomarkers to help more effectively plan personalized treatment strategies. Radiological images acquired before treatment may contain previously untapped predictive information that can be quantified in the form of computational imaging biomarkers. The vast majority of existing computational imaging biomarkers provides analysis limited to the tumor region itself. However, the tumor environment contains critical biological information pertinent to tumor progression and treatment outcome, such as tumor-associated vascularization and immune response. This dissertation focuses on the development of new, biologically-inspired computational imaging biomarkers targeting the tumor environment for the prediction of response to a wide range of chemotherapeutic and targeted treatment strategies in oncology. First, we explore measurements of textural heterogeneity within the tumor and surrounding peritumoral environment, and demonstrate the ability to predict therapeutic response and tumor biology to neoadjuvant chemotherapy in primary and targeted therapy in primary and metastatic breast cancer. Second, we introduce morphologic techniques for the quantification of the twistedness and organization of the tumor-associated vasculature, and demonstrate their association with response and survival following four different therapeutic strategies in breast cancer MRI and non-small cell lung canc (open full item for complete abstract)

Committee: Madabhushi Anant (Advisor); Wilson David (Committee Chair); Abraham Jame (Committee Member); Gilmore Hannah (Committee Member); Plecha Donna (Committee Member); Varadan Vinay (Committee Member) Subjects: Biomedical Engineering; Biomedical Research; Computer Science; Medical Imaging; Medicine; Oncology; Radiology

PhD, University of Cincinnati, 2014, Medicine: Cancer and Cell Biology

Innate immune signaling has an essential role in inflammation, and the dysregulation of signaling components within this pathway is increasingly being recognized as a mediator in cancer initiation and progression. The innate immune system is an evolutionarily conserved pathogen pattern recognition apparatus, which defends the host in a non-specific manner. Pathogens and cytokines signal to immune cells through the toll-like receptor (TLR) and interleukin-1 receptor (IL1R) superfamily. In order to mediate an inflammatory response, TLRs and IL1R require interleukin-1 associated receptor kinases (IRAKs). Herein, we demonstrate that IRAK1 is activated and overexpressed in Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML); two closely related hematologic malignancies. Furthermore, pharmacological (IRAK-Inh) and RNAi-mediated inhibition of IRAK1 is effective in eliminating disease-propagating cells. Integrated gene expression analysis revealed compensatory BCL2 upregulation following small-molecule IRAK1 inhibition. This proved to be a drugable vulnerability, as BCL2 inhibition potently synergized with IRAK-Inh to induce rapid cell death, even in IRAK-Inh-refractory cell lines. Importantly, suppression of IRAK1 signaling, through either RNAi or small-molecule inhibition, is tolerated in normal CD34+ cells, suggesting a potential therapeutic window for MDS and AML patients. To examine the effect of cancer-modifying therapies, like IRAK inhibition, we developed a novel xenograft model, utilizing an MDS-derived patient cell line, MDSL. Immunocompromised animals receiving MDSL xenografts developed progressive anemia and thrombocytopenia, thus recapitulating clinical features of the disease. These mice displayed rapid morbidity resulting from MDSL engraftment in bone marrow, spleen and peripheral blood. In this setting, both RNAi-mediated and small-molecule IRAK1 inhibition was effective in reducing MDSL cell burden, and provided a significant survival benefit. T (open full item for complete abstract)

Committee: Daniel Starczynowski Ph.D. (Committee Chair); Gang Huang Ph.D. (Committee Member); H. Leighton Grimes Ph.D. (Committee Member); Ashish R. Kumar M.D. Ph.D. (Committee Member); Maria Czyzyk-Krzeska M.D. Ph.D. (Committee Member); James Mulloy Ph.D. (Committee Member) Subjects: Cellular Biology

Master of Science, The Ohio State University, 2012, Electrical and Computer Engineering

Since co-expressed genes often are co-regulated by a group of transcription factors, different conditions (e.g., disease versus normal) may lead to different transcription factor activities and therefore different co-expression relationships. A method for identifying condition specific co-expression networks by combining the recently developed network quasi-clique mining algorithm and the Expected Conditional F-statistic has been proposed. This method has been applied to compare the transcriptional programs between the non-basal and basal types of breast cancers. This work is a translational bioinformatics study integrating network analysis which lifts the traditional gene list based disease biomarker discovery to the gene and protein interaction level. This work presents a method for identifying condition specific gene co-expression networks. The method involves construction of a Weighted Graph Co-expression Network (WGCN) and mining the WGCNs to identify dense co-expression networks followed by a chi-square test based enrichment analysis for detecting condition specific co-expression relationship. The expression values in all the conditions for the genes constituting a condition specific co-expression network are visualized as heat maps which suggest that the genes are highly correlated in a specific condition but the correlations are disrupted in other conditions.

Committee: Kun Huang PhD (Advisor); Raghu Machiraju PhD (Committee Member) Subjects: Bioinformatics; Computer Engineering; Computer Science; Engineering

Doctor of Philosophy (PhD), University of Toledo, 2013, College of Medicine

The overall goal in cancer therapeutics is to do induce cell death in the tumor cells. While many classical anticancer drugs have different targets, they generally induce cell death by stimulating signaling pathways that ultimately activate apoptosis. Unfortunately, many genetic alterations that help drive the progression of a tumor cell also lead to apoptosis resistance. Thus, cancers are often treated with drugs to which they are inherently resistant. In order to circumvent this problem, there is a strong interest in identifying new forms of non-apoptotic cell death, with the goal of developing therapies that can activate these forms of cell death. Our lab has recently identified a form of non-apoptotic cell death called methuosis, characterized by hyperstimulated macropinocytosis and disrupted trafficking of these vesicles to the lysosome. These vesicles overwhelm the cytoplasm, disrupt cellular metabolism, and compromise membrane integrity, resulting in cell death. Methuosis was originally characterized in glioblastoma cell culture by overexpression of activated Ras or Rac GTPases. However, our lab recently identified a class of small molecules that induce methuosis in cancer cells, providing a potential way to induce this form of cell death therapeutically. This dissertation describes studies aimed to further understand the molecules that induce methuosis. First, the structure activity relationships of compounds that induce methuosis were evaluated, resulting in the identification of our lead compound, MOMIPP. Next, we sought to identify the cellular targets of MOMIPP that lead to methuosis induction. Accordingly, various chemical tools were synthesized and used to identify MOMIPP target proteins. Ultimately, two proteins that specifically bind MOMIPP were identified as candidates for methuosis-triggering activity. These await further characterization to confirm their relationship to methuosis and cell death.

Committee: William Maltese PhD (Committee Chair); Paul Erhardt PhD (Committee Member); Kenneth Hensley PhD (Committee Member); Jean Overmeyer PhD (Committee Member); James Slama PhD (Committee Member); Kana Yamamoto PhD (Committee Member) Subjects: Biochemistry; Chemistry; Oncology; Organic Chemistry

Doctor of Philosophy, Case Western Reserve University, 2024, Nutrition

Drug resistance in both cancer and infectious disease is a major driver of mortality across the globe. In infectious disease, the emergence of antimicrobial resistance (AMR) outpaces our ability to develop novel drugs, and within-host evolution confounds the use of previously effective drugs during the course of treatment. In cancer, while targeted therapies have improved outcomes for some, many patients continue to face metastatic, drug-resistant disease, with limited therapeutic options available. As both disease types are driven by clonal evolution, a complementary approach to treatment that leverages tools and ideas from evolutionary biology has been beneficial. However, this evolutionary-inspired therapy has thus far been limited in its consideration of drug variation in time and space within a patient (pharmacokinetics) and variable pathogen response to drug (pharmacodynamics). In this dissertation, we describe novel computational and experimental approaches that integrate pharmacokinetics and pharmacodynamics to allow for more physically realistic models of the evolution of drug resistance. We apply these approaches to gain novel insights into drug dosing regimens and drug diffusion in tissue. In Chapters 1 and 2, we briefly review integrated pharmacokinetics and pharmacodynamics in the study of drug resistance and survey the current evidence of fitness costs to drug resistance in cancer. In Chapter 3, we developed a novel, fluorescence-based time-kill protocol for estimating drug dose-dependent death rates in bacteria. In Chapter 4, we described a software package, FEArS, that allows for efficient agent-based simulation of evolution under time-varying drug concentration. In Chapter 5, we leverage both of these methods to gain insight into why some antimicrobial treatments fail using computational modeling and simulated clinical pharmacokinetics. In Chapter 6, we use spatial agent-based modeling to examine how drug diffusion in tissue can promote tumor hetero (open full item for complete abstract)

Committee: Mark Chance (Committee Chair); Christopher McFarland (Committee Member); Jacob Scott (Advisor); Michael Hinzcewski (Committee Member); Drew Adams (Committee Member) Subjects: Bioinformatics; Biology; Biomedical Research; Biophysics

Doctor of Philosophy, The Ohio State University, 2024, Pharmaceutical Sciences

Cancers and leishmaniasis are distinct diseases, but the effects of each on people and communities are similarly devastating. Cancers cause over 10 million deaths worldwide each year, and are so widespread that nearly every person has lost a loved one to them, myself included. Leishmaniasis primarily affects tropical countries and in many places where access to medical care is limited, and the visceral form of the disease requires medical treatment to increase chances of survival above 5%. Both cancers and visceral leishmaniasis are diseases that the human immune system alone often cannot overcome, so the continued research into treatments is crucial to develop new and better tools to fight against these diseases. This dissertation details drug discovery efforts for two different projects, one against each disease; chapter 1 introduces readers to each disease state, chapter 2 describes the synthesis and biological evaluation of anticancer compounds, and chapter 3 describes the synthesis and biological evaluation of antileishmanial compounds. Following the serendipitous discovery of an antileukemia hit compound with an arylimidamide-azole scaffold, a series of analogs was synthesized to evaluate modifications to the scaffold. A robust structure-activity relationship (SAR) was developed through the synthesis of these compounds, and analysis of this relationship pointed to specific chemical modifications to the scaffold which improved their anticancer potency. Combining these favorable modifications led to compounds with >4-fold improved potency compared to the parent compound. Among the most potent compounds in this iv series was 2.9k, which displayed an IC50 value of 100 nM against the acute myeloid leukemia (AML) cell line OCI-AML3. Promising compounds in this series were then further evaluated for broad anticancer activity, pharmacokinetic properties, and mechanism of action as described in chapter 2. The antileishmanial compounds described in this dissertation (open full item for complete abstract)

Committee: Karl Werbovetz (Advisor); Xiaolin Cheng (Committee Member); James Fuchs (Committee Member) Subjects: Biology; Chemistry; Organic Chemistry; Pharmaceuticals; Pharmacology; Pharmacy Sciences

Master of Science (MS), Bowling Green State University, 2023, Biological Sciences

All epithelia are characterized by keratins, which make up a type of intermediate filament (IF). In epithelial tumors, which account for the majority of clinical cancers, the loss of cytoskeletal integration is considered one of the first alterations in epithelial metaplasia. This may have something to do with the expression of keratins or rearrangement of keratin filaments. In this study, I employed shotgun proteomic analysis and bioinformatic tools to identify proteins that interact with keratin filaments and thus may contribute to the disintegration of cytoskeleton. Using four airway epithelial cell lines in culture, I confirmed they highly expressed Keratin 14 (K14) and its obligatory partners, Keratin 5 (K5) or Keratin 6A (K6A). This suggests that the predominant IF is made up of K14 paired with K5/K6A. Although samples were enriched in keratin-associated proteins by immunoprecipitation (IP) with an antibody directed against K14 and K17, additional keratins not specifically targeted were also captured. Proteomic analysis revealed a list of non-keratin proteins enriched by IP. Some were associated with actin and microtubules, 23 and 6 proteins, respectively. Most of these were not linearly related to keratin content by abundance, but the motor protein, dynein I heavy chain, showed a Pearson correlation coefficient (CC) of -0.84 with keratin. Similarly, of 54 proteins associated with focal adhesions, intercellular junctions, or membranes, only septin-9 had a CC suggesting its abundance tracked with that of keratins. Finally, I analyzed IP-specific proteins that were cytosolic or had unknown subcellular distribution. A CC of -0.91 was found for one of these proteins, namely 26S proteasome regulatory subunit 8 (Psmc5). Further investigation and validation of the dataset was done by GO Enrichment Analysis. Using a subset of proteins highly concentrated by IP, compared to controls, I found the GO functions predicted were intracellular transport, (open full item for complete abstract)

Committee: Carol Heckman Ph.D (Committee Chair); Michael Geusz Ph.D (Committee Member); Xiaohong Tan Ph.D (Committee Member) Subjects: Bioinformatics; Biology; Biomedical Research; Cellular Biology; Molecular Biology; Oncology

Bachelor of Science, Wittenberg University, 2022, Biology

The fishing industry for the collection of Dungeness crabs is restricted to size, sex, and season. Dungeness crabs are found along the western coast of the United States. Data analysis showed that through the years all groups of the crab were found in high abundance in the shallowest depth, 5-20 fathoms and the lowest abundance was seen in the deepest depth of>60 fathoms. When considered by region the data showed that all three groups were common in the Georgia Basin and not as common in South Puget Sound. Of the regions where the trawl was conducted, the highest abundance of all three groups were clustered in the upper Northeast region of Washington State.

Committee: Kathy Reinsel (Advisor); Doug Andrews (Committee Member); Matthew Collier (Committee Member) Subjects: Animal Sciences; Animals; Aquatic Sciences; Biological Oceanography; Biology; Ecology; Environmental Science; Zoology

Doctor of Philosophy, Case Western Reserve University, 2020, Pharmacology

Aberrant signal transduction resulting from dysregulated phosphorylation is a hallmark of human cancer. Altered phosphorylation has broad implications on cancer biology. Much work has been done characterizing the effects of individual kinases with their cancer phenotypes. However, the structural complexity of their counterparts, phosphatases, has limited our knowledge of these signaling events. Protein Phosphatase 2A (PP2A), one such negative regulator of multiple oncogenic kinases, has been well characterized as a tumor suppressor protein that when inhibited can lead to cellular transformation. PP2A is a heterotrimeric complex whose substrate specificity is dependent on one of 23 different regulatory subunits that can bind to form over 60 distinct holoenzyme complexes. Although PP2A's function as a general tumor suppressor is well studied, the role of PP2A on specific tumor suppressive signaling pathways and the specific holoenzymes mediating this signaling are not completely understood. Through chemical and genetic approaches, this work characterizes a new role for PP2A in the regulation of DNA replication, and links PP2A effects on replication with its ability to induce apoptosis. 2 Utilizing both a gain of function chemical biology approach and loss of function genetic approaches to modulate PP2A activity, we demonstrate that increasing PP2A activity can interrupt ongoing DNA replication resulting in a collapse of replication forks, the induction of double-stranded DNA (dsDNA) breaks, and a replication stress response that is PP2A dependent. Additionally, we show that increasing PP2A activity during replication causes a dissociation of the replisome, a common mechanism of inhibiting ongoing replication. Furthermore, patients harboring mutations in PP2A are shown to have a higher fraction of their genome altered, suggesting that PP2A regulates ongoing replication as a mechanism for maintaining genomic integrity. Moreover, knockdown of the (open full item for complete abstract)

Committee: Goutham Narla M.D./Ph.D. (Advisor); Derek Taylor Ph.D. (Committee Chair); John Mieyal Ph.D. (Committee Member); Youwei Zhang Ph.D. (Committee Member); Amar Desai Ph.D. (Committee Member) Subjects: Biomedical Research; Cellular Biology; Pharmacology

Doctor of Philosophy, Case Western Reserve University, 2019, Pharmacology

Cellular signaling through reversible phosphorylation is an essential process of communication which allows cells to identify and respond to their microenvironment and is coordinated in a manner regulated both in time and space. This process is balanced by the opposing actions of phosphatases and kinases. Highlighting the importance of maintaining balanced cellular signaling, altered cellular signaling is dysregulated is multiple disease contexts. In particular, one of the hallmarks of cancer is sustained proliferative signaling, often through the dysregulation of phosphorylation. Work completed over the past several years has shown an important role for phosphatases in cellular transformation and disease progression. In particular, Protein Phosphatase 2A (PP2A) functions as a tumor suppressor by negatively regulating multiple oncogenic signaling pathways responsible for driving cancer progression. The canonical PP2A holoenzyme is comprised of a scaffolding subunit (PP2A A-alpha/beta), which serves as the platform for the binding of both the catalytic C subunit and one regulatory B subunit. While it has been established the PP2A holoenzyme and the A-alpha scaffold have tumor suppressive functions, the mechanisms responsible for these activities had not been well explored. The research presented in this dissertation sought to provide insight into the mechanisms of the tumor suppressive functions of the PP2A A-alpha scaffolding subunit by studying how mutations and deletions of this protein affect function. We showed how the most recurrent PP2A A-alpha mutation, R183W, altered holoenzyme formation, the downstream consequences on cellular signaling and decreased response to MEK inhibitors. Additionally, we investigated the functional consequences of homozygous deletion of the A-alpha subunit and identified that complete deletion of A-alpha is not tumor suppressive due to a compensatory upregulation of the A-beta scaffolding subunit. Collectively, these studies offer un (open full item for complete abstract)

Committee: Goutham Narla (Advisor); Jason Mears (Committee Chair); Ruth Keri (Committee Member); Mark Jackson (Committee Member); Derek Taylor (Committee Member) Subjects: Oncology; Pharmacology

PhD, University of Cincinnati, 2018, Medicine: Systems Biology and Physiology

Classically much of the focus in cancer biology has been on driver genes, i.e. tumor-suppressors and oncogenes, and how somatic mutations in these genes influence tumor phenotype. Large scale profiling studies like The Cancer Genome Atlas (TCGA) have produced massive repositories of genomic and transcriptomic data. This data has facilitated discovery and characterization of somatic drive mutations across cancers. In addition to these driver mutations cancer also have onco-passenger mutations that are passively acquired. These mutations are particularly common in tumors with extensive structural variations resulting in chromosomal deletions or amplifications. These variants are thought to target driver genes but result in copy number changes in hundreds of genes surrounding the driver genes- these genes are onco-passenger genes. Though individual instances of onco-passenger events have been characterized, a systematic understanding of their role in cancers is lacking. In addition to somatic changes, tumors also carry common heritable variants or germline polymorphisms. Recent studies have shown that these polymorphisms play critical roles in modulating gene expression across tissues. These regulatory polymorphisms are also related to numerous loci associated with predisposition to complex diseases. These studies indicate that germline polymorphisms could have a significant role in cancer biology. However, in contrast to somatic mutations we lack a systematic understanding of the functional role that germline polymorphisms play in cancers. The body of work presented here leverages the TCGA dataset, and using rigorous computational and statistical analysis hope to provide a more comprehensive picture of the role that onco-passenger genes and germline polymorphisms play in cancers.

Committee: Kakajan Komurov Ph.D. (Committee Chair); Christian Hong Ph.D. (Committee Member); Gang Huang Ph.D. (Committee Member); Nathan Salomonis M.D. (Committee Member); Yana Zavros Ph.D. (Committee Member) Subjects: Biology; Systematic

Doctor of Philosophy, Case Western Reserve University, 2018, Molecular Biology and Microbiology

In the United States, melanoma is the fifth leading cancer in men and sixth in women. The current course of treatment is tumor resection, which is extremely effective in early stage tumors. However, because of the aggressive nature of melanoma and the access to the underlying vascular “highway”, metastasis is common and deadly. Therefore, novel therapeutic strategies need to be devised to intervene and improve survival rates of patients diagnosed with metastatic disease; at the same time, prophylactic strategies are needed to prevent development of metastatic disease and/or recurrence. This work proposes the use of plant virus-like nanoparticles (VLPs) for application in cancer immunotherapy. Here the goals were to investigate the underlying mechanism of the potent antitumor response of cowpea mosaic virus (CPMV), as well as to define the engineering design parameters for future translational development. The central hypothesis was that by inserting plant VLPs into the tumor microenvironment, the particles will interact with and activate the innate immune response. Furthermore, this localized response can positively affect immune tumor recognition by removing tumor microenvironment tolerance and increase tumor antigen presentation. Three specific aims were used to test this hypothesis. Aim one set to determine the usability of flexible high aspect ratio particles for mono and combination therapies. Here monotherapy involved the use of potato virus X (PVX) while combination added doxorubicin (DOX) with varying forms of co-administration. The data showed that the combination of the two therapies was indeed synergistic, however, benefit in treatment outcome was only achieved when the PVX immunotherapy and DOX chemotherapy were administered separately (rather than combined into a single nanoparticle). Aim two set to determine the engineering design space of the VLPs and to determine the immunological changes upon tumor treatment with plant VLPs. Here antitumor efficacy (open full item for complete abstract)

Committee: Nicole Steinmetz PhD (Advisor); Alan Levine PhD (Committee Chair); Julian Kim MD (Committee Member); Susan Brady-Kalnay PhD (Committee Member); Robert Silverman PhD (Committee Member) Subjects: Biology; Biomedical Engineering; Immunology; Medicine; Microbiology; Molecular Biology; Nanoscience; Nanotechnology; Oncology; Plant Biology; Plant Pathology; Plant Sciences; Virology

Doctor of Philosophy, Case Western Reserve University, 2018, EECS - Computer and Information Sciences

Precision medicine is a promising new approach to medicine that takes into account the individual differences in people's genetic makeup and lifestyle to identify specific treatment and prevention strategies for diseases. However, many human diseases are complex, and are driven by multiple layers of dysregulation at the cellular level, in addition to environmental factors. In recent years, the advances in high throughput technologies enable interrogation of biological systems at multiple levels, offering valuable types of data representing various aspects of cellular systems. These data types include sequences and structures of genes, RNAs, proteins, quantitative measurements on the abundance of these molecules under different conditions, and the interactions among these molecules. However, these data are noisy, incomplete, high-dimensional, highly heterogeneous, and often provide static representations of a complex and dynamic system. In this thesis, we develop computational methods to make use of these useful, yet limited sources of biological data, with a view to gaining insights on the molecular mechanisms of complex diseases. In particular, we develop novel algorithms to integrate genomic (genome-wide association studies), transcriptomic (expression-quantitative trait locus interactions), proteomic (protein expression screened via mass spectrometry), phospho-proteomic (large scale data on the phosphorylation of signaling proteins screened via mass spectrometry), and interactomic (protein interaction networks, pathway databases) datasets. Using these integrative algorithms, we develop computational tools for the identification of disease-associated protein subnetworks, risk assessment for complex diseases, and prediction of kinase-substrate associations in specific biological contexts.

Committee: Mehmet Koyuturk (Advisor); Mark Chance (Committee Member); Soumya Ray (Committee Member); Liberatore Vincenzo (Committee Member) Subjects: Bioinformatics; Computer Science

Doctor of Philosophy, The Ohio State University, 2018, Biomedical Sciences

Lung cancer is the most deadly form of cancer, responsible for over 1.6 million deaths annually, the majority of which are due to non-small cell lung cancer, of which adenocarcinoma and squamous cell carcinoma are the major subtypes. Standard chemotherapy produces responses in a small minority of patients, and despite the tremendous growth of personalized therapies in the last decade, only a minority of patients benefit from these treatments in the North American setting. A greater understanding of the biology of non-small cell lung cancer is desperately needed to develop novel targeted therapies and their accompanying biomarkers. Understanding the function of cancer-associated genes requires the integration and analysis of multiple modalities of biological data. Cancer associated genes can be activated or repressed by DNA somatic mutations, RNA alternative splicing, epigenetic changes, microRNA-mediated silencing, post-translational regulation, and other mechanisms. To understand how tumors form and grow, we have to be able to measure DNA, RNA, protein, metabolites, and lipids. Further, integrative and analytical methods are necessary to leverage these data together, collectively termed integrative genomics. Here, we leverage DNA mutations and copy number measurements, RNA transcriptomics, proteomics, and clinical data to discover regulatory relationships in tumors, develop prognostic biomarkers, and identify mediators of tumor mutation burden. First, we focus on the RNA editing protein ADAR, and propose an immune-mediated function in lung adenocarcinoma. Second, we develop a method to integrate RNA and protein expression data to predict binary clinical variables, and test its ability to predict tumor recurrence in surgically resected lung adenocarcinoma samples. Finally, we define the relationship between tumor mutation burden and genome stability protein inactivation to better understand tumor immunogenicity in non-small cell lung cancer. T (open full item for complete abstract)

Committee: Kun Huang (Advisor); Jeffrey Parvin (Committee Member); David Carbone (Committee Member); Kai He (Committee Member) Subjects: Bioinformatics; Oncology

PHD, Kent State University, 2015, College of Arts and Sciences / Department of Biological Sciences

Protein translational regulation by RNA binding proteins (RBPs) is a critical process in maintaining homeostasis. Epithelial to mesenchymal transition (EMT) is a process in which epithelial cells de-differentiate and become mesenchymal, increasing the propensity toward tumorigenesis and/or metastasis. We have identified a heterogeneous nuclear riboprotein E1 (hnRNP E1)-mediated post-transcriptional operon that controls transcript-selective translational regulation of epithelial / mesenchymal transition (EMT)-associated genes. In this regulatory mechanism, hnRNPE1 binds to the 3'-UTR of select transcripts and silences their translation. TGFß reverses translational silencing through Akt2-dependent phosphorylation of hnRNP E1 at Ser-43, resulting in loss of hnRNP E1 binding to RNA. We have identified approximately forty pro-EMT / metastatic mRNAs that are regulated by this hnRNP E1 operon and our preliminary studies have revealed a short stretch of nucleic acids, that we have termed the BAT element (TGF-beta activated translational (BAT) element), present in their respective 3'-UTRs that may be responsible for hnRNP E1 binding. Herein, through the use of in-vitro and in-vivo assays, we demonstrate the contribution of BAT element mutations and constitutively high levels of pSer43 hnRNP E1 to cancer tumorigenesis and metastasis.

Committee: Philip Howe Ph.D. (Advisor); Derek Damron Ph.D. (Committee Member); Srinivasan Vijayaraghavan Ph.D. (Committee Member); Olena Piontkivska Ph.D. (Committee Member); Bidyut Mohanty Ph.D. (Committee Member) Subjects: Bioinformatics; Biology; Biomedical Research; Biostatistics

Doctor of Philosophy, Case Western Reserve University, 2014, Genetics

Regulation of protein tyrosine phosphorylation is important in maintaining appropriate cellular homeostasis. Accordingly, protein tyrosine phosphatases are frequently mutated in cancer. The most commonly mutated protein tyrosine phosphatase in colorectal cancer is PTPRT. Follow-up studies validated it as a tumor suppressor, especially through its activity on its substrates STAT3 phosphotyrosine-705 and paxillin phosphotyrosine-88. While the latter substrate is well characterized, further study is needed into pY88 paxillin. Since previous studies show that PTPRT is inactivated in colorectal carcinoma, understanding what kinase directly phosphorylates its substrates is an important question to investigate. Here, we show that paxillin Y88 is directly targeted by Src kinase for phosphorylation. Consequently, this finding has implications for cells that express high levels of pY88 paxillin, as they become sensitive to dasatinib treatment. Moreover, although prior work demonstrated that pY88 paxillin impacts Akt signaling, how this signal was transduced was not immediately clear. We show that pY88 paxillin promotes interaction between p130Cas and the p85alpha regulatory subunit of PI3K. Therefore, we shed further light into how PTPRT affects colorectal cancer tumorigenesis. Another important aspect of this and many other cancers is the role of obesity in tumor development. One of PTPRT's substrates, pY705 STAT3, plays a crucial role in energy homeostasis. Like PTPRT, there are other neuronally-expressed tyrosine phosphatases that target STAT3 for dephosphorylation. These proteins have a dramatic impact on obesity development, making PTPRT a good candidate for a similar study. Appropriately, the loss of PTPRT via a mouse knockout has a dramatic impact on the development of obesity. In the genetic background of a mouse strain that is sensitive to high-fat diet-induced obesity, PTPRT knockout mice resist the development of obesity by decreased food intake. Accordingly (open full item for complete abstract)

Committee: Zhenghe Wang PhD (Advisor); Hua Lou PhD (Committee Chair); Sanford Markowitz MD/PhD (Committee Member); Clark Distelhorst MD (Committee Member); Alex Huang MD/PhD (Committee Member) Subjects: Biology; Cellular Biology; Genetics

Doctor of Philosophy, The Ohio State University, 1999, Public Health

The purpose of these investigations was to evaluate hypotheses concerning associations between the acute phase response (APR), an adaptive response to cellular injury during which hepatocyte protein synthesis is altered, and preclinical cancer and myocardial infarction (MI). The goal of the first investigation (Chapter 2) was to determine how long prior to cancer or MI diagnoses alterations in serum albumin, transferrin (assessed as iron binding capacity [IBC]), and serum iron occur. Age-adjusted statistically significant decreases in serum albumin, IBC, and serum iron prior to both cancer and MI diagnoses are found. Men not diagnosed with either cancer or MI have initial IBC and serum iron levels significantly lower than men developing cancer and MI, and show significant increases in IBC and serum iron during the eight-year study period. Results from the second investigation (Chapter 3) indicate that routinely-measured acute phase reactants are altered at least three years prior to diagnoses of two smoking-related cancers: lung and bladder cancer, although results vary by sex. For example, among males, risk of bladder cancer is 8.24 times greater (95 percent confidence interval [CI]: 3.39-20.04), and risk for lung cancer is 2.95 times greater (95 percent CI: 1.90-4.56) in men with WBCC in the upper quartile compared to men in remaining quartiles. Results from the third investigation (Chapter 4) indicate that serum micronutrients are altered during the APR. Statistically significant inverse associations between the APR and the following micronutrients are found: serum iron, selenium, vitamin C, vitamin A, a-carotene, ß-carotene, and lycopene. Finally, results of the last investigation (Chapter 5) indicate that urinary albumin levels greater than 100 ug/dl are found associated with the APR independent of serum albumin (prevalence odds ratio = 1.80, 95 percent CI: 1.19-2.70), and urinary albumin excretion is associated with increased risk of prostate (RR = 1.88, 95 pe (open full item for complete abstract)

Committee: Judith Schwartzbaum (Advisor) Subjects: Epidemiology; Oncology; Public Health

Doctor of Philosophy, Miami University, 2014, Chemistry and Biochemistry

Metabonomics is a novel tool to investigate diseases and therapeutic treatments. This dissertation describes novel statistical methods for metabonomics based on nuclear magnetic resonance (NMR) spectroscopy and their application in studying the mechanism of human cancers. Chapter 1 introduces the currently used metabonomics data interpretation methods and instruments. Chapter 2 investigated how the reproducibility of metabolite resonances measured by NMR depends on signal-to-noise ratio (SNR) and normalization methods using the coefficient of variation (CV) method. An inverse correlation was detected between SNR and CV for all normalization methods, which will aid the researchers to optimize experiments. Chapter 3 demonstrates a new potential biomarker discovery method for metabonomics studies called Standard Deviation Step Down (SDSD). Unlike most of commonly used methods, SDSD gives weight to relative metabolite concentration and is progressively more sensitive for more concentrated metabolites. Chapter 4 provides a new algorithm for Principal Components Analysis (PCA) in protein sequence analysis. The method provides a way to know which amino acid position variations are most responsible for driving separation into sub-clusters. Chapter 5 describes metabonomics study of human neuroblastoma cell line induced by Neuropeptide Y (NPY) and its Y2 receptor. High conversion of glucose into lactate in abundance oxygen (Warburg effect) and lower intracellular nutrient in NPY Y2R group was observed. NPY and Y2R may influence glycolysis, glutaminolysis and possibly TCA cycle. Chapter 6 describes role of osteopontin-a in tumor progression by studying breast cancer cell metabolites. Osteopontin-a upregulates the levels of glucose in breast cancer cells, likely through STAT3 and its transcriptional targets apolipoprotein D and IGFBP5. The splice-variant-specific metabolic effects of osteopontin add a novel aspect to the pro-metastatic functions. Chapter 7 describes the microbi (open full item for complete abstract)

Committee: Michael Kennedy (Advisor); Neil Danielson (Committee Chair); Carole Dabney-Smith (Committee Member); Gary Lorigan (Committee Member); Michael Robinson (Committee Member) Subjects: Biochemistry; Biostatistics; Chemistry