Thesis (M. Med. Sc.)--University of Hong Kong, 2005.

<p> Cancer is a leading cause of morbidity and mortality, and one in three individuals in the U.S. will be diagnosed with cancer in their lifetime. At the molecular level, cancer is driven by the activity of oncogenes and the loss of activity of tumor suppressors. The availability of genomic data from large sets of tumor tissue have facilitated the identification of subgroups of patients whose tumors share molecular patterns of expression. These molecular signatures, in turn, can help identify clinically-useful patient subgroups and inform potential therapeutic strategies against cancer.</p><p> In chapter 1, I review the current theories behind carcinogenesis, the molecular factors that regulate gene expression, and statistical methods for analyzing genomic data. In chapter 2, I describe an approach, termed oncomix, developed to identify oncogene candidates from expression data obtained from tumor and adjacent normal tissue. I apply oncomix to breast cancer expression data and identify an oncogene candidate, <i>CBX2</i>, whose expression is gained in a subset of breast tumors. <i>CBX2</i> is expressed at low levels in most normal adult tissue, and the CBX2 protein contains a drug-targetable chromodomain, both of which are desirable properties in a potential therapeutic target. We then provide the first experimental evidence that <i>CBX2</i> regulates the growth of breast cancer cells. In chapter 3, I develop a method for identifying nuclear hormone receptors whose expression is lost in endometrial cancers relative to normal tissue. I report, for the first time, that the loss of expression of Thyroid Hormone Receptor Beta (<i>THRB</i>) is associated with better 5-year survival in endometrial cancer. The loss of <i>THRB</i> expression is independent of the loss of estrogen and progesterone receptor expression, two genes whose loss of expression is known to be associated with poor survival. <i> THRB</i> expression could be considered as a biomarker to risk-stratify endometrial cancer patients. In Chapter 4, I develop a user-friendly application for visualizing chromosomal copy number state obtained from three types of copy number input in single cells &ndash; fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), and whole genome sequencing (WGS). This web application, termed aneuvis, automatically creates novel visualizations and summary statistics from a set of user-uploaded files that contain chromosomal copy number information.</p><p> In this thesis, I develop new computational approaches for identifying candidate molecular regulators of cancer. I also develop a new user-friendly tool to enable biological researchers to identify aneuploidy and chromosomal instability within populations of single cells. Applying these tools to breast and endometrial cancer genomic datasets has highlighted novel aspects of breast and endometrial cancer biology and may inform novel therapeutic strategies based on molecular patterns of genomic heterogeneity. The freely available software developed as part of these projects has the potential to enable other researchers to advance our understanding of cancer genomics and to inform novel therapeutic strategies against cancer.</p><p>

<p> Prostate cancer is among the most prevalent and deadly of malignancies in both the United States and worldwide. Ongoing diagnostic challenges in prostate cancer include differentiating low-risk and high-risk tumors, and monitoring responses to therapy in patients with aggressive disease. Prostate cancer metabolism is characterized by a shift to aerobic glycolysis with lactate production and efflux, as well as increased tricarboxylic acid cycle activity, which has led to the investigation and development of metabolic imaging strategies such as hyperpolarized 13C MRI. However, it is nontrivial to study human prostate cancer metabolism in vivo, and the capability to better characterize tumor metabolism from a variety of disease states would be valuable for metabolic imaging biomarker development. This dissertation focuses on developing ex vivo strategies to measure metabolism in benign and malignant living human prostate tissue. First, because prostate tissue heterogeneity can impact metabolic measurements, we present the engineering of a 600 MHz radiofrequency (RF) microcoil to assess the heterogeneity of freshly acquired human prostate biopsies using microscale diffusion-weighted imaging (DWI). Next, we demonstrate the capability of micro-DWI to determine the biopsy percentage of glandular tissue, setting the stage for establishing the percentage and grade of cancer using this approach. After this, we develop a protocol for nuclear magnetic resonance (NMR) quantification of lactate production and efflux and glutamate fractional enrichment in freshly acquired living human prostate biopsies cultured with [1,6-13C2]glucose. In this study we demonstrate a significantly higher lactate efflux rate coming from low-grade prostate cancer versus benign biopsies in an early-stage patient population. This sets the stage for studies of metabolic fluxes and steady-state metabolite levels in biopsies from patients with aggressive disease before and after non-surgical therapy. Finally, due to recent interest in the potential role of Myc amplification and glutaminolysis upregulation in treatment insensitive castrate-resistant prostate cancer (CRPC) and neuroendocrine prostate cancer (NEPC), we present metabolic labeling results from a study of primary human prostate tissue slice cultures (TSCs) obtained at surgery and cultured with either [1,6-13C2]glucose or [3-13C]glutamine. Our results are consistent with prior thinking on the role of glucose and glutamine metabolism in treatment-na&iuml;ve prostate cancer.</p><p>

Thesis (Ph.D)--Boston University / The purpose of the research was to investigate the action of prostatic acid phosphatase on a spectrum of physiologically significant phosphate esters under varying environmental conditions. The effects of varying pH, substrate concentration, and enzyme concentration, the influence of inhibitors, and the influence of time on enzymatic hydrolysis were studied with each substrate. The enzymes extracted from both normal and cancerous prostatic tissue were used in an attempt to discover any differences existing between enzymes. A survey of the literature was made. A historical review of the history of acid phosphatase, its distribution in animal tissues and the influence of experimental conditions on enzyme activity is included in the body of the dissertation. Little work has been done to investigate the action of acid phosphatases on physiologically significant substrates, and the comparison of normal and cancerous enzyme preparations from human tissues has attracted the attention of only several investigators. [TRUNCATED]

BACKGROUND: The aging population in the United States will correlate with an increased number of cancer diagnoses as cancer is primarily a disease of the elderly. Providing this ever-growing group of individuals with quality surgical management, while taking into account the unique needs and desires of this cohort, is a great challenge facing both geriatricians and surgeons going forward. The best approach to ensure that oncogeriatric patients receive the best tailored treatment is through the completion of a pre-surgical geriatric assessment. However, only a minority of oncogeriatric patients is undergoing a comprehensive pre-surgical geriatric assessment despite the majority of geriatricians and surgeons acknowledging its importance in order to properly risk stratify their patients. LITERATURE REVIEW FINDINGS: Multiple theories exist as to why geriatric assessments are not being utilized more frequently, but the most probable answer is that these assessments are very time-consuming, making it virtually impossible for incorporation into a healthcare provider’s busy schedule. Comprehensive literature review regarding geriatric assessments amongst the oncogeriatric population found that the most sensitive and specific domains of the geriatric assessments predicting morbidity and mortality include Frailty Index, Social Support Survey, Mini-Nutritional Assessment, and Geriatric Depression Screening. PROPOSED METHODS: A novel educational intervention will be proposed to teach Physician Assistant and Medical Students about the domains of the geriatric assessment most predictive of post-surgical risk during their surgical clerkship. The curriculum will utilize both simulation- and competency-based education training under the guidance of geriatricians and surgeons. Students will first learn the necessary skills in a controlled classroom environment and then proceed to incorporate these skills during their clerkship with patients on their service. CONCLUSIONS: The goal of the proposed method is to instill the confidence and skills necessary to provide an accurate geriatric assessment for oncogeriatric patients in future clinicians. The field of geriatric oncology is going to grow exponentially in the up-coming years and familiarizing future clinicians with the most predictive domains regarding surgical outcome will improve treatment outcomes for oncogeriatric patients in the immediate and foreseeable future.

Thesis (B.A.)--Boston University. University Professors Program Senior theses. / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / 2031-01-01

<p> Glioblastoma (GBM) is a hypervascular and hypoxic neoplasia of the central nervous system with an extremely high rate of mortality. Owing to its hypervascularity, anti-angiogenic therapies (AAT) have been used as an adjuvant to the traditional surgical resection, chemotherapy, and radiation to normalize blood vessels, control abnormal vasculatures and prevent recurrence. The benefits of AAT have been transient and the tumors were shown to relapse faster and demonstrated particularly high rates of AAT-induced therapy resistance due to activation of alternative neovascularization mechanisms. Vascular Mimicry (VM) is the uncanny ability of tumor cells to acquire endothelial-like properties, lay down vascular patterned networks reminiscent of host endothelial blood vessels and served as an irrigation system for the tumors to meet with the increasing metabolic and nutrient demands in the event of the ensuing hypoxia resulting from AAT. In our studies, we have demonstrated that AAT accelerates VM. We observed that Vatalanib (a VEGFR2 tyrosine kinase inhibitor) induced VM vessels are positive for periodic acid-Schiff (PAS) matrix but devoid of any endothelium on the inner side and lined by tumor cells on the outer side. Interestingly, 20-HETE synthesis inhibitor HET0016 significantly decreased GBM tumors through decreasing VM structures both at the core and at the periphery of the tumors. During our extensive studies to understand the tumor-inherent mechanisms of AAT-induced resistance, we identified a crucial chemokine, CXCL8 or IL-8, to be highly upregulated in the GBM tumors treated with AAT. IL-8 has been well established as a highly prevalent cytokine in GBM with potent pro-migratory and pro-angiogenic functions. AAT-treated groups had significantly higher populations of CXCR2+ glioma stem cells and endothelial-like subpopulations and these populations were decreased following treatment with HET0016 and SB225002 (a CXCR2 antagonist). CXCR2+ GBM tumor cells were shown to form VM-like vascular channels carrying functional RBCs. Knocking down CXCR2 led to smaller tumor size in the animals and improperly developed vascular structures without CXCR2+ GBM cells lining them. This confirms our hypothesis that CXCR2+ GBM cells initiate VM and contribute to AAT resistance in GBM. Our present study suggests that HET0016 and SB225002 have potential to target therapeutic resistance and can be combined with other antitumor agents in preclinical and clinical trials.</p><p>

<p> Advances in next-generation sequencing and algorithm design have revealed the evolutionarily conserved expression of large numbers of circular RNAs (circRNAs) that are endogenous to eukaryotic cells, many being abundant and in some cases the exclusive output of a given gene. CircRNAs are produced when the pre-mRNA splicing machinery &ldquo;backsplices&rdquo; to join a 3&rsquo; downstream splice donor to a 5&rsquo; upstream splice acceptor. Their circular nature gives them superior resistance to exonucleases and extended half-lives when compared to linear RNAs. CircRNAs are produced in a regulated manner to carry out specific cellular functions, as supported by the identification of alternative splicing factors required for circularization. A generalized biological function for circRNAs has not been unequivocally identified. Aberrantly expressed circRNAs may contribute to tumorigenesis, maintenance or progression of cancer cells. In particular, altered circRNA can contribute to important aspects of melanoma biology, and even harbor prognostic and/or therapeutic value. This work is the first comprehensive, unbiased identification and characterization of circRNAs in melanoma, focusing particularly on circARID1A, a gained circRNA when comparing melanoma to non-transformed melanocytes. Silencing of either linear (protein coding) or circular ARID1A in melanoma cells results in impaired proliferation and distinct transcriptional outputs. SERBP1 was identified as an interacting partner of circARID1A, and as a potential mediator of its function. These studies shed light on the roles of circRNAs in cancer and their mechanisms of action, setting the path for future work on these RNA species in other malignancies.</p><p>

<p> Blood supply is crucial for tumor growth and metastasis. However, current anti-angiogenic therapy is not as effective as predicted, thus a better understanding of the tumor angiogenic process and new anti-angiogenic agent are urgently required. Anthrax lethal toxin (LeTx) has an anti-angiogenic effect on tumors. Tumors treated with LeTx are smaller, paler, and have lower mean vessel density compared to control treated tumors. Most interestingly, compared to current anti-angiogenic treatment, LeTx does not cause normalization of tumor vessels. Instead, tumors treated with LeTx have massive hemorrhages, pointing to a potential alternative mechanism to inhibit tumor angiogenesis. I hypothesize that instead of causing &ldquo;normalization&rdquo; of tumor vasculature, LeTx&rsquo;s anti-angiogenic effects works in a manner similar to a hemorrhagic toxins. To test this hypothesis, I compared the effect of LeTx to snake venom metalloproteinase, a known hemorrhagic toxin, in tumor vasculature. Quantified by Nuance multispectral imaging system, both LeTx and SVMP caused an increase in tumor hemorrhage. Futher analysis of vasculature integrity using continued vessel length showed disruption of vessels by LeTx and SVMP. With these results, I conclude that the anti-angiogenic effects of LeTx are due to its hemorrhagic nature, and not due to normalization of tumor vasculature. Further understanding of LeTx mechanism can help design novel anti-angiogenic agent that compliments current therapy.</p><p>

<p> With researchers showing greater interest in the relationship between longitudinal and survival outcomes, joint models are being used with greater frequency. Joint models of longitudinal and time to event outcomes offer distinct advantages. First, joint models can reduce bias in estimates of the relationship between surrogate markers and survival endpoints. Second, this class of model can provide sensitivity analysis of longitudinal estimates in the presence of potential missing data when the longitudinal outcome and survival outcome are related. The aim of this paper is to demonstrate the usefulness of this methodology when dealing with potentially related outcomes. Using a data set from a clinical trial aimed at reducing fatigue with physical activity amongst non-resectable lung cancer patients, several joint models and conventional models such as a linear mixed model and Cox proportional hazards model were generated. Both the longitudinal and survival estimates from these models were compared to demonstrate the utility of joint models. Furthermore, the implementation of joint models is discussed as a result of the analysis. </p><p>