Dissertation (Ph.D.)--University of Toledo, 2010. / "Submitted to the Graduate Faculty as partial fulfillment of the requirement for the Doctoral of Philosophy Degree in Biomedical Sciences." Title from title page of PDF document. "A Dissertation entitled"--at head of title. Bibliography: p. 80-98.

Thesis (M.S.)--University of Michigan, 2002. / Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (p. 105-112).

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 163-183).

Abstract Prostate cancer is the most common solid tumor among men in Western industrialized countries. A major problem in prostate cancer treatment is the development of androgen-independence, as androgen-deprivation therapy is the basic therapy for the disease. Molecular mechanisms behind prostate cancer and androgen-independent growth development are poorly known. In this study, subtractive hybridization was used for the generation of a cDNA library specific for prostate cancer. Analysis of the cDNA library revealed over-expression of several ribosomal proteins namely L4, L5, L7a, L23a, L30, L37, S14 and S18, in prostate cancer cell lines. Over-expression of L7a and L37 was also confirmed in prostate cancer tissue samples. Further, cDNA array was used in order to examine differentially expressed genes in androgen-dependent and androgen-independent prostate cancer cell line LNCaP. Monoamine oxidase A, an Expressed Sequence Tag (EST) similar to rat P044, and EST AA412049 were highly over-expressed in androgen-dependent LNCaP cells. Tissue-type plasminogen activator, interferon-inducible protein p78 (MxB), an EST similar to galectin-1, follistatin, fatty acid-binding protein 5, EST AA609749, annexin I, the interferon-inducible gene 1-8U and phospholipase D1 were highly over-expressed in androgen-independent LNCaP cells. The EST similar to rat P044, the EST similar to galectin-1, follistatin, annexin I and the interferon-inducible gene 1-8U were also expressed in benign prostatic hyperplasia tissue. The Y-linked ribosomal protein S4, Mat-8, and EST AA307912 were highly expressed in benign prostatic hyperplasia tissue. In situ hybridization of mouse embryos and adult mouse tissues revealed the expression of TMPRSS2 in the epithelium throughout the gastrointestinal, urogenital and respiratory tracts during development. In human multiple tissue RNA dot blot, the highest level of expression was detected in prostate, and lower levels in colon, stomach and salivary gland. TMPRSS2 transcript levels were significantly higher in prostate cancer tissue between benign and malignant epithelium of prostate cancer patients with untreated disease. Similarly, in poorly differentiated adenocarcinomas, expression in malignant tissue was significantly higher. Enzymatic mutation detection and direct sequencing of TMPRSS2 coding region revealed only one deletion in aggressive disease among 9 non-aggressive and 9 aggressive prostate cancer samples. No other mutations were found. Detected 7-base pair deletion leads to premature stop codon and disruption of serine protease substrate binding and catalytic active site. We cloned several potential genes whose expression is changed during prostate cancer initiation or progression. These genes may serve as prostate cancer markers, and further studies are needed to clarify the expression of these proteins during the disease.

Abstract Dentin forms the hard tissue portion of the dentin-pulp complex, while the dental pulp is soft connective tissue that retains the vitality of the dentin. Odontoblasts form the outermost cell layer of pulp and play a central role during dentin formation by producing and mineralizing the dentin matrix. The understanding of the defensive reactions in the dentin-pulp complex is limited. Information about the transcriptome and proteome of pulp tissue and odontoblasts would facilitate understanding of their functions during health and disease. The aim of this study was to investigate the expression profiles of human pulp tissue and odontoblasts in vivo and in vitro using large-scale expression analysis methods. Also, the suitability of these methods in pulp biological research in vivo and in vitro was evaluated. cDNA microarray revealed only minor variation and 2-D electrophoresis combined with mass spectrometry revealed no differences between healthy and carious teeth pulp tissue in vivo. The effect of transforming growth factor β1 (TGF-β1) on pulp and odontoblasts was studied in vitro using oligonucleotide-based microarrays, and marked changes in the transcriptome were revealed, especially in the expression of chemokine- and cytokine-related genes. Transiently increased interleukin expression was confirmed at the protein level by antibody array. DNA microarray analysis of native pulp tissue and odontoblasts was used to search for potential odontoblast markers. Only one gene related to extracellular matrix organization and biogenesis, matrilin 4, and two expressed sequence tags (ESTs), which represent transcribed sequences encoding possibly unknown genes, were identified in odontoblasts but not in pulp. Analysis of mature native odontoblasts and cultured odontoblast-like cells by DNA microarray revealed a high similarity (84%) between native and cultured cells. Also, differential expression levels of selected neuronal proteins were observed and confirmed at the mRNA and protein levels. In conclusion, microarray is a powerful tool for pulp biology, especially for in vitro studies. TGF-β1 was revealed as a potent regulator of proinflammatory responses in the dentin–pulp complex. In addition, several potential odontoblast markers were identified by microarray, and the similarity of cultured odontoblast-like cells used in the study with native odontoblasts was confirmed.

Stroke is an acute neurological deficit that results from abnormal blood flow to the brain. The term stroke encompasses two primary subgroups: hemorrhagic stroke that is due to extravasation of blood and ischemic stroke that is due to vessel obstruction. Determining stroke type and underlying etiology is a crucial step in patient management as it influences treatment strategies. Currently diagnosis of stroke relies on clinical examination and neuroimaging, but there is a lack of rapid diagnostic and prognostic testing. Using microarray technology we identified a novel association between elevated peripheral blood expression of MCEMP1 and stroke. We have also shown that MCEMP1 discriminates between primary stroke types and predicts one-month post-stroke prognosis. Since genetic mechanisms underlying stroke remain incompletely understood we next conducted a global gene network analysis. Network analysis identified four large groups of co-expressed genes associated with ischemic stroke. NLRC4, CKLF, and HS.546375 were the most interconnected genes within unique modules and each was also independently associated with ischemic stroke. We show that multi-gene models have greater discriminative capacity for stroke and stroke prognosis, than single gene models. In addition to stroke biomarkers we also identified biomarkers of atrial fibrillation (AF), a known risk factor of stroke. Currently our understanding of the molecular mechanisms underlying AF remains incompletely understood. Thus we conducted whole blood expression profiling in patients with persistent AF before and after successful electrical cardioversion, a procedure that aims to restore sinus rhythm to the heart. We identified elevated expression of SLC25A20 and PDK4 during AF as compared with sinus rhythm. Furthermore we show that SLC25A20, PDK4 and NT-proBNP have incremental utility to discriminate AF from sinus rhythm. Taken together, the thesis implicates new genes with stroke and AF, and also indicates that whole blood RNA biomarkers may have clinical utility. / Thesis / Doctor of Philosophy (PhD)

No description available.

Obstructive sleep apnea syndrome (OSAS) is a complex disorder characterized by repetitive bouts of upper airway collapse during sleep, causing subsequent intermittent hypoxia, hypercapnia, and fragmented sleep and is also associated with significant morbidity including daytime sleepiness, hypertension, and elevated cardiovascular risk. OSAS affects at least 4% of men and 2% of women; unfortunately, it is estimated that 80% to 90% of adults with OSAS remain undiagnosed. Both clinical characteristics and complex genetic and environmental interactions have made it difficult to understand OSAS disease etiology and identifying patients at risk is still elusive. A pattern of gene expression in cells or tissues related to a disease state for OSAS would provide beneficial information to be most effective in screening or diagnosing this disease. Objectives: The objectives of this study were to: 1) map out the study design and bench assay strategies by which to investigate this issue; 2) find out if there are specific differences in the global gene expression profiles of adult females with OSAS compared to those without OSAS, under conditions in which subjects were clinically similar (BMI, diabetes, cardiovascular disease, etc.); and 3) assess the protein expression differences that could potentially be linked via well-established molecular pathways associated with any differences found in global gene expression profiles in the presence and absence of OSAS. Methods: Subjects were overweight premenopausal Caucasian women with untreated OSAS (n=6; age = 40.7 ± 3.4; BMI = 49.04 ± 6.97; apnea-hypopnea index = 27.3 ± 16.02), and control subjects (n=10) (age = 38.2 ± 7.6; BMI = 47.94 ± 6.15; apnea-hypopnea index < 5), and matched for other clinical characteristics (diabetes, cardiovascular disease status, medications, etc.) recruited from either Carilion Clinic Pulmonary/Sleep Medicine or Carilion Clinic Bariatric Surgery practices. Subjects provided a fasting blood sample in which the monocytes were isolated from whole blood. The RNA was extracted from the monocytes, assessed for purity and quantity, frozen and shipped to collaborators at Dana-Farber Cancer Institute and hybridized to Affymetrix whole human genome chips on a gene chip. The initial computational evaluation and interpretation generated the hypothesis. Two-step quantitative real time polymerase chain reaction (qPCR) was performed to verify the results from the microarray analysis. The laminin enzyme immunoassay (EIA), and cellular adhesion assays were performed to determine if genomic changes resulted in proteomic and phenotypic assessments. Results: OSAS subjects had nine aberrantly regulated genes, of which three genes (LAMC-1, CDC42, and TACSTD2) showed a pattern in segregation between OSAS and controls subjects based on expression patterns. In addition, qPCR indicated a 2.1 fold increase in LAMC-1 and a 1.1 fold increase CDC42 expression unique to the tissue samples of patients with OSAS. Though the serum laminin EIA did not differ between groups, a statistically significant increase in peripheral blood mononuclear cells (PBMC) cellular adhesion in OSAS patients versus control subjects was found. The OSAS subjects had a well cell count of 9.27 ± 1.54 cells vs. controls 5.75 ± 0.78 cells (p Ë‚ 0.05), which is relative to the 103 cells/field that were plated. Conclusions: Cells isolated from women with moderate-severe OSAS show an abnormality in cellular adhesion, a process driven in part by the gene LAMC-1, which was also aberrantly expressed in these subjects. This suggests that inflammation may be linked to the pathogenesis of OSAS. This pilot study has provided the framework and preliminary data needed to propose a larger study with extramural research funding. / Ph. D.

Hepatitis C Virus (HCV) infects 170 million people worldwide. The current treatment regimen, which is combination therapy with pegylated interferon (PegIFN) and Ribavirin (Rib), cures only 50% of the patients infected with the most prevalent HCV genotype. Therefore, there is a pressing need to understand the molecular mechanism of interferon resistance and to develop a prognostic tool to predict who will respond to treatment before initiation of therapy. It has been firmly established that the virus-host interaction plays an important role in determining treatment outcomes. My thesis investigated the host factors that are involved in interferon resistance with an aim to provide insights into the molecular mechanism of IFN resistance. cDNA microarray analysis identified 18 differentially expressed hepatic genes from pretreatment liver tissues of responders (Rs) and non-responders (NRs). Based on the differential expression levels of these 18 genes, a prognostic tool was developed to predict who will respond to therapy, with a positive predicting value (PPV) of 96%. Most of these 18 genes are interferon stimulated genes (ISGs) and they are more highly expressed in NR livers, indicating that preactivation of interferon signaling in the pre-treatment liver tissues contributes to NR. 3 out of the 18 genes are involved in an ubiquitin-like ISG15/USP18 signaling pathway that plays an important role in interferon response. Over-expression of USP18 and ISG15 in the pretreatment liver tissues of NR promotes HCV production and blunts interferon anti-HCV activity. There exists a distinct cell-type specific ISG activation in the pretreatment liver tissues of Rs and NRs. Up-regulation of the two ISGs that I tested (ISG15 and MxA) was found mainly in hepatocytes in NRs while ISG activation was preferentially observed in macrophages in Rs. Taking all these data together, pre-activation of interferon signaling and cell-type specific gene activation in the pretreatment liver tissues of patients infected with HCV are associated with treatment non-response. HCV exploits the host interferon system to favour its persistence by enhanced replication /secretion stimulated by a few ISGs (ISG15, USP18) in response to IFN. The developed prognostic tool can be used to stratify patients for treatment and the novel insights of the molecular mechanism of IFN resistance in HCV patients offer potential drug targets for future development.