Early detection of prostate cancer is problematic due to the lack of a marker that has high diagnostic sensitivity and specificity. The prostate specific antigen test, in combination with digital rectal examination, is the gold standard for prostate cancer diagnosis. However, this modality suffers from low specificity. Therefore, specific markers for clinically relevant prostate cancer are needed. Our objective was to proteomically characterize the conditioned media from human prostate cancer cell lines to identify secreted proteins that could serve as novel prostate cancer biomarkers. An initial proof of principle study of the PC3 prostate cancer cell line was conducted. From this study over 200 proteins were identified in the conditioned media. Through gene ontology analysis and literature searches Mac-2 binding protein was selected as a candidate biomarker for validation in the serum of prostate cancer patients. A preliminarily validation showed that Mac-2 binding protein has discriminatory ability in prostate cancer diagnosis. However, an extended validation did not confirm this. Based on our proof of principle study we optimized our workflow and extended our analysis by culturing three different prostate cell lines [PC3 (bone metastasis), LNCaP (lymph node metastasis), and 22Rv1 (localized to prostate)]. We conducted a bottom-up analysis of each cell line by 2-dimensional liquid chromatography and tandem mass spectrometry. Of the 2124 proteins identified, 12% (329) were classified as extracellular and 18% (504) as membrane-bound. Among the identified proteins were known prostate cancer biomarkers such as PSA and KLK2. To select the most promising candidates for further investigation, tissue specificity, biological function, disease association based on literature searches, and comparison of protein overlap with the proteome of seminal plasma and serum were examined. Based on these results, several candidates were selected for validation in serum of patients with and without prostate cancer. Of these four novel candidates: follistatin, chemokine (C-X-C motif) ligand 16, pentraxin 3 and spondin 2 showed discriminatory ability. Of the four candidates, follistatin was further studied in an extended validation in serum of patients with biopsy confirmed prostate cancer and tissues of prostate cancer patients of low and high grade tumours by immunohistochemistry. In addition, follistatin was also investigated in the tissue of colon and lung cancer where intense staining was observed in one specimen of lung squamous carcinoma.

Background: The International Agency for Research on Cancer has classified diesel exhaust as a carcinogen, and specific polycyclic aromatic hydrocarbons (PAHs) as probable carcinogens. Urban air pollution is one source of PAH exposure. These facts provided motivation to pursue three thesis objectives: 1) to critically review environmental inequity research in Canada and methods used in previous studies; 2) to determine associations between socio-demographic factors and residential traffic exposure; and, 3) to assess correlations between two PAH biomarkers and their relationship with a newer geographic information system (GIS) method (a proxy of PAH exposure measurement), and explore determinants of these two PAH biomarkers. Methods: The first objective was achieved through an extensive and critical literature review. The second and third objectives were achieved through conducting a cross-sectional study in Montreal where 107 female and 93 male volunteers completed a questionnaire and provided a urine sample for measurement of 1-hydroxypyrene (1-OHP) and 1-hydroxypyrene glucuronide (1-OHPG). GIS-based distance-weighted traffic density (DWTD) at participants’ residences and time- and distance-weighted traffic density (TDWTD) for all participants’ locations in the 48 hours before urine collection were calculated. Results: Participants with lower household income and unemployment/student status were more likely to be exposed to higher traffic density at their residence. DWTD was related to self-reported living within 100 meters of highway/major roads. Detection rates for the two biomarkers were over 95%, and females have higher 1-OHP and 1-OHPG levels (exp β: 1.56, 95% CI: 1.17 to 2.09; exp β: 1.49, 95% CI: 1.05 to 2.11, respectively) than males. Smoking in the 48-hour period before urine collection significantly predicted levels of biomarkers, and among non-smokers barbecued/grilled meat consumption was implicated in increases in 1-OHP. Conclusions: Those with lower household income and unemployment/student status experienced increased traffic exposure, while education, marital status and ethnicity were not associated with traffic exposure. While higher levels among females and an interaction with sex needs further study, PAH biomarkers are useful in capturing recent PAH exposure from smoking, and barbecued/grilled meat consumption. PAH biomarkers can be easily used in epidemiologic studies to assess general population exposures. / Thesis (Ph.D, Community Health & Epidemiology) -- Queen's University, 2013-07-30 10:41:50.321

Epigenetics refers to the mitotically heritable modifications in gene expression without a change in the genetic code. A combination of molecular, chemical and environmental factors constituting the epigenome is involved, together with the genome, in setting up the unique functionality of each cell type. DNA methylation is the most studied epigenetic mark in mammals, where a methyl group is added to the cytosine in a cytosine-phosphate-guanine dinucleotides or a CpG site. It has been shown to have a major role in various biological phenomena such as chromosome X inactivation, regulation of gene expression, cell differentiation, genomic imprinting. Furthermore, aberrant patterns of DNA methylation have been observed in various diseases including cancer. In this thesis, we have utilized machine learning methods and developed new methods and tools to analyze DNA methylation patterns as a biomarker of ageing, cancer subtyping and mental disorders. In Paper I, we introduced a pipeline of Monte Carlo Feature Selection and rule-base modeling using ROSETTA in order to identify combinations of CpG sites that classify samples in different age intervals based on the DNA methylation levels. The combination of genes that showed up to be acting together, motivated us to develop an interactive pathway browser, named PiiL, to check the methylation status of multiple genes in a pathway. The tool enhances detecting differential patterns of DNA methylation and/or gene expression by quickly assessing large data sets. In Paper III, we developed a novel unsupervised clustering method, methylSaguaro, for analyzing various types of cancers, to detect cancer subtypes based on their DNA methylation patterns. Using this method we confirmed the previously reported findings that challenge the histological grouping of the patients, and proposed new subtypes based on DNA methylation patterns. In Paper IV, we investigated the DNA methylation patterns in a cohort of schizophrenic and healthy samples, using all the methods that were introduced and developed in the first three papers.

Luminescent semiconductor quantum dots (QDs) are extensively researched for use in biological applications. They have unique optical and physical properties that make them excellent candidates to replace conventional organic dyes for cellular labeling, multiplexing, nucleic acid detection, and as generalized probes. The primary focus of this dissertation was to utilize quantum dots for improvement in immunoassays. Specifically, atherosclerosis biomarkers were detected simultaneously in an effort to demonstrate advances in early detection diagnostics. Quantum dot-antibody bioconjugates were prepared by encapsulation into mesoporous silica and functionalized with thiol and amine groups to enable bioconjugation. Functionalization of the mesoporous silica quantum dot composites facilitated biocompatibility for use with biological buffers in immunoassays. These bioconjugates were used in a sandwich immunoassay to detect atherosclerosis biomarkers IL-15 and MCP-1. Sandwich assays employ capture antibodies immobilized onto a well plate to bind as much of the antigen as possible. The capture antibodies increased binding by at least 4 times the amount of antigen bound to the surface of a direct detection assay. The sandwich immunoassay was able to detect 1 pg/mL of IL-15 and 50 pg/mL of MCP-1 biomarkers. Human serum albumin nanoparticles (HSAPs) were synthesized via a desolvation and crosslinking method. Human serum albumin is a versatile protein being used in a variety of applications. Quantum dots were loaded into HSAPs as potential detection probes for immunoassays. Efficient loading was not achieved, and the assay was unable to improve current detection limits. Controlled release studies were explored using HSAPs loaded with superparamagnetic iron oxide nanoparticles and a fluorescent drug analog. Exposure to a magnetic field resulted in degradation of the HSAPs. The fluorophore was released and measured to examine how cancer drugs might be controlled through a magnetic field. Gold nanorods and an anticancer drug, Sorafenib, were also encapsulated into HSAPs for treatment of renal cell carcinoma in vivo. Laser irradiation treatment combined with Sorafenib resulted in 100% tumor necrosis and total elimination of any viable tumor present. HSAPs have demonstrated remarkable potential as drug delivery nanocarriers.

Many anticancer therapies, including radiotherapy, act by damaging the deoxyribosenucleic acid (DNA) that is fundamental to cell function and proliferation. H2AX is a histone protein associated with DNA that is phosphorylated to produce γH2AX in response to DNA double strand breaks (DSBs), the most lethal lesions caused in cancer cells. This thesis examines the translation of γH2AX detection assays to clinical situations in order to provide biomarkers of response that might help to guide the treatment of cancer patients. γH2AX immunohistochemistry was developed in preclinical xenograft models, and validated over a range of radiation doses and over time after irradiation. The method was prepared for translation to archived clinical biopsy and surgical specimens. The DSB Biomarkers Pilot Study was established in order to develop a method for γH2AX quantification in direct tumour cell specimens obtained using the clinical technique of fine needle aspiration (FNA) cytology. Eleven patients undergoing anticancer therapy were recruited to the study, and the method evaluated. The coefficient of variation of the measure was 49%. Non-invasive imaging for γH2AX would allow DNA damage to be quantified in all tumour sites, and on multiple occasions. An antibody-based nuclear medicine imaging agent was re-engineered using Fab fragments of the antibody. The novel agent demonstrated improved pharmacokinetics when compared to the whole antibody agent, but reduced target specificity. The findings further develop the potential to exploit DNA damage biomarker measurements in clinical oncology.

Each year in the U.S., approximately 7-8 million patients with non-traumatic chest pain visit hospital emergency departments (ED) for medical evaluation. It is estimated that approximately 2-5% of these patients are experiencing acute cardiac ischemia, but due to the shortcomings of current test methods, they are incorrectly diagnosed and discharged without appropriate treatment provided, thus leading to poor patient outcome and potential medical malpractice litigation.The goals of this research were to evaluate plasma samples for potential biomarker(s) of acute cardiac ischemia prior to heart tissue necrosis, and to ultimately develop a rapid method for detection of the potential biomarker(s) in human plasma. Initial experiments were performed using the mouse model, with subsequent evaluations on human plasma samples using high performance liquid chromatographic ultraviolet detection (HPLC-UV). The final phase of this research involved the development of a rapid luminometer test method (An HPLC-UV detection method was developed and utilized for inosine, hypoxanthine and other adenosine triphosphate (ATP) catabolic by-products in Krebs-Henseleit (Krebs) buffer solution, with analysis on perfusate samples from isolated mouse hearts undergoing 20 min acute global ischemia. The HPLC-UV method was modified for subsequent use on human plasma samples, obtained from hospital emergency department (ED) patients presenting with non-traumatic chest pain (potential acute cardiac ischemia) and from healthy normal individuals. The HPLC-UV (component quantification) and HPLC-MS (component identification) test methods utilized C18 column technology, mobile phases consisting of aqueous trifluoroacetic acid (0.05% TFA in deionized water pH 2.2, v/v) and methanol gradient to achieve component separation, with both utilizing simple sample preparations (e.g. direct injection of Krebs perfusate samples and centrifugal membrane filtration on plasma samples).Results of the animal experiments using isolated mouse hearts undergoing 20 min acute global ischemia demonstrated significant levels of endogenous inosine effluxed from the heart tissue, indicating its use as a potential candidate biomarker of acute cardiac ischemia. The HPLC results from human plasma representing ED non-traumatic chest pain patients demonstrated elevated levels of inosine (hypoxanthine precursor) and significant levels of hypoxanthine, which provided additional support for the use of these candidate biomarker(s) as a potential diagnostic tool for the initial acute cardiac ischemic event, prior to heart tissue necrosis.The final phase of this research focused on the development of a rapid, simple and sensitive chemiluminescence test method. Using a microplate luminometer with direct injectors and continuous mixing, the measurement of inosine and hypoxanthine in human plasma was achieved for healthy normal individuals and on patients with confirmed acute MI, with an analysis time of less than 5 minutes. The utility of this rapid luminescence technique would be the potential use at point-of-care (POC) services (e.g. hospital clinical laboratory or emergency medical services) as part of the initial ED treatment protocol on patients presenting with non-traumatic chest pain and signs/symptoms of acute myocardial ischemia or acute MI.

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La variabilité du rythme cardiaque « Heart Rate Variability (HRV) » consiste en des fluctuations perpétuelles du rythme cardiaque autour de sa fréquence moyenne. L’analyse de l’HRV constitue un biomarqueur du fonctionnement du système nerveux autonome (SNA), par l’intermédiaire de ses effets sur le cœur. De nombreuses études ont montré qu’une diminution de l’HRV est associée à un pronostic péjoratif, notamment dans le post infarctus et dans l’insuffisance cardiaque (IC). Nous nous sommes proposés d’élargir le champ d’investigation de l’HRV à de nouveaux domaines d’application, qu'il s'agisse de pathologies cardiaque ou extra cardiaque. Nous avons ciblé des contextes pathologiques dans lesquels le SNA joue un rôle important : 1-Accidents sur la Voie Publique (AVP) et le risque de développement d’un syndrome de stress post traumatique (PTSD). 2-Effet de la douleur et de l’analgésie péridurale sur l’HRV maternelle au cours de l’accouchement. 3-Lien avec les polymorphismes génétique des récepteurs bêta adrénergiques (β;-AR) chez des patients présentant une dysfonction ventriculaire gauche et implanté d’un défibrillateur automatique implantable (DAI) en prévention secondaire. L'analyse temporelle de l'HRV sur 24 heures est un facteur prédictif de survenue d'un PTSD et aussi de sa sévérité chez les victimes d'AVP. L'indice de variabilité est le meilleur paramètre prédictif de PTSD à 6 mois, avec une aire sous la courbe de 0.92 (IC 95% : 0.785; 1.046). Le seuil de 2.19% confère une sensibilité de 85,7 £ et une spécificité e 81.8 % pour prédire la survenue d'un PTSD. les valeurs prédictives positives et négatives sont de 75 % et 90 % respectivement. L'ANI, reflétant l'influence de la ventilation sur le rythme cardiaque, permet une mesure objective de la douleur chez les parturientes. Enfin, les patients ayant subi les substitutions Arg (pour Gly) en 16 et Gln (pour Glu) en 27 pour les récepteurs β2-AR, présentent une HRV plus faible que les patients ayant la forme sauvage du gène. / The heart rate variability (HRV) has arisen as a promising simple and non invasive biomarker of autonomic nervous system (ANS) function, through its effects on the heart. Multiple studies have shown that the decrease in the HRV is associated usually with poor prognosis. We proposed to further investigate the HRV in other domains of clinical application, including cardiac or extra-cardiac pathologies. In particular, the pathological contexts in which the ANS plays an important role :1-Traffic road accident (RTA) and the risk of development of post traumatic stress disorders (PTSD) in survivors.2-Effect of pain and of epidural analgesia on maternal HRV during childbirth.3-Genetic polymorphisms of beta adrenergic receptors (β-AR) in patients with left ventricular dysfunction and implanted with an implantable cardioverter defibrillator (ICD) for secondary prevention. At first, our study is the first to show that the temporal analysis of 24-h HRV is not only a predictive factor of the occurrence of PTSD but also its severity among victims of RTA AVP. The variability index was the best predictor of PTSD with the area under the receiver-operating curve for discriminating PTSD at 6 month at 0.92 (95% CI:0.785;1.046). Acut-off at 2.19% yielded a sensitivity of 85.7% and a specificity of 81.8% for PTSD. Positive and negative predictive values were respectively 75% and 90%. At next, we showed that the ANI, which reflects the influence of ventilation on heart rate, allows an objective measure of pain in conscious subjects? At last, we found that patients with the substitutions Arg (instead of Gly) at position 16 and Gln (instead of Glu) at position 27 for β2-AR have a lower HRV value than patients with wild type receptor.

Ovarian carcinoma is a serious illness with the highest mortality rate among all female cancers. No suitable methods for early diagnosis, precise determination of prognosis or prediction of therapy efficacy are currently available, which leads to diagnosis in advanced stages of disease and therapy efficacy limitation. Consequently, the development of chemoresistance to conventional drugs and frequent relapse of the disease pose a fundamental complication too. The main goal of the current study was identification of new putative prognostic and therapeutic biomarkers, whose introduction into clinical practice could help to improve the dismal outcome of ovarian carcinoma patients. The present master thesis provides results of expression analysis of genes whose products take part in the transport, metabolism and mechanism of action of platinum based drugs and taxanes, and also the regulation of cell cycle and signaling. Transcript levels of these genes have been assessed in series of tumor and control ovarian tissue samples and the difference between both tissue types was evaluated. Gene expression level in tumors was then compared with patient's clinical data and candidate genes, ABCA2 and PRC1, were selected from the obtained results for more detailed analysis. The protein level of candidate genes...

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