IP25 is a highly branched isoprenoid alkene derived from certain Arctic sea ice diatoms that, when detected in marine sediments, has been used as a proxy for past Arctic sea ice over the last decade. In the current study, the structure of this biomarker was determined following large-scale extraction from sediment material collected from the Canadian Arctic. After purification, the structure of IP25 was confirmed by NMR spectroscopy as being the same as that of a laboratory standard. The purified IP25 was subsequently used to obtain a quantitative (GC-MS) instrumental response factor that could be used to improve the future quantification of IP25 and would help to produce a robust database. IP25, other highly branched isoprenoid (HBI) lipids and some other phytoplanktonic lipids (sterols) were analysed to provide modern and past sediment-based sea ice reconstructions for the Barents Sea. First, a surface sediment study was conducted and biomarker distributions were compared to satellite sea ice records. The occurrence of IP25 was consistent with the presence/absence of seasonal sea ice but there was also evidence of lateral transport of IP25 and other biomarkers in sediments from the southern Barents Sea. In contrast to some previous studies, abundances of IP25, and of those combined with other biomarkers, including sterols, did not show strong quantitative relationships to sea ice concentration. The surface study was used to relate biomarker distributions to recent sea ice and oceanographic conditions and apply this information to long-term sediment records in the eastern and western Barents Sea covering ca. 2 kyr and 11 kyr (Holocene) respectively. IP25 concentrations for the former were found to be very variable and were used to identify the period with maximum sea ice cover occurring from ca. 900 - 400 cal. yr BP where the highest abundances of IP25 and IRD were observed. Similarly, biomarker results from the eastern Barents Sea provided evidence for a dynamic advance of the marginal sea ice zone potentially situated at ca. 78° N (maximum extent) during ca 9.4 – 5.9 cal. kyr BP, to late Holocene and modern day maximum MIZ advance ca. 75° N. Replicate analysis of various biomarkers in individual push-cores collected from a box core obtained from Rijpfjorden (north Svalbard) demonstrated some variability between cores. Variability in individual biomarker concentrations was lowest for HBI lipids and greatest for sterols. These data are consistent with a selective and relatively minor source of the former. In contrast, the somewhat more generic origins of sedimentary sterols likely explain the greater variability in their distributions between cores Finally, the strong abundance relationship between IP25 and a structurally related di-unsaturated HBI (C25:2) was confirmed in all sediments, similar to that found between two tri-unsaturated HBIs, consistent with co-production by certain marine phytoplankton. The progressive use of novel HBIs with two or three degrees of unsaturation (e.g. C25:2 and C25:3) could provide further valuable insights into environmental conditions.

Wilms’ tumor gene 1 (WT1) is a zinc finger transcriptional regulator with crucial functions in embryonic development. Originally WT1 was described as a tumor suppressor gene, but later studies have shown oncogenic properties of WT1 in a variety of tumors. Because of its dual functions in tumorigenesis, WT1 has been described as a chameleon gene. In this thesis, the significance of WT1 as a biomarker was investigated in acute myeloid leukemia (AML), clear cell renal cell carcinoma (ccRCC), ovarian carcinoma (OC) and childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Previous studies have suggested that expression of WT1 is a potential marker for detection of minimal residual disease (MRD) in AML. We aimed to define expression of WT1 as an MRD marker in AML. In adult AML patients, we found that a reduction of WT1 expression in bone marrow (≥ 1-log) detected less than 1 month after diagnosis was associated with an improved overall survival (OS) and freedom from relapse (FFR). In peripheral blood, a reduction of WT1 expression (≥ 2-log) detected between 1 and 6 months after treatment initiation was associated with an improved OS and FFR. WT1 harbor pathogenic genetic variants in a considerable proportion of AML and T-lymphoblastic leukemia (T-ALL), but mutations have not been reported in BCP-ALL. We aimed to evaluate the clinical impact of WT1 mutations and single nucleotide polymorphisms (SNPs) in BCP-ALL. Pathogenic mutations in the WT1 gene were rarely seen in childhood BCP-ALL. However, five WT1 SNPs were identified. In survival analyses, WT1 SNP rs1799925 was found to be associated with worse OS, indicating that WT1 SNP rs1799925 may be a useful marker for clinical outcome in childhood BCP-ALL. We also explored whether WT1 mutations and SNPs in ccRCC could be used as biomarkers for risk and treatment stratification. We therefore examined whether SNPs or mutations in WT1 were associated with WT1 expression and clinical outcome. Sequencing analysis revealed that none of the previously reported WT1 mutations were found in ccRCC; however, we identified six different WT1 SNPs. Our data suggest that pathogenic WT1 mutations are not involved in ccRCC, and the prognostic significance of WT1 SNPs in ccRCC is considerably weak. However, a favorable OS and disease-specific survival were found in the few cases harboring the homozygous minor allele. OC has a poor prognosis, and early effective screening markers are lacking. Serous OCs are known to express the WT1 protein. Overexpressed oncogenic proteins can be considered potential candidate antigens for cancer vaccines and T-cell therapy. It was therefore of great interest to investigate whether anti-WT1 IgG antibody (Ab) measurements in plasma could serve as biomarkers of anti-OC response. We found limited prognostic impact, but the results indicated that anti-WT1 IgG Ab measurements in plasma and WT1 staining in tissue specimens could be potential biomarkers for patient outcome in the high-risk subtypes of OCs. In conclusion, the results of this thesis indicate that WT1 gene expression can provide information about MRD of patients with AML, and WT1 SNP rs1799925 may be used as a biomarker for predicting clinical outcome in childhood BCP-ALL. In ccRCC, the prognostic significance of WT1 SNPs is weak and limited to the subgroup of patients that are homozygous for the minor allele. In OCs anti-WT1 IgG Ab measurement in plasma and WT1 staining in tissue specimens could possibly be used as biomarkers for predicting patient outcome in the high-risk subtypes of OCs.

No description available.

Ovarian cancer (OC) is the second most common gynecologic cancer; however it is responsible for the most gynecologic cancer-related deaths. Apoptosis evasion is an important mechanism in OC tumorigenesis, and the prototypic anti-apoptotic protein, B-cell lymphoma 2 (Bcl-2), is often overexpressed in OC tumors. Gaining a better understanding of the mechanism(s) behind Bcl-2 overexpression and potential extra-anti-apoptotic functions of Bcl-2 could elucidate the importance of elevated Bcl-2 in OC. In the current study, I show through immunohistochemical analysis of normal, benign, and OC tissue sections, that both epithelial and stromal Bcl-2 expression decreases with OC progression. However, the number of Bcl-2-positive lymphocyte nests and the size of these lymphocyte nests increase dramatically with OC progression. Additionally, this study shows that lysophosphatidic acid (LPA), a glycerophospholipid frequently elevated in serum and ascites fluid of OC patients, upregulates Bcl-2 in OC cells. Bcl-2 enzyme-linked immunosorbant assay (ELISA), western blot analysis, reverse transcriptase polymerase chain reaction (RT-PCR), and luciferase reporter assays reveal that LPA increases Bcl-2 promoter, messenger RNA (mRNA), and protein levels in OC cells, but not in normal immortalized ovarian surface epithelial (IOSE) cells. LPA also increases secreted levels of Bcl-2. In vitro human umbilical vein endothelial cell (HUVEC) tube formation assays show that OC-derived Bcl-2 or recombinant human (rh) Bcl-2 promotes aberrant formation of tube-like structures. Though extracellular Bcl-2 does not affect HUVEC cell viability, it may cause aberrant tube formation by inhibiting HUVEC migration. Finally, Bcl-2 ELISA reveals that urinary Bcl-2 levels in OC patients are higher than those in normal individuals and patients with benign gynecologic disease. Urinary Bcl-2 also complements serum CA125 when the two are compared in parallel samples. Furthermore, urinary Bcl-2 decreases following cytoreductive surgery. Altogether, the results suggest that Bcl-2 is important in OC tumorigenesis and angiogenesis. Additionally, urinary Bcl-2 may be a valuable non-invasive biomarker for OC diagnosis and/or screening. Consequently, further elucidation of mechanisms of Bcl-2 overexpression and its extra-apoptotic functions could lead to improved treatment and diagnostic strategies for OC patients.

The enzyme spermidine/spermine N1-acetyltransferase (SSAT) is a candidate biomarker for various cancers as its activity in cancerous tissues is significantly increased. An artificial molecule, amantadine, is exclusively acetylated by SSAT to acetylamantadine (AcAm), levels of which in urine can serve as a proxy biomarker for malignancy. Current method of AcAm detection is laborious, time-consuming, and lacks the possibility of transforming to a point-of-care device. In this thesis, two different approaches were applied to detect AcAm in deionized water and in human urine using optical methods. The first one was fluorescence-based indicator displacement assay using cucurbit[7]uril as the receptor molecule. The second was programmed gold nanoparticle disaggregation with cucurbit[7]uril as a molecular linker. / Graduate

Raman spectroscopy has been used to characterise both organic and geological samples in order to build a database for the future characterization of biomarker molecules that are of astrobiological relevance. Characteristic geological features and hydrated minerals recently found on the surface of Mars by the NASA planetary rovers Spirit and Opportunity suggest that a possible biosphere could have once existed there. Analytical instrumentation protocols for the unequivocal detection of biomarkers in suitable geological matrices are critical for future unmanned explorations, including the forthcoming ESA ExoMars mission scheduled for 2018. Several geological features found on the surface of Mars by planetary rovers suggest that a possible extinct biosphere could exist based on similar sources of energy as occurred on Earth. For this reason, analytical instrumental protocols for the detection of isolated biomarkers preserved in suitable geological matrices unequivocally and non-destructively have to be evaluated for future unmanned missions. Raman spectroscopy is currently part of the Pasteur instrumentation suite of the ExoMars mission for the remote detection of extant or extinct life signatures in the Martian surface and subsurface. Terrestrial analogues of Martian sites have been identified and the biogeological modifications resulting from extremophilic survival activity have been studied. Here we present the Raman spectral characterization of several examples of organic compounds which have been recorded using 785 nm, 633 nm and 514 nm laser excitation -polycyclic aromatic hydrocarbons (PAHs), organic acids, chlorophyll and carotenoids. Experimental mixtures of ß-carotene in usnic acid, PAHs in usnic acid and PAHs in mineral matrices have also been investigated. Organic compounds and PAHs located under crystalline minerals samples were identified using a 5x objective lens and 785 nm III excitation. The pure compounds and compound mixtures were also analysed using X-ray powder diffraction and scanning electron microscopy (SEM). The results of this study indicate that near infrared laser at 785 nm provided the clearest and the most informative spectra due to the reduction of fluorescence emission. Higher energy lasers operating in the visible region have resulted in the emission of significant background fluorescence. Few samples fluoresce even with the use of 785 nm excitation and FT-Raman spectroscopy remains the instrument of choice for the analysis of these samples.

<p>In this thesis, methods to study gene and protein expression in cells and tissues were developed and utilized in combination with protein-specific antibodies, with the overall objective to attain greater understanding of protein function.</p><p>To analyze protein expression in <i>in vitro</i> cultured cell lines, a cell microarray (CMA) was developed, facilitating antibody-based protein profiling of cell lines using immunohistochemistry (IHC). Staining patterns in cell lines were analyzed using image analysis, developed to automatically identify cells and immunohistochemical staining, providing qualitative and quantitative measurements of protein expression. Quantitative IHC data from CMAs stained with nearly 3000 antibodies was used to evaluate the adequacy of using cell lines as models for cancer tissue. We found that cell lines are homogenous with respect to protein expression profiles, and generally more alike each other, than corresponding cancer cells <i>in vivo</i>. However, we found variability between cell lines in regards to the level of retained tumor phenotypic traits, and identified cell lines with a preserved link to corresponding cancer, suggesting that some cell lines are appropriate model systems for specific tumor types. </p><p>Specific gene expression patterns were analyzed in vitiligo vulgaris and malignant melanoma. Transcriptional profiling of vitiligo melanocytes revealed dysregulation of genes involved in melanin biosynthesis and melanosome function, thus highlighting some mechanisms possibly involved in the pathogenesis of vitiligo. Two new potential markers for infiltrating malignant melanoma, Syntaxin-7 and Discs large homolog 5, were identified using antibody-based protein profiling of melanoma in a tissue microarray format. Both proteins were expressed with high specificity in melanocytic lesions, and loss of Syntaxin-7 expression was associated with more high-grade malignant melanomas.</p><p>In conclusion, the combination of antibody-based proteomics and microarray technology provided valuable information of expression patterns in cells and tissues, which can be used to better understand associations between protein signatures and disease.</p>

Telomerase, discovered in 1985, is considered a near-universal marker of malignancy and therefore has a potential use in cancer therapeutics and diagnostics. In this study, I used several approaches to gain a better understanding of telomerase and its potential applications in the canine context, for both cancer therapeutics and diagnosis. Having already developed an effective siRNA viral vector in vitro, the challenge still remained to deliver it efficiently in vivo. Thus, I initially investigated two possible approaches for in vivo delivery. First, I investigated a cell-based system for direct delivery to the tumours. Specifically I optimised a system for efficient gene-transfer to endothelial cells using a green fluorescent protein plasmid vector, and monitored systemic delivery by ex vivo imaging of dye-labelled cells in a canine xenograft tumour mouse model. In parallel, in vitro I investigated the gene transfer mediated by a novel dendrimer vector that can form nanoparticles with DNA and accumulate in tumour sites in vivo after i.v. administration. In order to utilize these delivery systems, I developed a DNA plasmid-based siRNA vector and tested its efficacy on canine tumour cells. To investigate telomerase as a cancer biomarker, I conducted a study that aimed to detect circulating telomerase reverse transcriptase (TERT) mRNA in serum taken from canine cancer patients. For this I developed several systems for effective RNA isolation from serum and used both conventional and quantitative PCR assays to detect TERT expression. Although for the first time I can confirm the existence of mRNA in serum of canine cancer patients, in this clinical study, I could only detect telomerase transcripts in a very small proportion of canine cancer patients. In a final pilot study to investigate anti-ageing technologies, I looked at the potential for drug-dependant telomerase induction rather than inhibition. For this I investigated the ability of three candidate drugs to induce TERT mRNA activation in canine embryonic fibroblasts. In this study, telomerase induction was measured using the quantitative PCR method that I had developed for serum detection. In summary, I have demonstrated that a cell-based delivery vehicle has a potential application in cancer therapy, but that more development is required before it can be applied clinically. I have also reported here that PPIG3 dendrimer-based gene transfer in vitro is low in canine cancer cells and thus require more optimisation and development before it can be utilised as an efficient systemic delivery vehicle. For the siRNA experiment, unfortunately, I did not observe any telomerase genesilencing in canine cancer cells using the plasmid-based siRNA expression vector, and therefore the gene sequence of cTR that we were targeting as well as the siRNA plasmid-vector that we used needs further validation in canine cells. I also suggest that TERT mRNA may not be a good serum biomarker for canine cancer diagnostics as I did not find TERT transcript in most of our serum samples from canine cancer patients, although circulating mRNA of a housekeeping gene was detected. Finally, in a pilot study, I have demonstrated that telomerase can be induced in normal canine somatic cells using small molecules. However, the long-term effects of telomerase induction on ageing must be determined in future studies.

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