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The purposes of this research are (1) to bridge this gap of deficiency by developing a simple, precise and reproducible routine analytical technique by using attenuated total reflectance, and (2) to serve as an atlas for identification of renal calculi.

The two studies follow free nucleic acids in urine in search for biomarkers to distinguish urinary bladder cancer patients from controls. Bladder cancer forms 4 % of newly diagnosed oncological diseases in the Czech Republic. Nowadays, there is no accredited non-invasive method for its diagnosis, which is sufficiently accurate. Urine supernatant, which is washing the bladder mucosa and which does not contain cell debris, seems to be an appropriate source of biomarkers for non-invasive diagnosis. miRNAs, as a non-invasive biomarker of urinary bladder cancer, were studied in one of the studies. miRNAs are short noncoding RNA, which block the process of translation. miRNAs occur in all body fluids and are relatively stable. A study with three phases was assessed to find a suitable miRNA marker. 109 individuals were examined in total (36 controls and 73 bladder cancer patients). The analysis of miRNAs was based on RT-PCR (Reverse Transcription Polymerase Chain Reaction). In the first phase, the urine of 59 individuals was analyzed on TaqMan array card with 381 miRNAs. In the second phase, the results of the first phase were confirmed on the same cohort by a single miRNA assay. In the third phase, a new cohort was used (23 controls and 27 bladder cancer patients), analyzed by a single miRNA assay again....

Exposure to arsenic (As) is a major public health concern globally. Inorganic As (InAs) undergoes hepatic methylation to form monomethyl (MMAs)- and dimethyl (DMAs)-arsenical species, facilitating urinary As elimination. MMAsIII is considerably more toxic than either InAsIII or DMAsV, and a higher proportion of MMAs in urine has been associated with risk for a wide range of adverse health outcomes. One-carbon metabolism (OCM) is a biochemical pathway that provides methyl groups for the methylation of As, and is influenced by folate and other micronutrients, such as vitamin B12, choline, betaine and creatine. A growing body of evidence has demonstrated that OCM-related micronutrients play a critical role in As methylation. To analyze the impact of As exposure, it needs to be properly quantitated. Urinary As (uAs) is a biomarker of As exposure. Urinary creatinine (uCr) or specific gravity (SG) are used to correct uAs for urine dilution. However, uCr is correlated with As methylation, whereas SG has limitations in individuals with kidney damage. Therefore, it is important to determine which urine dilution proxy is appropriate in As-related research. In Chapter 2 we conducted a review that summarized observational epidemiological studies, interventions, and relevant experimental evidence examining the role that OCM-related micronutrients have on As methylation, toxicity of As, and risk for associated adverse health-related outcomes. People with higher relative percentage of MMAs (%MMAs) in urine (inefficient As methylation), have been shown to have a higher risk of cardiovascular disease and several cancers but appear to have a lower risk of diabetes and obesity in populations from the US, Mexico, and Taiwan. It is unknown if this opposite pattern with obesity is present in Bangladesh, a country with lower adiposity and higher As exposure in drinking water. Efficiency of As methylation differs substantially between species, between individuals, and across populations. In Chapter 3, we aimed to evaluate which urine dilution correction methods for uAs most accurately predicted blood As (bAs). We used data from the Folic Acid and Creatine Trial (FACT; N = 541) and Folate and Oxidative Stress (FOX; N = 343) study in Bangladesh. Three linear regression models were assessed using uAs (1) adjusted for uCr or SG as separate covariates, (2) standardized for uCr or SG, i.e., uAs/uCr, and (3) adjusted for residual corrected uCr or SG following adjustment for age, sex and BMI. Median uAs/bAs for FACT and FOX were 114/8.4 and 140/12.3 µg/L. In FACT, two-fold increases in uAs adjusted for uCr or SG were related to 34% and 22% increases in bAs, respectively, with similar patterns in FOX. In Chapter 4, we investigated the effects of folic acid (FA) and/or creatine supplementation on the concentrations of As species and primary (PMI: MMAs/InAs) and secondary (SMI: DMAs/MMAs) methylation indices in blood in Bangladeshi adults having a wide range of folate status. In a randomized, double-blinded, placebo-controlled trial, 622 participants were assigned to FA (400 or 800 μg/day), 3 g creatine/day, 3 g creatine + 400 μg FA/day, or placebo for 12 weeks. For the following 12 weeks, half of the FA participants were randomly switched to receive placebo. All participants received As-removal water filters at baseline. Blood As species were measured at baseline, and weeks 1, 12, and 24. In all groups, blood As species concentrations decreased due to filter use. After 1 week, the mean within-person increase in SMI for the creatine + 400FA group was greater than that of the placebo group (p = 0.05). The mean percent decrease (95% CI) in blood concentrations of MMAs (bMMAs) between baseline and week 12 was greater for all treatment groups compared to the placebo group [400FA: -10.3 (-11.9, -8.8); 800FA: -9.5 (-11.1, -8.0); creatine: -5.9 (-8.6, -3.0); creatine + 400FA: -8.4 (-10.0, -6.9); placebo: -2.0 (-4.0, 0.0)], and the percent increase in blood DMAs (bDMAs) concentrations for the FA treated groups all significantly exceeded that of placebo [400 FA: 12.8 (10.5, 15.2); 800 FA: 11.3 (8.90, 13.8); creatine + 400 FA: 7.40 (5.20, 9.70); placebo: -0.10 (-2.80, 2.60)]. The mean decrease in PMI and increase in SMI in all FA groups significantly exceeded placebo (p < 0.05). Data from week 24 showed evidence of a reversal of treatment effects on As species from week 12 in those who switched from 800FA to placebo, with significant decreases in SMI [-9.0% (-3.5, -14.8)] and bDMAs [-5.9% (-1.8, -10.2)] in those who switched from 800FA to placebo, whereas for those who remained on 800FA, PMI and bMMAs concentrations continued to decline [-7.2% (-0.5, -14.3) and -3.1% (-0.1, -6.2), respectively] for those who remained on 800FA supplementation. This trial was registered at https://clinicaltrials.gov as NCT01050556. In Chapter 5, we characterized the association between body mass index (BMI) and As methylation in Bangladeshi adults and adolescents participating in the FACT; FOX; and Metals, Arsenic, and Nutrition in Adolescents Study (MANAS). Arsenic species (InAs, MMAs, DMAs) were measured in urine and blood. Height and weight were measured to calculate BMI. The associations between concurrent BMI with urine and blood As species were analyzed using linear regression models, adjusting for nutrients involved in OCM such as choline. In FACT, we also evaluated the prospective association between weight change and As species. Mean BMIs were 19.2/20.4, 19.8/21.0, and 17.7/18.7 kg/m2 in males/females in FACT, FOX, and MANAS, respectively. BMI was associated with As species in female but not in male participants. In females, after adjustment for total urine As, age, and plasma folate, the adjusted mean differences (95% confidence) in urinary %MMAs and %DMAs for a 5 kg/m2 difference in BMI were -1.21 (-1.96, -0.45) and 2.47 (1.13, 3.81), respectively in FACT, -0.66 (-1.56, 0.25) and 1.43 (-0.23, 3.09) in FOX, and -0.59 (-1.19, 0.02) and 1.58 (-0.15, 3.30) in MANAS. The associations were attenuated after adjustment for choline. Similar associations were observed with blood As species. In FACT, a 1-kg of weight increase over 2 to 10 (mean 5.4) years in males/ females was prospectively associated with mean %DMAs that was 0.16%/0.19% higher. BMI was negatively associated with %MMAs and positively associated with %DMAs in females but not males in Bangladesh; associations were attenuated after plasma choline adjustment. In conclusion, we found that FA supplementation lowers bMMAs and increases bDMAs in a sample of primarily folate-replete adults, while creatine supplementation lowers bMMAs. Evidence of the reversal of treatment effects on As species following FA cessation suggests short-term benefits of supplementation and underscores the importance of long-term interventions such as FA fortification. Additionally, there is fairly robust evidence supporting the impact of folate on As methylation, and some evidence from case-control studies indicating that folate nutritional status influences risk for As-induced skin lesions and bladder cancer. However, the potential for folate to be protective for other As-related health outcomes, adverse health risks of high folate/FA levels (particularly in areas where folate supplements are common), and beneficial effects of other OCM-related micronutrients on As methylation and risk for health outcomes are not as well studied and warrant additional research. We also found that the role of body fat on estrogen levels that may influence OCM, e.g. by increasing choline synthesis. Research is needed to determine whether the associations between BMI and As species are causal and their influence on As-related health outcomes. Finally, we found that in assessing urine dilution correction approaches, models with uCr consistently had lower AIC values than SG across methods. The uAs associations with bAs were stronger after adjustment for uCr vs. SG. Decisions regarding urine dilution methods should consider whether the study outcomes are influenced by factors such as methylation or medical conditions.

Polycyclic aromatic hydrocarbons (PAH) are a class of environmental pollutants consisting of a minimum of two fused aromatics rings originating from the incomplete combustion of organic matter and/or anthropogenic sources. Numerous possible anthropogenic and natural sources make the presence of PAH ubiquitous in the environment. The carcinogenic nature of some PAH and their ubiquitous presence makes their chemical analysis a topic of environmental and toxicological importance. Although environmental monitoring of PAH is an important step to prevent exposure to contaminated sites, it provides little information on the actual uptake and subsequent risks. Parent PAH are relatively inert and need metabolic activation to express their carcinogenicity. Covalent binding to DNA appears to be the first critical step in the initiation of the tumor formation process. To this end, the determination of short term biomarkers – such as monohydroxy-PAH metabolites (OH-PAH) - fills an important niche to interpret actual PAH exposure levels, prevent extreme body burdens and minimize cancer risk. One would certainly prefer an early warning parameter over a toxicological endpoint – such as DNA-adducts – indicating that extensive damage has already been done. Several methods have been developed to determine OH-PAH in specific tissue or excreta and food samples. The general trend for the analysis of OH-PAH follows the pattern of sample collection, sample clean-up and pre-concentration, chromatographic separation and quantification. Popular approaches for sample clean-up and preconcentration include liquid-liquid extraction (LLE) and solid-phase extraction (SPE). Chromatographic separation and quantification has been based on high-performance liquid iv chromatography-room temperature fluorescence detection (HPLC) and gas chromatographymass spectrometry (GC-MS). Although chromatographic techniques provide reliable results in the analysis of OHPAH, their experimental procedures are time consuming and expensive. Elution times of 30-60 minutes are typical and standards must be run periodically to verify retention times. If the concentrations of target species are found to lie outside the detector’s response range, the sample must be diluted and the process repeated. On the other end of the concentration range, many samples are “zeroes,” i.e. the concentrations are below detection limits. Additional problems arise when laboratory procedures are scaled up to handle thousands of samples under mass screening conditions. Under the prospective of a sustainable environment, the large usage of organic solvents is one of the main limitations of the current chromatographic methodology. This dissertation focuses on the development of a screening methodology for the analysis of OH-PAH in urine and milk samples. Screening techniques capable of providing a “yes or no” answer to OH-PAH contamination prevent unnecessary scrutiny of un-contaminated samples via conventional methods, reduce analysis cost and expedite the turnaround time for decision making purposes. The proposed methodology is based on capillary zone electrophoresis (CZE) and synchronous fluorescence spectroscopy (SFS). Metabolites extraction and pre-concentration is achieved with optimized SPE, LLE and/or QuEChERS (quick, easy, cheap, effective, rugged and safe) procedures. The small sample and extracting solvent volumes facilitate the simultaneous extraction of numerous samples via an environmentally friendly procedure, which is well-suited for routine monitoring of numerous samples. Sample stacking is successfully implemented to improve CZE limits of detection by two orders of magnitude. The unique electrophoretic pattern of positional isomers of OH-PAH demonstrates the potential of CZE for v the unambiguous determination of metabolites with similar chromatographic behaviors and virtually similar fragmentation patterns. The direct determination of OH-PAH without chromatographic separation is demonstrated via SFS. The non-destructive nature of SFS provides ample opportunity for further metabolite confirmation via chromatographic techniques

The primary aim was to validate and implement a urinary pharmacokinetic method for terbutaline to determine the relative lung and systemic bioavailability following inhalation and to measure the in-vitro characteristics of the emitted dose by these inhalation methods. Two new robust, accurate and sensitive high performance liquid chromatography methods for the determination of terbutaline in aqueous and urine samples were validated in accordance with the FDA and ICH guidelines. Terbutaline was extracted using solid phase extraction with salbutamol and bamethane as internal standards. The accuracy, precision, lower limit of detection and recovery for both methods were within recognized limits. The in-vitro characteristics of terbutaline sulphate inhalers were measured according to standard compendial methodology as well as adaptation of this methodology to simulate routine patient use. The dose emission of terbutaline sulphate from a Bricanyl Turbuhaler was determined using an inhalation volume of 4 L at inhalation flows of 10-60 L min-1. The particle size distribution was measured using an Anderson Cascade Impactor (ACI) with a mixing inlet valve to allow measurement at different flows. A steady increase in total emitted dose (TED) and the fine particle dose (FPD) was observed as the inhalation flow increased thereby highlighting the flow dependent dose emission characteristics of the Turbuhaler. The in-vitro dose emission characteristics of terbutaline sulphate from Bricanyl MDIs were measured according to the standard compendial methodology at a flow of 28.3 L min-1 using a 4 L inhalation volume. The TED and particle size distribution of terbutaline sulphate from the Bricanyl MDI were determined alone and with different spacers [AeroChamber Max (AMAX), AeroChamber Plus (APLUS), Fisonair and Nebuhaler]. The TED from the MDI alone was significantly higher than all MDI+spacers (p<0.001). The MDI with APLUS resulted in the smallest mass median aerodynamic diameter (MMAD) and the highest fine particle fraction (FPF). The MDI with AMAX resulted in the highest FPD. The in-vitro characteristics of terbutaline sulphate from Bricanyl respules using the Aeroneb Pro (vibrating mesh) and Sidestream jet nebulisers were determined by the CEN methodology and the Next Generation Impactor (NGI) methodology. The Aeroneb Pro was found to have significantly better aerodynamic properties than the Sidestream. The results from the NGI method were significantly different from the CEN method suggesting further evaluation of both methods. Cooling the NGI decreased the evaporation effect. Twelve healthy volunteers (6 females) completed in-vivo urinary terbutaline pharmacokinetic studies to determine the relative bioavailability following inhalation. The differences between the amounts excreted 0.5, 1, 2, 4, 6 and 24 hour post inhalation from a Bricanyl MDI (I) and oral (O) dosing of 500 µg terbutaline sulphate and with the co-administration of oral charcoal (IC and OC, respectively) were studied. No terbutaline was found in OC samples. The amount of terbutaline excreted 30 minutes post I and IC were significantly (p<0.001) higher than post O suggesting that the amount of terbutaline excreted 30 minutes post dosing can be used as an index of the lung deposition. The amount of terbutaline excreted 24 hour post I was significantly (p<0.01) higher than post O suggesting that the amount of terbutaline excreted 24 hour post dosing can be used as an index of the relative systemic bioavailability. The dose response relationships and the low inter and intra-subject variability studies confirm the feasibility of this method. To demonstrate the application of the method the effect of inhalation technique on the lung and systemic bioavailability following inhalation from a dry powder inhaler was evaluated. The effect of different spacers on the dose emitted from the Bricanyl MDI and the effect of different nebulisers on the dose emitted were also studied using twelve healthy volunteers (6 females) for each study. A fast inhalation flow using the Bricanyl Turbuhaler resulted in significantly higher amounts of terbutaline excreted 0.5 and 24 hour post dosing (2 doses of 500µg terbutaline sulphate from Bricanyl Turbuhaler) than slow inhalation flow (p<0.001). The Bricanyl MDI alone resulted in a significantly higher amount of terbutaline excreted 24 hour post dosing (2 doses of 250µg terbutaline sulphate from Bricanyl MDI) and significantly lower amounts excreted 30 minutes post dosing than the MDI+Spacers. The AMAX provided a greater amount of urinary terbutaline excreted 30 minutes post dosing than the APLUS and Nebuhaler. The Aeroneb Pro resulted in significantly higher amounts of terbutaline excreted 0.5 and 24 hour post dosing (1 dose of 5mg/2ml terbutaline sulphate from Bricanyl respule) than a Sidestream Jet nebuliser (p<0.001). Further application of the method was demonstrated by 12 (6 female) COPD non-invasive mechanically ventilated patients. One dose of 2mg in 0.8ml terbutaline sulphate respiratory solution from Aeroneb Pro and one dose of 5mg in 2ml terbutaline sulphate respiratory solution from Sidestream jet nebuliser resulted in a similar amounts of urinary terbutaline excreted 0.5 and 24 hour post dosing. The results were consistent with the results of the ex-vivo study performed on the same patients. The thesis highlights extension of the urinary pharmacokinetic method following inhalation to terbutaline and its application in volunteer and patient studies. / Egyptian Culture Office in UK, Missions Department in Egypt

Transcriptome studies disentangle functional mechanisms of gene expression regulation and may lend key insights into disease mechanisms. However, the cost of RNA-sequencing and types of tissues currently assayed pose major limitations to study expansion and disease-relevant discovery. This thesis develops methods for sampling noninvasive biospecimens for transcriptome studies, investigating their technical and biological characteristics, and assessing the feasibility of using noninvasive samples in transcriptomic and clinical applications. Chapter 1 explores the technical and biological features of four potential noninvasive sample types (buccal swabs, hair follicles, saliva, and urine cell pellets) in a pilot study of 19 individuals whereby four separate collections of each tissue were performed (i.e. 76 samples/tissue, 304 samples in total). From this data, consistency of library preparation, cell type content, replication of GTEx cis-eQTLs, and disease applications were assessed. In all, hair follicles and urine cell pellets were found to be most promising for future applications. Chapter 2 investigates the scaling potential of noninvasive sampling in SPIROMICS, a COPD clinical cohort. To do so, 140 hair follicle and 110 buccal swab samples were collected from seven different clinical sites. Consistency of sample quality was observed to be high for hair follicles, and hair cell type abundance estimates were consistent within SPIROMICS and compared to the 19 subject pilot study. Mapping of cis-eQTLs in hair revealed 339 associations not identified in any prior study. These cis-eQTLs show higher replication in GTEx tissues that share cell types with hair follicles, indicating hair follicles may indeed capture gene expression regulatory mechanisms found in more invasive tissue types of the body. This thesis suggests future use of noninvasive sampling will facilitate discovery by increasing sample sizes in more diverse populations and in tissues with greater cell type diversity and biological relatedness to disease mechanisms. Moreover, the nature of noninvasive sampling enables complex, longitudinal study designs with greater ability to capture context-dependent mechanisms of genetic regulation not currently able to be interrogated.

Exposomics aims to characterize the totality of exposures over the lifespan, and their impact on human health. Currently, chronic exposure to harmful chemicals from air pollution and/or tobacco smoke, along with a suboptimal diet, remain leading causes for preventable mortality and morbidity worldwide. As a result, new analytical methods are needed to measure robust biomarkers of smoke exposure and food intake for improved risk assessment of clinical events. This thesis aims to develop high throughput methods to rapidly quantify urinary biomarkers of environmental smoke in high-risk occupations, and diverse global populations using multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) technology. Chapter II outlines an inter-laboratory method comparison for the targeted analysis of urinary 1-hydroxypyrene (HP) when using gas chromatography-high resolution mass spectrometry (GC-HRMS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) on urine samples collected from firefighters. This work revealed the critical role of incomplete enzymatic deconjugation on method bias and underreporting of true smoke exposures. Chapter III introduces a high throughput MSI-CE-MS/MS method (< 3 min/sample) to directly analyze the intact glucuronide conjugate of HP (HP-G) in urine without complex pre-column enzyme deconjugation and derivatization procedures. Importantly, firefighters deployed under emergency conditions at the 2016 Fort McMurray wildfire had creatinine normalized HP-G concentrations below the biological exposure index, likely caused by delays in urine collection under emergency conditions, at early stages of firefighting. Chapter IV extends from targeted biomonitoring of occupational smoke exposure, towards elucidating the relative risk of tobacco smoking in an international cohort of participants (n=1000) from the Prospective Urban and Rural Epidemiological (PURE) study. Comprehensive analysis of nicotine metabolites in urine by MSI-CE-MS allowed for reliable determination of the total nicotine equivalent and nicotine metabolic ratio as robust indicators of recent tobacco smoke exposure and nicotine dependence, respectively. This method also offers a more accurate approach for biochemical verification of smoking status in large-scale epidemiological studies that are prone to social desirability and gender bias when relying on standardized questionnaires. Lastly, Chapter V employs a nontargeted metabolomics workflow using MSI-CE-MS to identify urinary metabolites that may serve as objective dietary biomarkers of food intake in participants across 14 countries from the PURE cohort. A panel of robust and generalizable metabolites were validated for biomonitoring of complex dietary exposures, that may further exacerbate the hazards of tobacco smoking. In summary, this thesis contributes high throughput analytical tools for characterizing the human urine exposome to better decipher the roles of smoke exposure, and suboptimal diet on chronic disease burden among diverse populations and regions worldwide. / Thesis / Doctor of Philosophy (PhD)

No description available.

Irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) are two of the most commonly diagnosed chronic digestive disorders in Western countries with increasing prevalence among Canadians. However, the etiology of IBS and IBD remain poorly understood due to a complex interplay of genetic, psychosocial and environmental factors, which hampers efforts at early detection/screening, accurate diagnosis and effective treatments notably in children. This thesis aims to reveal new biochemical insights into the pathophysiology underlying IBS and IBD when using an untargeted metabolite profiling (i.e., metabolomics) approach on urine and stool specimens based on multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS). Chapter I reviews brief history and current challenges in diagnosis and treatment, as well as current metabolomics literature of IBS and IBD. Chapter II first develops a robust method for high throughput profiling of anionic metabolites in human urine samples when using MSI-CE-MS. For the first time, we demonstrate that incidental capillary fractures are caused by irreversible aminolysis of the outer polyimide coating due to the frequent use of volatile ammonia based buffers under alkaline conditions (pH > 9) in electrospray ionization-MS. Chapter III subsequently applies this validated method to investigate differentially excreted urinary metabolites between adult IBS patients and healthy controls, which indicated significantly accelerated rates of collagen degradation and cell turn-over in IBS patients. Chapter IV later develops a novel stool extraction protocol for characterization of the fecal metabolome together with meta-genomic data for elucidating complex host-gut microflora interactions from a cohort of pediatric IBD patients, including Crohn’s disease and ulcerative colitis. In this pilot study, a panel of discriminating metabolites in urine is shown to allow for differential diagnosis of major pediatric IBD sub-types as an alternative to colonoscopy and histopathology that are invasive, expensive and prone to ambiguous test results. Finally, Chapter V involves a longitudinal metabolomics study that aims to identify metabolic trajectories that predict treatment responses of a cohort of pediatric Crohn’s disease patients following initiation of exclusive enteral nutrition (EEN) therapy. In the end, Chapter VI highlights major outcomes of thesis and future direction of metabolomics in IBS and IBD with a specific focus on improved stool specimen collection and validation of biomarker specificity relative to other related gastrointestinal disorders. In summary, this thesis has demonstrated metabolic processes that are associated with exacerbation of symptoms or remission in subset of IBS and pediatric IBD patients. With follow up studies with larger cohort of patients, potential biomarkers identified in this thesis will contribute the development of more accurate and non-invasive decision making process for diagnosis and treatment, resulting in long-lasting remission and improved quality of life of patients suffering from chronic digestive disorders. / Thesis / Doctor of Science (PhD)