Design issues in cross-sectional biomarkers studies: urinary biomarkers of PAH exposure and oxidative stress

Unbiased data analytic strategies to improve biomarker discovery in precision medicine

Omics technologies promised improved biomarker discovery for precision medicine. The foremost problem of discovered biomarkers is irreproducibility between patient cohorts. From a data analytics perspective, the main reason for these failures is bias in statistical approaches and overfitting resulting from batch effects and confounding factors. The keys to reproducible biomarker discovery are: proper study design, unbiased data preprocessing and quality control analyses, and a knowledgeable application of statistics and machine learning algorithms. In this review, we discuss study design and analysis considerations and suggest standards from an expert point-of-view to promote unbiased decision-making in biomarker discovery in precision medicine.

Predictors of polycyclic aromatic hydrocarbon exposure and internal dose in inner city Baltimore children

Polycyclic aromatic hydrocarbons (PAHs), the by-products of incomplete combustion of organic materials, are commonly found on particulate matter (PM) and have been associated with the development of asthma and asthma exacerbation in urban populations. We examined time spent in the home and outdoors as predictors of exposures to airborne PAHs and measured urinary 1-hydroxypyrene-glucuronide (1-OHPG) as internal dose of PAHs in 118 children aged 5-12 years from Baltimore, MD. During weeklong periods (Saturday-Saturday) in each of four seasons: daily activities were assessed using questionnaires, indoor air nicotine and PM concentrations were monitored, and urine specimens were collected on Tuesday (day 3) and Saturday (day 7) for measurement of 1-OHPG. Time spent in non-smoking homes was associated with significantly decreased 1-OHPG concentration in urine (β=-0.045, 95% CI (-0.076, -0.013)), and secondhand smoke (SHS) exposures modified these associations, with higher urinary 1-OHPG concentrations in children spending time in smoking homes than non-smoking homes (P-value for interaction=0.012). Time spent outdoors was associated with increased urinary 1-OHPG concentrations (β=0.097, 95% CI (0.037, 0.157)) in boys only. Our results suggest that SHS and ambient (outdoor) air pollution contribute to internal dose of PAHs in inner city children.

Photomodified fluoranthene exerts more harmful effects as compared to intact fluoranthene by inhibiting growth and photosynthetic processes in wheat

Polycyclic aromatic hydrocarbons (PAHs) are toxic to plants. Exposure of PAHs to sunlight can result in the formation of photomodified PAHs, which are generally more toxic than the parent compounds. In the present study, biochemical and physiological effects of intact fluoranthene (FLT) and photomodified FLT (P.FLT) in wheat were investigated. Our results demonstrated that the treatment of FLT and P.FLT, inhibited germination, seedling growth and pigment content. However, inhibition observed on primary photochemistry and photosystem II heterogeneity was more prominent in P.FLT treated plants. Both FLT and P.FLT affected the levels of antioxidant enzymes such as POD, SOD, CAT and GR to similar extent. Greater inhibitory effects of P.FLT than FLT may be ascribed to its effects on growth parameters and photochemistry rather than on the activities of various antioxidant enzymes.

Modified ion source triple quadrupole mass spectrometer gas chromatograph for polycyclic aromatic hydrocarbon analyses

We describe modified gas chromatography electron-impact/triple-quadrupole mass spectrometry (GC-EI/MS/MS) utilizing a newly developed hydrogen-injected self-cleaning ion source and modified 9mm extractor lens. This instrument, with optimized parameters, achieves quantitative separation of 62 polycyclic aromatic hydrocarbons (PAHs). Existing methods historically limited rigorous identification and quantification to a small subset, such as the 16 PAHs the US EPA has defined as priority pollutants. Without the critical source and extractor lens modifications, the off-the-shelf GC-EI/MS/MS system was unsuitable for complex PAH analysis. Separations were enhanced by increased gas flow, a complex GC temperature profile incorporating multiple isothermal periods, specific ramp rates, and a PAH-optimized column. Typical determinations with our refined GC-EI/MS/MS have a large linear range of 1-10,000pgμl(-1) and detection limits of <2pgμl(-1). Included in the 62 PAHs, multiple-reaction-monitoring (MRM) mode enabled GC-EI/MS/MS identification and quantitation of several constituents of the MW 302 PAH isomers. Using calibration standards, values determined were within 5% of true values over many months. Standard curve r(2) values were typically >0.998, exceptional for compounds which are archetypally difficult. With this method benzo[a]fluorene, benzo[b]fluorene, benzo[c]fluorene were fully separated as was benzo[b]fluoranthene, benzo[k]fluoranthene, and benzo[j]fluoranthene. Chrysene and triphenylene, were sufficiently separated to allow accurate quantitation. Mean limits of detection (LODs) across all PAHs were 1.02±0.84pgμl(-1) with indeno[1,2,3-c,d] pyrene having the lowest LOD at 0.26pgμl(-1) and only two analytes above 2.0pgμl(-1); acenaphthalene (2.33pgμl(-1)) and dibenzo[a,e]pyrene (6.44pgμl(-1)).

The effect of glutathione S-transferase M1 and T1 polymorphisms on blood pressure, blood glucose, and lipid profiles following the supplementation of kale (Brassica oleracea acephala) juice in South Korean subclinical hypertensive patients

BACKGROUND/OBJECTIVES

Glutathione S-transferase (GST) forms a multigene family of phase II detoxification enzymes which are involved in the detoxification of reactive oxygen species. This study examines whether daily supplementation of kale juice can modulate blood pressure (BP), levels of lipid profiles, and blood glucose, and whether this modulation could be affected by the GSTM1 and GSTT1 polymorphisms.

SUBJECTS/METHODS

84 subclinical hypertensive patients showing systolic BP over 130 mmHg or diastolic BP over 85 mmHg received 300 ml/day of kale juice for 6 weeks, and blood samples were collected on 0-week and 6-week in order to evaluate plasma lipid profiles (total cholesterol, triglyceride, HDL-cholesterol, and LDL-cholesterol) and blood glucose.

RESULTS

Systolic and diastolic blood pressure was significantly decreased in all patients regardless of their GSTM1 or GSTT1 polymorphisms after kale juice supplementation. Blood glucose level was decreased only in the GSTM1-present genotype, and plasma lipid profiles showed no difference in both the GSTM1-null and GSTM1-present genotypes. In the case of GSTT1, on the other hand, plasma HDL-C was increased and LDL-C was decreased only in the GSTT1-present type, while blood glucose was decreased only in the GSTT1-null genotype.

CONCLUSIONS

These findings suggest that the supplementation of kale juice affected blood pressure, lipid profiles, and blood glucose in subclinical hypertensive patients depending on their GST genetic polymorphisms, and the improvement of lipid profiles was mainly greater in the GSTT1-present genotype and the decrease of blood glucose was greater in the GSTM1-present or GSTT1-null genotypes.

Acute exposure to 3-methylcholanthrene induces hepatic oxidative stress via activation of the Nrf2/ARE signaling pathway in mice

Polycyclic aromatic hydrocarbons (PAHs) are the most common contaminants in the environment. The primary focus on the toxicity of PAHs is their ability to activate the aryl hydrocarbon receptor (AhR)-mediated pathway and lead to carcinogenesis in different organisms. However, the influence of PAHs on the antioxidant system in mammalian systems has received only limited attention. In the present study, we observed that the intraperitoneal injection of 100 mg/kg 3-methylcholanthrene (3MC) into mice significantly increased reactive oxygen species (ROS) levels and malondialdehyde (MDA) contents and decreased glutathione (GSH) contents and the activity of total antioxidant capacity (T-AOC), indicating that serious oxidative stress had been induced in the liver of mice. Then, the oxidative stress signal activated the nuclear factor erythroid 2-related factor 2/antioxidant response element (Nrf2/ARE) pathway by enhancing the mRNA levels of Nrf2, p38, and Erk2. Moreover, the mRNA levels of Nrf2/ARE target genes, including glutathione peroxidase (Gpx), glutathione reductase (GR), glutathione synthetase (GS), NAD(P)H: quinone oxidoreductase 1 (Nqo1), superoxide dismutase 1 (Sod1), and Sod2, increased significantly after treatment with 3MC for 24 hours. The hepatic levels of NQO1 and the activities of GR and GS were also significantly enhanced at 24 hours after 3MC treatment. Because the expression of NQO1 is co-regulated by Nrf2/ARE and AhR/XRE in mammalian tissues, NQO1 may play an important role in protecting against the oxidative stress induced by 3MC. Taken together, our findings suggested that acute exposure to 3MC altered the cellular redox balance in hepatocytes to trigger Nrf2-regulated antioxidant responses, which may represent an adaptive cell defense mechanism against the oxidative stress induced by PAHs.

Polycyclic aromatic hydrocarbon (1-OHPG and 2-naphthol) and oxidative stress (malondialdehyde) biomarkers in urine among Korean adults and children

Using the urinary biomarkers 1-hydroxypyrene-glucuronide (1-OHPG), 2-naphthol, and malondialdehyde (MDA), we evaluated seasonal and regional variations in polycyclic aromatic hydrocarbon (PAH) exposure and oxidative stress among Korean adults and children. In total, 322 children (175 male and 147 female) and 332 adults (47 male and 285 female) were recruited in two regions of Korea, one representing a metropolitan area (Seoul/Incheon) and the other an industrial (Pohang) area, from winter 2002 to spring 2003. The subjects voluntarily gathered their first morning urine void, which was immediately transported to our laboratory and stored at -20 °C. Urinary 1-OHPG was measured by synchronous fluorescence spectroscopy, 2-naphthol by HPLC, and urinary MDA by HPLC with a UV detector. The median urinary 1-OHPG concentration tended to be higher in the industrial region than in the metropolitan region (0.92 vs. 0.77 ng/mL; p=0.03), and higher in winter than in spring (0.95 vs. 0.73 ng/mL; p<0.001). The median 2-naphthol concentration was also higher in the industrial region than in the metropolitan region (21.0 vs. 12.3 ng/mL; p<0.0001), but was higher in spring than in winter (19.7 vs. 10.3 ng/mL; p<0.0001). The median MDA concentration was significantly higher in winter than in spring (2.19 vs. 1.03 μmol/L; p<0.0001), whereas regional variation in MDA was observed only in female adults (p=0.02). In winter, the level of 1-OHPG was higher in children exposed to environmental tobacco smoke than in unexposed children (0.94 vs. 0.86 ng/mL; p=0.02). Our results indicate that both region and season can significantly influence the levels of PAH exposure and oxidative stress biomarkers.

Identification and application of biomarkers in molecular and genomic epidemiologic research

Biomarkers are characteristic biological properties that can be detected and measured in a variety of biological matrices in the human body, including the blood and tissue, to give an indication of whether there is a threat of disease, if a disease already exists, or how such a disease may develop in an individual case. Along the continuum from exposure to clinical disease and progression, exposure, internal dose, biologically effective dose, early biological effect, altered structure and/or function, clinical disease, and disease progression can potentially be observed and quantified using biomarkers. While the traditional discovery of biomarkers has been a slow process, the advent of molecular and genomic medicine has resulted in explosive growth in the discovery of new biomarkers. In this review, issues in evaluating biomarkers will be discussed and the biomarkers of environmental exposure, early biologic effect, and susceptibility identified and validated in epidemiological studies will be summarized. The spectrum of genomic approaches currently used to identify and apply biomarkers and strategies to validate genomic biomarkers will also be discussed.

Validation of biomarkers for the study of environmental carcinogens: a review

There is a need for validation of biomarkers. Our aim is to review published work on the validation of selected biomarkers: bulky DNA adducts, N-nitroso compounds, 1-hydroxypyrene, and oxidative damage to DNA. A systematic literature search in PubMed was performed. Information on the variability and reliability of the laboratory tests used for biomarkers measurements was collected. For the evaluation of the evidence on validation we referred to the ACCE criteria. Little is known about intraindividual variation of DNA adduct measurements, but measurements have a good repeatability irrespective of the technique used for their identification; reproducibility improved after the correction for a laboratory factor. A high-sensitivity method is available for the measurement of 1-hydroxypyrene in urine. There is consensus on validation of biomarkers of oxidative damage DNA based on the comet assay and chromatographic measurement in blood while urinary measurements by chromatographic assays are well validated, and ELISA-based assays appear to lack specificity. Immunoassays for the quantification of adducts of N-nitroso compounds are useful for large epidemiological studies, given their sensitivity, the small amount of DNA required and their potential for rapid and high-throughput analysis.

Determinants of urinary 1-hydroxypyrene glucuronide in South Korean children

OBJECTIVES

This study was conducted to investigate the dominant sources of the urinary pyrene metabolite, 1-hydroxypyrene glucuronide (1-OHPG), in South Korean children.

METHODS

Urine samples were collected from 102 non-smoking children (aged 10-14). Urinary 1-OHPG was assayed by synchronous fluorescence spectroscopy, following immuno-affinity purification using monoclonal antibody 8E11. Urinary cotinine, a metabolite of nicotine, was measured by GC/MS. Information on environmental tobacco smoke (ETS) exposure, diet, fuel type for heating home, and other possible sources of PAH exposure was collected by self-administered questionnaires.

RESULTS

Mean (+/-SE) 1-OHPG levels were 1.64 (+/-0.06) ng/ml (range 0.04-3.27 ng/ml). Two multiple linear regression analyses (differing in how ETS was approximated: by parental smoking or urinary cotinine) revealed a positive association between urinary 1-OHPG levels and parental smoking at home (P = 0.007), log urinary cotinine (P = 0.165), frequent grilled (shell)fish consumption (P = 0.061), and living in a commercial/other zone (P = 0.007) versus a residential or industrial zone. No consistent associations were found between 1-OHPG and the child's sex, grilled meat consumption, or fuels used to heat the home.

CONCLUSIONS

These results support that ETS, frequent grilled fish consumption, and the ambient environment are important predictors of urinary 1-OHPG levels in South Korean children.

Stability and intra-individual variation of urinary malondialdehyde and 2-naphthol

OBJECTIVES

Malondialdehyde (MDA), a lipid peroxidation by-product, has been widely used as an indicator of oxidative stress. Urinary 2-naphthol, a urinary PAH metabolite, is used as a marker of ambient particulate exposure and is associated with lung cancer and chronic obstructive pulmonary disease. However, the stability and intra-individual variation associated with urinary MDA and 2-naphthol have not been thoroughly addressed. The objective of this study was to assess the stability and intraindividual variation associated with urinary MDA and 2-naphthol.

METHODS

Urine samples were collected from 10 healthy volunteers (mean age 34, range 27 approximately 42 years old). Each sample was divided into three aliquots and stored under three different conditions. The levels of urinary MDA and 2-naphthol were analyzed 1) just after sampling, 2) after storage at room temperature (21 degrees C) for 16 hours, and 3) after storage in a -20 degrees C freezer for 16 hours. In addition, an epidemiological study was conducted in 44 Chinese subjects over a period of 3 weeks. The urinary MDA and 2-naphthol were measured by HPLC three times.

RESULTS

There was no difference in the levels of urinary MDA and 2-naphthol between the triplicate measurements (n=10, p=0.84 and p=0.83, respectively). The intra-class correlation coefficients (ICC) for urinary MDA and 2-naphthol were 0.74 and 0.42, respectively. However, the levels of PM2.5 in the air were well correlated with the levels of both MDA and 2-naphthol in the epidemiological study.

CONCLUSIONS

These results suggest that urinary MDA and 2-naphthol remain stable under variable storage conditions, even at room temperature for 16 hours, and indicate that these markers can be used in epidemiological studies involving various sample storage conditions. The intra-CC of urinary 2-naphthol and MDA were acceptable for application to epidemiological studies.

Estimating exposure to polycyclic aromatic hydrocarbons: a comparison of survey, biological monitoring, and geographic information system-based methods

Our objective was to compare polycyclic aromatic hydrocarbon (PAH) exposure estimates based on survey, biological monitoring, and geographic information system (GIS) methods. The 304 participants in this study supplied a urine sample and completed questionnaires about exposure to potential PAH sources. We assayed urine samples for 1-hydroxypyrene-O-glucuronide (1-OHPG), the major metabolite of pyrene, a common PAH. We used a GIS to estimate traffic exhaust exposure using vehicle count data at the residence and workplace. The five subjects who reported smoking during the 48-hour period had median 1-OHPG concentrations 10-fold that of nonsmokers (1.6 versus 0.16 pmol/mL; P = 0.01). Among nonsmokers, those who reported eating grilled, roasted, or broiled meat had significantly higher 1-OHPG concentrations than those who did not reported eating meat prepared by these methods (0.25 versus 0.06 pmol/mL; P = 0.02). Nonsmokers who reported traveling on roads for > or =3 hours during the 48-hour period also had significantly higher 1-OHPG levels than those who traveled <3 hours (0.23 versus 0.11 pmol/mL; P = 0.03). 1-OHPG levels were also correlated with hours of secondhand smoke exposure among nonsmokers (P = 0.04). In this study, 1-OHPG urine concentrations were not associated with self-reported exposures to cooking smoke, wood burning, or traffic levels near the home or to traffic density or urban/rural status determined using a GIS. Self-reported indicators of residential proximity to high traffic volume were, however, associated with GIS traffic density measures.