Toxicogenomic analysis of susceptibility to inhaled urban particulate matter in mice with chronic lung inflammation

A hypothesis: Potential contributions of metals to the pathogenesis of pulmonary artery hypertension

Pulmonary artery hypertension (PAH) is characterized by vasoconstriction and vascular remodeling resulting in both increased pulmonary vascular resistance (PVR) and pulmonary artery pressure (PAP). The chronic and high-pressure stress experienced by endothelial cells can give rise to inflammation, oxidative stress, and infiltration by immune cells. However, there is no clearly defined mechanism for PAH and available treatment options only provide limited symptomatic relief. Due to the far-reaching effects of metal exposures, the interaction between metals and the pulmonary vasculature is of particular interest. This review will briefly introduce the pathophysiology of PAH and then focus on the potential roles of metals, including essential and non-essential metals in the pathogenic process in the pulmonary arteries and right heart, which may be linked to PAH. Based on available data from human studies of occupational or environmental metal exposure, including lead, antimony, iron, and copper, the hypothesis of metals contributing to the pathogenesis of PAH is proposed as potential risk factors and underlying mechanisms for PAH. We propose that metals may initiate or exacerbate the pathogenesis of PAH, by providing potential mechanism by which metals interact with hypoxia-inducible factor and tumor suppressor p53 to modulate their downstream cellular proliferation pathways. These need further investigation. Additionally, we present future research directions on roles of metals in PAH.

Effects of Urban Particulate Matter on the Olfactory System in a Mouse Model

BACKGROUND

Exposure to urban particulate matter (UPM) is linked to the aggravation of various health problems. Although the nasal cavity is the first barrier to encounter UPM, there is a lack of studies on the impact of UPM on the olfactory area. The purpose of this study was to investigate the cytotoxic effects of UPM on mouse olfactory epithelium, the underlying pathophysiology involved, and changes in cytokine levels.

METHODS

Mice were divided into 4 groups: control, 400UPM (administered 400 µg UPM daily; standard reference material 1649b; average particle diameter 10.5 μm) 1week, 400UPM 2weeks, and recovery 1week after 400UPM 2weeks (n = 10, 6, 6, and 6, respectively). Olfactory function was evaluated by conducting a food-finding test once a week. The olfactory neuroepithelium was harvested for histologic examination, gene ontology, quantitative real-time polymerase chain reaction, and western blotting.

RESULTS

Compared to those in the control group, olfactory marker protein, olfactory receptor 1507, adenylyl cyclase 3, and GNAL mRNA levels were lower and S-100, 2',3'-cyclic nucleotide 30-phosphodiesterase, nerve growth factor receptor-associated protein, brain-derived neurotrophic factor, and tachykinin receptor mRNA levels were higher in the 400UPM group olfactory neuroepithelium. There were no significant differences in neuroepithelial inflammatory marker levels between the 400UPM and saline group.

CONCLUSIONS

UPM decreased olfactory function and might have cytotoxic effects on the olfactory epithelium. Olfactory ensheathing cells and trigeminal nerve might be related to the regeneration of the olfactory epithelium after olfactory destruction associated with UPM.

Interactions of particulate matter and pulmonary surfactant: Implications for human health

Particulate matter (PM), which is the primary contributor to air pollution, has become a pervasive global health threat. When PM enters into a respiratory tract, the first body tissues to be directly exposed are the cells of respiratory tissues and pulmonary surfactant. Pulmonary surfactant is a pivotal component to modulate surface tension of alveoli during respiration. Many studies have proved that PM would interact with pulmonary surfactant to affect the alveolar activity, and meanwhile, pulmonary surfactant would be adsorbed to the surface of PM to change the toxic effect of PM. This review focuses on recent studies of the interactions between micro/nanoparticles (synthesized and environmental particles) and pulmonary surfactant (natural surfactant and its models), as well as the health effects caused by PM through a few significant aspects, such as surface properties of PM, including size, surface charge, hydrophobicity, shape, chemical nature, etc. Moreover, in vitro and in vivo studies have shown that PM leads to oxidative stress, inflammatory response, fibrosis, and cancerization in living bodies. By providing a comprehensive picture of PM-surfactant interaction, this review will benefit both researchers for further studies and policy-makers for setting up more appropriate regulations to reduce the adverse effects of PM on public health.

Acellular oxidative potential assay for screening of amorphous silica nanoparticles

Silica nanoparticles (SiNPs) are used in a wide range of consumer products, engineering and medical applications, with likelihood of human exposure and potential health concerns. It is essential to generate toxicity information on SiNP forms and associated physicochemical determinants to conduct risk assessment on these new materials. To address this knowledge gap, we screened a panel of custom synthesized, well-characterized amorphous SiNPs pristine and surface-modified (-C3-COOH, -C11-COOH, -NH₂, -PEG) of 5 different sizes: (15, 30, 50, 75, 100 nm) for their oxidative potential using an acellular assay. The assay is based on oxidation of dithiothreitol (DTT) by reactive oxygen species and can serve as a surrogate test for oxidative stress. These materials were characterized for size distribution, aggregation, crystallinity, surface area, surface modification, surface charge and metal content. Tests for association between oxidative potential of SiNPs and their physicochemical properties were carried out using analysis of variance and correlation analyses. These test results suggest that the size of amorphous SiNPs influenced their oxidative potential irrespective of the surface modification, with 15 nm exhibiting relatively higher oxidative potential compared to the other sizes. Furthermore, SiNP surface area, surface modification and agglomeration in solution also appeared to affect oxidative potential of these SiNPs. These findings indicate that physicochemical properties are critical in influencing the oxidative behaviour of amorphous SiNPs, with potential to trigger cellular oxidative stress and thus toxicity, when exposed. This information advances our understanding of potential toxicities of these amorphous SiNPs and supports risk assessment efforts and the design of safer forms of silica nanomaterials.

Stress axis variability is associated with differential ozone-induced lung inflammatory signaling and injury biomarker response

Ozone (O₃), a ubiquitous urban air pollutant, causes adverse pulmonary and extrapulmonary effects. A large variability in acute O₃-induced effects has been observed; however, the basis for interindividual differences in susceptibility is unclear. We previously demonstrated a role for the hypothalamic-pituitary-adrenal (HPA) stress axis and glucocorticoid response in acute O₃ toxicity. Glucocorticoids have important anti-inflammatory actions, and have been shown to regulate lung inflammatory responses. We hypothesised that a hyporesponsive HPA axis would be associated with greater O₃-dependent lung inflammatory signaling. Two genetically-related rat strains with known differences in stress axis reactivity, highly-stress responsive Fischer (F344) and less responsive Lewis (LEW), were exposed for 4 h by nose-only inhalation to clean air or 0.8 ppm O₃, and euthanized immediately after exposure. As expected, baseline (air-exposed) plasma corticosterone was significantly lower in the hypo-stress responsive LEW. Although O₃ exposure increased plasma corticosterone in both strains, corticosterone remained significantly lower in LEW when compared to F334. LEW exhibited greater O₃-induced inflammatory cytokine/chemokine signaling compared to F344, consistent with the lower corticosterone levels. Since we observed strain-specific differences in inflammatory signaling, we further investigated injury biomarkers (total protein, albumin and lactate dehydrogenase). Although the hyper-responsive F344 exhibited lower inflammatory signaling in response to O₃ compared with LEW, they had greater levels of lung injury biomarkers. Our results indicate that stress axis variability is associated with differential O₃-induced lung toxicity. Given the large variability in stress axis reactivity among humans, stress axis regulation could potentially be a determining factor underlying O₃ sensitivity.

The effect of urban particulate matter on cultured human nasal fibroblasts

BACKGROUND

Exposure to urban particulate matter (UPM) has been linked to aggravation of various health problems. Although the effects of UPM on the lower respiratory tract have been extensively studied, more research is required on the impact of UPM on the upper respiratory tract and the underlying mechanisms. Thus, we investigated the cytotoxic effects of UPM on cultured human nasal fibroblasts, the underlying signaling pathways involved, and changes in cytokine levels.

METHODS

Human turbinate tissue specimens were collected during partial turbinectomies performed on 6 patients, and then cultured. The effect of UPM on nasal fibroblast viability was explored. Real-time reverse transcription-polymerase chain reaction was used to measure the mRNA levels of genes encoding cytokines and chemokines (interleukin [IL]-4, IL-6, IL-8, and tumor necrosis factor-α) before and after 24 hours of UPM treatment. Enzyme-linked immunosorbent assays were employed to measure IL-6 and IL-8 levels. The status of the p38 and nuclear factor (NF)-κB signaling pathways was analyzed by Western blotting.

RESULTS

UPM reduced cell viability in a dose-dependent manner and increased IL-6 and IL-8 expression at both the mRNA and protein levels. UPM induced the phosphorylation of p38 and NF-κB p65; inhibitors of the actions of these proteins repressed phosphorylation and the expression of IL-6 and IL-8.

CONCLUSION

UPM induced IL-6 and IL-8 expression by fibroblasts via p38 and NF-κB classical signaling, suggesting that UPM can induce or aggravate allergic and/or chronic rhinitis.

Particulate air pollution: major research methods and applications in animal models

Ambient air pollution is composed of a heterogeneous mixture of gaseous and solid particle compounds in which primary particles are emitted directly into the atmosphere, such as diesel soot, while secondary particles are created through physicochemical transformation. Particulate matter (PM), especially fine and ultrafine particles, can be inhaled and deposited in the alveolar cavities and penetrate into circulation. An association between high levels of air pollutants and human disease has been known for more than half a century and increasing evidences demonstrate a strong link between exposure on PM and the development of systemic diseases, such as cardiovascular and neurological disorders. Experimental animal models have been extensively used to study the underlying mechanism caused by environmental exposure to ambient PM. Due to their availability, quality, cost, and genetically modified strains, rodent models have been widely used. Some common exposure approaches include intranasal instillation, intratracheal instillation, nose-only inhalation, whole-body inhalation, and intravenous injection have been reviewed with brief summary of its performance, merit, limitation, and application. We hope this would provide useful reference in advancing experimental researches about air pollution human health and disease development.

Comprehensive pulmonary metabolome responses to intratracheal instillation of airborne fine particulate matter in rats

Airborne fine particulate matter (PM2.5) has been closely related with a variety of lung diseases. Although some modes of action (e.g. oxidative stress, inflammations) have been proposed, but the pulmonary toxicological mechanism remains obscure. In this paper, in order to understand the comprehensive pulmonary response to PM2.5 stress, a non-targeted high-throughput metabolomics strategy was adopted to characterize the overall metabolic changes and relevant toxicological pathways. PM2.5 samples were collected from Tangshan, one of the most polluted cities in China. Adult male rats were treated with PM2.5 suspension once a week at the dose of 1mg/kg/week through intratracheal instillation in three months. Aqueous and organic metabolite extracts of the lung tissues were subjected to metabolomics analysis using ultra-high performance liquid chromatograph/mass spectrometry. Along with a significant increase of oxidative stress, significant metabolome alterations were observed in the lung tissues of the treated rats. Nineteen metabolites were found decreased and 31 metabolites increased, which are mainly involved in lipid and nucleotide metabolism. Integrated pathway analysis suggests that PM2.5 can induce pulmonary toxicity through disturbing pro-oxidant/antioxidant balance, which may further correlate with metabolism changes of phospholipid, glycerophospholipid, sphingolipid and purine. These findings improve our understanding of the toxicological pathways of PM2.5 exposure.

Contrasting biological potency of particulate matter collected at sites impacted by distinct industrial sources

BACKGROUND

Industrial sources contribute a significant proportion of anthropogenic particulate matter (PM) emissions, producing particles of varying composition that may differentially impact health. This study investigated the in vitro toxicity of ambient PM collected near industrial sites in relation to particle size and composition.

METHODS

Size-fractionated particles (ultrafine, PM_0.1-2.5, PM_2.5-10, PM_>10) were collected in the vicinity of steel, copper, aluminium, and petrochemical industrial sites. Human lung epithelial-like A549 and murine macrophage-like J774A.1 cells were exposed for 24 h to particle suspensions (0, 30, 100, 300 μg/cm²). Particle potency was assessed using cytotoxic (resazurin reduction, lactate dehydrogenase (LDH) release) and inflammatory (cytokine release) assays, and regressed against composition (metals, polycyclic aromatic hydrocarbons (PAHs), endotoxin).

RESULTS

Coarse (PM_2.5-10, PM_>10) particle fractions were composed primarily of iron and aluminium; in contrast, ultrafine and fine (PM_0.1-2.5) fractions displayed considerable variability in metal composition (especially water-soluble metals) across collection sites consistent with source contributions. Semi-volatile and PM-associated PAHs were enriched in the fine and coarse fractions collected near metal industry. Cell responses to exposure at equivalent mass concentrations displayed striking differences among sites (SITE x SIZE and SITE x DOSE interactions, p < 0.05), suggesting that particle composition, in addition to size, impacted particle toxicity. While both J774A.1 and A549 cells exhibited clear particle size-dependent effects, site-dependent differences were more pronounced in J774A.1 cells, suggesting greater sensitivity to particle composition. Plotting particle potency according to cytotoxic and inflammatory response grouped particles by size and site, and showed that particles of similar composition tended to cluster together. Cytotoxic effects in J774A.1 cells correlated with metal and PAH content, while inflammatory responses were associated primarily with endotoxin content in coarse particles.

CONCLUSIONS

Industrial sources produce particulate emissions with varying chemical composition that differ in their in vitro potency in relation to particle size and the levels of specific constituents.

Cytotoxic and inflammatory potential of size-fractionated particulate matter collected repeatedly within a small urban area

Background

Exposure to coarse, fine, and ultrafine particles is associated with adverse population health impacts. We investigated whether size-fractionated particles collected repeatedly in the vicinity of industrial (steel mills and associated coking operations, wastewater treatment), high traffic, and residential areas display systematic differences in biological potency.

Methods

Particulate matter (PM_<0.1, PM_0.1–0.5, PM_0.5–2.5, PM_2.5–10, PM_>10) samples collected at sites within Windsor, Ontario, were screened for biological potency in human A549 lung epithelial and murine J774A.1 macrophage-like cells using cytotoxicity bioassays (cellular ATP, resazurin reduction, lactate dehydrogenase (LDH) release), cytokine production, and transcript profiles. Potency was determined from the slope of each dose-effect relationship.

Results

Cytotoxic potency varied across size fractions and within a fraction across sites and sampling periods, suggesting that particle composition, in addition to size and mass, affected particle toxicity. While ATP and LDH profiles showed some similarity, resazurin reduction (a measure of metabolic activity) exhibited a unique pattern of response, indicating that the cytotoxicity assays were sensitive to distinct particle characteristics. Chemical speciation varied in relation to prevailing winds, consistent with enrichment of source emissions (e.g. higher metal and polycyclic aromatic hydrocarbon content downwind of the industrial site). Notwithstanding this variability, site-dependent differences in particle toxicity were evident, including greater potency of coarse fractions at the industrial site and of ultrafine particles at the traffic site (Site × Size interactions, p < 0.05). Regression of potency against particle constituents revealed correlations between resazurin reduction, induction of metal-responsive genes, and metal content, which were particularly strong for the coarse fraction, and between cytokine release and endotoxin, suggesting that these factors were important drivers of biological effects that explain, at least in part, the contrasting potencies of particles compared on an equivalent mass basis.

Conclusions

The data show that 1) particle potency and composition can exhibit significant temporal variation in relation to source contributions; 2) sources may differentially impact the potency of specific size fractions; and 3) particle constituents, notably metals and endotoxin, may elicit distinct biological responses. Together, the data are consistent with the notion that sources and composition, in addition to size and mass concentration, are relevant to particle toxicity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12989-015-0099-z) contains supplementary material, which is available to authorized users.

Modulation of macrophage activities in proliferation, lysosome, and phagosome by the nonspecific immunostimulator, mica

It was reported that the aluminosilicate material mica activated macrophages and showed its immunostimulating effects. However, the mechanisms by which it exerts these effects are unclear. To address this, we evaluated the effects of mica fine particles (MFP, 804.1 ± 0.02 nm) on the murine macrophage cell line, RAW 264.7. Specifically, RAW 264.7 cells were treated with 100 and 500 μg/mL MFP and their proliferative response was determined using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Changes in global gene expression upon MFP treatment for 12 and 48 h were also determined using microarrays. Following the MFP treatment, RAW 264.7 cells showed a low level of proliferation compared to nontreated cells (p < 0.01). There was a change in an expression level of 1,128 genes after 48 h treatment. Specifically, genes associated with the cell cycle, DNA replication, and pyrimidine and purine metabolisms, were down-regulated in cells treated with MFP, which resulted in reduction of cell proliferation. MFP treatment also up-regulated genes associated with lysosome and phagosome function, which are both required for macrophage activities. We speculate that activation of macrophages by mica is in part derived from up-regulation of these pathways.

Perspective: ambient air pollution: inflammatory response and effects on the lung's vasculature

Particulates from air pollution are implicated in causing or exacerbating respiratory and systemic cardiovascular diseases and are thought to be among the leading causes of morbidity and mortality. However, the contribution of ambient particulate matter to diseases affecting the pulmonary circulation, the right heart, and especially pulmonary hypertension is much less documented. Our own work and that of other groups has demonstrated that prolonged exposure to antigens via the airways can cause severe pulmonary arterial remodeling. In addition, vascular changes have been well documented in a typical disease of the airways, asthma. These experimental and clinical findings link responses in the airways with responses in the lung's vasculature. It follows that particulate air pollution could cause, or exacerbate, diseases in the pulmonary circulation and associated pulmonary hypertension. This perspective details the literature for support of this concept. Data regarding the health effects of particulate matter from air pollution on the lung's vasculature, with emphasis on the lung's inflammatory responses to particulate matter deposition and pulmonary hypertension, are discussed. A deeper understanding of the health implications of exposure to ambient particulate matter will improve our knowledge of how to improve the management of lung diseases, including diseases of the pulmonary circulation. As man-made ambient particulate air pollution is typically linked to economic growth, a better understanding of the health effects of exposure to particulate air pollution is expected to integrate the global goal of achieving healthy living for all.

Microarray analysis of gene expression alteration in human middle ear epithelial cells induced by micro particle

OBJECTIVES

The primary aim of this study is to reveal the effect of particulate matter (PM) on the human middle ear epithelial cell (HMEEC).

METHODS

The HMEEC was treated with PM (300 μg/ml) for 24 h. Total RNA was extracted and used for microarray analysis. Molecular pathways among differentially expressed genes were further analyzed by using Pathway Studio 9.0 software. For selected genes, the changes in gene expression were confirmed by real-time PCR.

RESULTS

A total of 611 genes were regulated by PM. Among them, 366 genes were up-regulated, whereas 245 genes were down-regulated. Up-regulated genes were mainly involved in cellular processes, including reactive oxygen species generation, cell proliferation, apoptosis, cell differentiation, inflammatory response and immune response. Down-regulated genes affected several cellular processes, including cell differentiation, cell cycle, proliferation, apoptosis and cell migration. A total of 21 genes were discovered as crucial components in potential signaling networks containing 2-fold up regulated genes. Four genes, VEGFA, IL1B, CSF2 and HMOX1 were revealed as key mediator genes among the up-regulated genes. A total of 25 genes were revealed as key modulators in the signaling pathway associated with 2-fold down regulated genes. Four genes, including IGF1R, TIMP1, IL6 and FN1, were identified as the main modulator genes.

CONCLUSIONS

We identified the differentially expressed genes in PM-treated HMEEC, whose expression profile may provide a useful clue for the understanding of environmental pathophysiology of otitis media. Our work indicates that air pollution, like PM, plays an important role in the pathogenesis of otitis media.

Mapping acute systemic effects of inhaled particulate matter and ozone: multiorgan gene expression and glucocorticoid activity

Recent epidemiological studies have demonstrated associations between air pollution and adverse effects that extend beyond respiratory and cardiovascular disease, including low birth weight, appendicitis, stroke, and neurological/neurobehavioural outcomes (e.g., neurodegenerative disease, cognitive decline, depression, and suicide). To gain insight into mechanisms underlying such effects, we mapped gene profiles in the lungs, heart, liver, kidney, spleen, cerebral hemisphere, and pituitary of male Fischer-344 rats immediately and 24h after a 4-h exposure by inhalation to particulate matter (0, 5, and 50mg/m³ EHC-93 urban particles) and ozone (0, 0.4, and 0.8 ppm). Pollutant exposure provoked differential expression of genes involved in a number of pathways, including antioxidant response, xenobiotic metabolism, inflammatory signalling, and endothelial dysfunction. The mRNA profiles, while exhibiting some interorgan and pollutant-specific differences, were remarkably similar across organs for a set of genes, including increased expression of redox/glucocorticoid-sensitive genes and decreased expression of inflammatory genes, suggesting a possible hormonal effect. Pollutant exposure increased plasma levels of adrenocorticotropic hormone and the glucocorticoid corticosterone, confirming activation of the hypothalamic-pituitary-adrenal axis, and there was a corresponding increase in markers of glucocorticoid activity. Although effects were transient and presumably represent an adaptive response to acute exposure in these healthy animals, chronic activation and inappropriate regulation of the hypothalamic-pituitary-adrenal axis are associated with adverse neurobehavioral, metabolic, immune, developmental, and cardiovascular effects. The experimental data are consistent with epidemiological associations of air pollutants with extrapulmonary health outcomes and suggest a mechanism through which such health effects may be induced.

The role of in vitro gene expression profiling in particulate matter health research

Exposure to particulate matter (PM) is consistently associated with increased morbidity and mortality rate. The mechanisms for these adverse health effects have been vigorously investigated for many years, but remain uncertain, in part due to the complex interactions between host and exposure. Over the past decade, the use of global gene expression profiling has increased to investigate molecular changes in an attempt to gain more insight into the complex mechanisms that underlie the adverse health effects induced by PM. These experiments have been performed mostly in cell cultures, in part due to the easy availability and maneuverability of different cell types. Whether or not the results obtained from these in vitro experiments are relevant to human exposure is unclear. In this study, cell culture studies were reviewed that used microarray technology to measure global gene expression in response to PM and the findings discussed in the context of global gene expression results obtained from animal and human exposure studies. Ten in vitro studies were identified from PubMed that reported global gene expression results in response to PM exposure. Despite difference in cell types, microarray platforms, incubation time, and PM sources and doses, these experiments showed commonality in the expression of genes and pathways, especially xenobiotic metabolism, oxidative stress, and inflammation. These gene expression profiles were consistent with results from animal and human controlled exposure experiments. The in vitro experiments also uncovered novel biological mechanisms that may be important in PM-induced health effects reported in epidemiological studies. Data indicate that in vitro microarray experiments complement animal and human exposure studies and allow the PM-associated health research to focus on the "toxic" components in PM and novel mechanisms, and may enhance risk assessment beyond the current mass-based standards.

Non-specific abdominal pain and air pollution: a novel association

Background

We studied whether short-term exposure to air pollution was associated with non-specific abdominal pain in epidemiologic and animal studies.

Methods

Patients visiting the emergency department with non-specific abdominal pain were identified in Edmonton (1992 to 2002, n = 95,173) and Montreal (1997 to 2002, n = 25,852). We calculated the daily concentrations for ozone (O₃), nitrogen dioxide (NO₂), sulfur dioxide (SO₂), carbon monoxide (CO), and particles <10 (PM₁₀) or <2.5 (PM_2.5) µm. A case crossover study design was used to estimate the odds ratio (OR) and 95% confidence interval (CI) associated with an increase in the interquartile range of the air pollutants. We investigated differential effects by age and sex. Mice were gavaged with urban particle extracts. In animal models, colonic motility was tested, and visceral abdominal pain was measured using a writhing test, and behavioral response to oil of mustard and neostigmine. Motility and pain was measured acutely (1.5 hours after gavage) and chronically (7-days and 21-days after gavage).

Results

Emergency department visits for non-specific abdominal pain were primarily by women between the ages of 15–24 years. Individuals aged 15 to 24 years were at increased risk of non-specific abdominal pain in Edmonton (same day CO: OR = 1.04, 95% CI = 1.02–1.06; and NO₂: OR = 1.06, 95% CI = 1.03–1.09). The risk of air pollution among 15–24 year olds in Montreal was significantly positive (same day CO: OR = 1.11, 95% CI = 1.05–1.17; NO₂: OR = 1.09, 95% CI = 1.01–1.16; SO₂: OR = 1.17, 95% CI = 1.10–1.25; PM_2.5: OR = 1.09, 95% CI = 1.04–1.15). Abdominal pain was increased by an acute gavage of pollution extract but not to chronic exposure to pollutants. Colonic transit was delayed following chronic but not acute exposure with the pollutants.

Conclusions

Epidemiological and animal data suggest that short-term exposure to air pollution may trigger non-specific abdominal pain in young individuals.

Genomics and the respiratory effects of air pollution exposure

Adverse health effects from air pollutants remain important, despite improvement in air quality in the past few decades. The exact mechanisms of lung injury from exposure to air pollutants are not yet fully understood. Studying the genome (e.g. single-nucleotide polymorphisms (SNP) ), epigenome (e.g. methylation of genes), transcriptome (mRNA expression) and microRNAome (microRNA expression) has the potential to improve our understanding of the adverse effects of air pollutants. Genome-wide association studies of SNP have detected SNP associated with respiratory phenotypes; however, to date, only candidate gene studies of air pollution exposure have been performed. Changes in epigenetic processes, such DNA methylation that leads to gene silencing without altering the DNA sequence, occur with air pollutant exposure, especially global and gene-specific methylation changes. Respiratory cell line and animal models demonstrate distinct gene expression signatures in the transcriptome, arising from exposure to particulate matter or ozone. Particulate matter and other environmental toxins alter expression of microRNA, which are short non-coding RNA that regulate gene expression. While it is clearly important to contain rising levels of air pollution, strategies also need to be developed to minimize the damaging effects of air pollutant exposure on the lung, especially for patients with chronic lung disease and for people at risk of future lung disease. Careful study of genomic responses will improve our understanding of mechanisms of lung injury from air pollution and enable future clinical testing of interventions against the toxic effects of air pollutants.

Overexpression of tumor necrosis factor-α in the lungs alters immune response, matrix remodeling, and repair and maintenance pathways

Increased production of tumor necrosis factor (TNF)-α and matrix metalloproteinases (MMPs) is a feature of inflammatory lung diseases, including emphysema and fibrosis, but the divergent pathological characteristics that result indicate involvement of other processes in disease pathogenesis. Transgenic mice overexpressing TNF-α in type II alveolar epithelial cells under the control of the surfactant protein (SP)-C promoter develop pulmonary inflammation and emphysema but are resistant to induction of fibrosis by administration of bleomycin or transforming growth factor-β. To study the molecular mechanisms underlying the development of this phenotype, we used a microarray approach to characterize the pulmonary transcriptome of SP-C/TNF-α mice and wild-type littermates. Four-month-old SP-C/TNF-α mice displayed pronounced pulmonary inflammation, airspace enlargement, increased MMP-2 and MMP-9 levels, and altered expression of 2332 probes. The functional assessment of genes with increased expression revealed enrichment of inflammatory/immune responses and proteases, whereas genes involved in protease inhibition, angiogenesis, cross-linking of basement membrane proteins, and myofibroblast differentiation were predominantly decreased. Comparison with multiple lung disease models identified a set of genes unique to the SP-C/TNF-α model and revealed that lack of extracellular matrix production distinguished SP-C/TNF-α mice from fibrosis models. Activation of inflammatory and proteolytic pathways and disruption of maintenance and repair processes are central features of emphysema in this TNF-overexpression model. Impairment of myofibroblast differentiation and extracellular matrix production may underlie resistance to induction of fibrosis.

Effects of scanning sensitivity and multiple scan algorithms on microarray data quality

Background

Maximizing the utility of DNA microarray data requires optimization of data acquisition through selection of an appropriate scanner setting. To increase the amount of useable data, several approaches have been proposed that incorporate multiple scans at different sensitivities to reduce the quantification error and to minimize effects of saturation. However, no direct comparison of their efficacy has been made. In the present study we compared individual scans at low, medium and high sensitivity with three methods for combining data from multiple scans (either 2-scan or 3-scan cases) using an actual dataset comprising 40 technical replicates of a reference RNA standard.

Results

Of the individual scans, the low scan exhibited the lowest background signal, the highest signal-to-noise ratio, and equivalent reproducibility to the medium and high scans. Most multiple scan approaches increased the range of probe intensities compared to the individual scans, but did not increase the dynamic range (the proportion of useable data). Approaches displayed striking differences in the background signal and signal-to-noise ratio. However, increased probe intensity range and improved signal-to-noise ratios did not necessarily correlate with improved reproducibility. Importantly, for one multiple scan method that combined 3 scans, reproducibility was significantly improved relative to individual scans and all other multiple scan approaches. The same method using 2 scans yielded significantly lower reproducibility, attributable to a lack-of-fit of the statistical model.

Conclusions

Our data indicate that implementation of a suitable multiple scan approach can improve reproducibility, but that model validation is critical to ensure accurate estimates of probe intensity.

Impact of nose-only exposure system on pulmonary gene expression

Nose-only exposure is used to study the distribution and toxicity of airborne contaminants. Restraint of animals in nose-only tubes causes stress, but the impact on pulmonary mRNA levels is unknown. Since stress and xenobiotics activate common pathways, we assessed whether nose-only exposure would alter expression of toxicologically relevant genes in the lungs. To identify candidate genes for further analysis, we first interrogated microarray data to examine time-dependent changes in gene expression in air-control animals from a nose-only inhalation study involving male wild-type C57BL/6 mice and transgenic tumor necrosis factor (TNF)-alpha over-expressing littermates. Comparison of transcript levels immediately and 24 h after a single 4-h nose-only exposure to air revealed differential expression of 280 genes (false discovery rate-adjusted, p < .05). Functional analysis revealed enrichment of immune response, apoptosis, and signalling terms, consistent with effects of restraint stress. We then selected a subset of target genes for comparison of naive animals and air-exposed animals from the inhalation study by real-time polymerase chain reaction (PCR). Expression of genes involved in stress (BNIP, sestrin-1, CDKN1A [p21], GADD45 gamma), glucocorticoid-response (GILZ, Sgk), and signal transduction (MAP3K6, C/EBP-delta) was increased as a result of nose-only exposure (p < .05). In contrast, proinflammatory factors (lymphotoxin-beta, chemokine receptor CXCR5) were decreased (p < .05). Immune gene responses observed in wild-type animals were reduced in animals with lung inflammation, indicating that pathological states can modify the response to nose-only exposure. Observed responses may warrant consideration in the evaluation of materials delivered by nose-only inhalation, and suggest that incorporation of naive animals into nose-only studies should be considered as a best practice.

Tungsten carbide cobalt nanoparticles exert hypoxia-like effects on the gene expression level in human keratinocytes

Background

Tungsten carbide (WC) and tungsten carbide cobalt (WC-Co) nanoparticles are of occupational health relevance because of the increasing usage in hard metal industries. Earlier studies showed an enhanced toxic potential for WC-Co compared to WC or cobalt ions alone. Therefore, we investigated the impact of these particles, compared to cobalt ions applied as CoCl₂, on the global gene expression level in human keratinocytes (HaCaT) in vitro.

Results

WC nanoparticles exerted very little effects on the transcriptomic level after 3 hours and 3 days of exposure. In contrast, WC-Co nanoparticles caused significant transcriptional changes that were similar to those provoked by CoCl₂. However, CoCl₂ exerted even more pronounced changes in the transcription patterns. Gene set enrichment analyses revealed that the differentially expressed genes were related to hypoxia response, carbohydrate metabolism, endocrine pathways, and targets of several transcription factors. The role of the transcription factor HIF1 (hypoxia inducible factor 1) is particularly highlighted and aspects of downstream events as well as the role of other transcription factors related to cobalt toxicity are considered.

Conclusions

This study provides extensive data useful for the understanding of nanoparticle and cobalt toxicity. It shows that WC nanoparticles caused low transcriptional responses while WC-Co nanoparticles are able to exert responses similar to that of free cobalt ions, particularly the induction of hypoxia-like effects via interactions with HIF1α in human keratinocytes. However, the enhanced toxicity of WC-Co particles compared to CoCl₂ could not be explained by differences in gene transcription.