Transcriptomic and metabolomic data integration.

Many studies now produce parallel data sets from different omics technologies; however, the task of interpreting the acquired data in an integrated fashion is not trivial. This review covers those methods that have been used over the past decade to statistically integrate and interpret metabolomics and transcriptomic data sets. It defines four categories of approaches, correlation-based integration, concatenation-based integration, multivariate-based integration and pathway-based integration, into which all existing statistical methods fit. It also explores the choices in study design for generating samples for analysis by these omics technologies and the impact that these technical decisions have on the subsequent data analysis options.

Free radical scavenging and formation by multi-walled carbon nanotubes in cell free conditions and in human bronchial epithelial cells.

BACKGROUND: Certain multi-walled carbon nanotubes (MWCNTs) have been shown to elicit asbestos-like toxicological effects. To reduce needs for risk assessment it has been suggested that the physicochemical characteristics or reactivity of nanomaterials could be used to predict their hazard. Fibre-shape and ability to generate reactive oxygen species (ROS) are important indicators of high hazard materials. Asbestos is a known ROS generator, while MWCNTs may either produce or scavenge ROS. However, certain biomolecules, such as albumin - used as dispersants in nanomaterial preparation for toxicological testing in vivo and in vitro - may reduce the surface reactivity of nanomaterials. METHODS: Here, we investigated the effect of bovine serum albumin (BSA) and cell culture medium with and without BEAS 2B cells on radical formation/scavenging by five MWCNTs, Printex 90 carbon black, crocidolite asbestos, and glass wool, using electron spin resonance (ESR) spectroscopy and linked this to cytotoxic effects measured by trypan blue exclusion assay. In addition, the materials were characterized in the exposure medium (e.g. for hydrodynamic size-distribution and sedimentation rate). RESULTS: The test materials induced highly variable cytotoxic effects which could generally be related to the abundance and characteristics of agglomerates/aggregates and to the rate of sedimentation. All carbon nanomaterials were found to scavenge hydroxyl radicals (•OH) in at least one of the solutions tested. The effect of BSA was different among the materials. Two types of long, needle-like MWCNTs (average diameter >74 and 64.2 nm, average length 5.7 and 4.0 µm, respectively) induced, in addition to a scavenging effect, a dose-dependent formation of a unique, yet unidentified radical in both absence and presence of cells, which also coincided with cytotoxicity. CONCLUSIONS: Culture medium and BSA affects scavenging/production of •OH by MWCNTs, Printex 90 carbon black, asbestos and glass-wool. An unidentified radical is generated by two long, needle-like MWCNTs and these two CNTs were more cytotoxic than the other CNTs tested, suggesting that this radical could be related to the adverse effects of MWCNTs.

Oxidative stress, DNA damage, and inflammation induced by ambient air and wood smoke particulate matter in human A549 and THP-1 cell lines.

Combustion of biomass and wood for residential heating and/or cooking contributes substantially to both ambient air and indoor levels of particulate matter (PM). Toxicological characterization of ambient air PM, especially related to traffic, is well advanced, whereas the toxicology of wood smoke PM (WSPM) is poorly assessed. We assessed a wide spectrum of toxicity end points in human A549 lung epithelial and THP-1 monocytic cell lines comparing WSPM from high or low oxygen combustion and ambient PM collected in a village with many operating wood stoves and from a rural background area. In both cell types, all extensively characterized PM samples (1.25-100 µg/mL) induced dose-dependent formation of reactive oxygen species and DNA damage in terms of strand breaks and formamidopyrimidine DNA glycosylase sites assessed by the comet assay with WSPM being most potent. The WSPM contained more polycyclic aromatic hydrocarbons (PAH), less soluble metals, and expectedly also had a smaller particle size than PM collected from ambient air. All four types of PM combined increased the levels of 8-oxo-7,8-dihydro-2'-deoxyguanosine dose-dependently in A549 cells, whereas there was no change in the levels of etheno-adducts or bulky DNA adducts. Furthermore, mRNA expression of the proinflammatory genes monocyte chemoattractant protein-1, interleukin-8, and tumor necrosis factor-α as well as the oxidative stress gene heme oxygenase-1 was upregulated in the THP-1 cells especially by WSPM and ambient PM sampled from the wood stove area. Expression of oxoguanine glycosylase 1, lymphocyte function-associated antigen-1, and interleukin-6 did not change. We conclude that WSPM has small particle size, high level of PAH, low level of water-soluble metals, and produces high levels of free radicals, DNA damage as well as inflammatory and oxidative stress response gene expression in cultured human cells.

Daily measurement of organic compounds in ambient particulate matter in Augsburg, Germany: new aspects on aerosol sources and aerosol related health effects.

Several epidemiological studies have shown that in the human population ambient particulate matter (PM) is associated with adverse health effects. Little is known, however, about the relative effects of aerosol constituents. Since 2002, diurnal samples of ambient PM2.5 were analysed by automated methods for the quantification of particle-associated organic compounds (POC). Data on chemical composition have been investigated in epidemiological and biological effect studies. As a result of these studies, the associations found between PAH concentration and symptoms of myocardial infarction survivors suggest a major influence of combustion sources on cardiovascular health effects. The correlations found between formation of reactive oxygen species and the presence of specific organic compounds suggests an important influence of biomass combustion particles in PM2.5-associated oxidative stress.

Concentration of oxygenated polycyclic aromatic hydrocarbons and oxygen free radical formation from urban particulate matter.

PM2.5 filter samples were collected in summer 2005 at an urban background site in Augsburg, Germany. They were analyzed for polycyclic aromatic hydrocarbons (PAH) and their oxygenated derivatives (O-PAH) using gas chromatography/mass spectrometry. Oxygen free radical formation (reactive oxygen substances, ROS) was measured by electron spin resonance (ESR) spectroscopy after addition of spin trapping agent directly on the same filters. The concentrations of ambient, high-boiling PAH and O-PAH were highly correlated to ROS formation, even better than to particulate mass or number concentration. Correlations were most pronounced for some polycyclic aromatic monoketones (e.g., benz[de]anthracene-7-one), which are not yet reported in literature to be redox cycling active. The association found between ESR measurements and the presence of specific semivolatile organic compounds suggests an important influence of wood burning in PM2.5-associated ROS formation. These results indicate that further research on the relationship between radical formation and presence of specific O-PAH and semivolatile organic compounds (SVOC) are likely to provide a better understanding of the relationship between the source-dependent chemical composition of PM and the toxicological risks associated with PM exposure.

DTW4Omics: comparing patterns in biological time series.

When studying time courses of biological measurements and comparing these to other measurements eg. gene expression and phenotypic endpoints, the analysis is complicated by the fact that although the associated elements may show the same patterns of behaviour, the changes do not occur simultaneously. In these cases standard correlation-based measures of similarity will fail to find significant associations. Dynamic time warping (DTW) is a technique which can be used in these situations to find the optimal match between two time courses, which may then be assessed for its significance. We implement DTW4Omics, a tool for performing DTW in R. This tool extends existing R scripts for DTW making them applicable for "omics" datasets where thousands entities may need to be compared with a range of markers and endpoints. It includes facilities to estimate the significance of the matches between the supplied data, and provides a set of plots to enable the user to easily visualise the output. We illustrate the utility of this approach using a dataset linking the exposure of the colon carcinoma Caco-2 cell line to oxidative stress by hydrogen peroxide (H2O2) and menadione across 9 timepoints and show that on average 85% of the genes found are not obtained from a standard correlation analysis between the genes and the measured phenotypic endpoints. We then show that when we analyse the genes identified by DTW4Omics as significantly associated with a marker for oxidative DNA damage (8-oxodG), through over-representation, an Oxidative Stress pathway is identified as the most over-represented pathway demonstrating that the genes found by DTW4Omics are biologically relevant. In contrast, when the positively correlated genes were similarly analysed, no pathways were found. The tool is implemented as an R Package and is available, along with a user guide from http://web.tgx.unimaas.nl/svn/public/dtw/.