Web-based multi-omics integration using the Analyst software suite.

The growing number of multi-omics studies demands clear conceptual workflows coupled with easy-to-use software tools to facilitate data analysis and interpretation. This protocol covers three key components involved in multi-omics analysis, including single-omics data analysis, knowledge-driven integration using biological networks and data-driven integration through joint dimensionality reduction. Using the dataset from a recent multi-omics study of human pancreatic islet tissue and plasma samples, the first section introduces how to perform transcriptomics/proteomics data analysis using ExpressAnalyst and lipidomics data analysis using MetaboAnalyst. On the basis of significant features detected in these workflows, the second section demonstrates how to perform knowledge-driven integration using OmicsNet. The last section illustrates how to perform data-driven integration from the normalized omics data and metadata using OmicsAnalyst. The complete protocol can be executed in ~2 h. Compared with other available options for multi-omics integration, the Analyst software suite described in this protocol enables researchers to perform a wide range of omics data analysis tasks via a user-friendly web interface.

Characterizing Variability and Uncertainty Associated with Transcriptomic Dose-Response Modeling.

Transcriptomics dose-response analysis (TDRA) has emerged as a promising approach for integrating toxicogenomics data into a risk assessment context; however, variability and uncertainty associated with experimental design are not well understood. Here, we evaluated n = 55 RNA-seq profiles derived from Japanese quail liver tissue following exposure to chlorpyrifos (0, 0.04, 0.1, 0.2, 0.4, 1, 2, 4, 10, 20, and 40 µg/g; n = 5 replicates per group) via egg injection. The full dataset was subsampled 637 times to generate smaller datasets with different dose ranges and spacing (designs A-E) and number of replicates (n = 2-5). TDRA of the 637 datasets revealed substantial variability in the gene and pathway benchmark doses, but relative stability in overall transcriptomic point-of-departure (tPOD) values when tPODs were calculated with the "pathway" and "mode" methods. Further, we found that tPOD values were more dependent on the dose range and spacing than on the number of replicates, suggesting that optimal experimental designs should use fewer replicates (n = 2 or 3) and more dose groups to reduce uncertainty in the results. Finally, tPOD values ranged by over ten times for all surveyed experimental designs and tPOD types, suggesting that tPODs should be interpreted as order-of-magnitude estimates.

EcoToxModules: Custom Gene Sets to Organize and Analyze Toxicogenomics Data from Ecological Species.

Traditional results from toxicogenomics studies are complex lists of significantly impacted genes or gene sets, which are challenging to synthesize down to actionable results with a clear interpretation. Here, we defined two sets of 21 custom gene sets, called the functional and statistical EcoToxModules, in fathead minnow (Pimephales promelas) to (1) re-cast predefined molecular pathways into a toxicological framework and (2) provide a data-driven, unsupervised grouping of genes impacted by exposure to environmental contaminants. The functional EcoToxModules were identified by re-organizing KEGG pathways into biological processes that are more relevant to ecotoxicology based on the input from expert scientists and regulators. The statistical EcoToxModules were identified using co-expression analysis of publicly available microarray data (n = 303 profiles) measured in livers of fathead minnows after exposure to 38 different conditions. Potential applications of the EcoToxModules were demonstrated with two case studies that represent exposure to a pure chemical and to environmental wastewater samples. In comparisons to differential expression and gene set analysis, we found that EcoToxModule responses were consistent with these traditional results. Additionally, they were easier to visualize and quantitatively compare across different conditions, which facilitated drawing conclusions about the relative toxicity of the exposures within each case study.

Selenium and stable mercury isotopes provide new insights into mercury toxicokinetics in pilot whales.

High exposures of mammalian species to inorganic mercury (HgII) and methylmercury (MeHg) have been associated with adverse effects on behavior and reproduction. Different mammalian species exhibit varying responses to similar external exposure levels, reflecting potential differences in Hg toxicokinetics. Here, we use Hg stable isotopes, total Hg, MeHg and selenium (Se) concentrations measured in multiple tissues of North Atlantic pilot whales (Globicephala melas) to investigate processes affecting the distribution and accumulation of HgII and MeHg. We find that simple mixing of two distinct isotopic end-members: MeHg (1.4‰) and HgII (-1.6‰) can explain the observed variability of δ202Hg in brain tissue. A similar isotopic composition for the MeHg end-member in the brain, muscle, heart, and kidney suggests efficient exchange of MeHg in blood throughout the body. By contrast, the Hg isotopic composition of the liver of adult whales is different from younger whales and other tissues that follow the two-end member mixing model. Measured Se:Hg ratios are lowest in adult whales with the highest levels of MeHg exposure. In these individuals, Se availability is likely reduced by complexation with demethylated HgII. We speculate that this results in a higher fraction of labile HgII eliminated from the liver of adult whales compared to young whales and subsequent redistribution to other tissues, potentially affecting toxicity.

Organ-specific differences in mercury speciation and accumulation across ringed seal (Phoca hispida) life stages.

Methylmercury (MeHg) is a central nervous system toxicant and exposures can adversely affect the health of marine mammals. Mercuric selenide (HgSe) in marine mammal tissues is hypothesized to result from a protective detoxification mechanism, but toxicokinetic processes contributing to its formation are poorly understood. Here, new data is reported on speciated Hg concentrations in multiple organs of n = 56 ringed seals (Phoca hispida) from Labrador, Canada, and compare concentrations to previously published data from Greenland seals. A higher proportion of Hg is found to accumulate in the kidney of young-of-the-year (YOY) ringed seals compared to adults. A toxicokinetic model for Hg species is developed and evaluated to better understand factors affecting variability in Hg concentrations among organs and across life stages. Prior work postulated that HgSe formation only occurs in the liver of mature seals, but model results suggest HgSe formation occurs across all life stages. Higher proportions of HgSe in mature seal livers compared to YOY seals likely results from the slow accumulation and elimination of HgSe (total body half-life = 500 days) compared to other Hg species. HgSe formation in the liver reduces modeled blood concentrations of MeHg by only 6%. Thus, HgSe formation may not substantially reduce MeHg transport across the blood-brain barrier of ringed seals, leaving them susceptible to the neurotoxic effects of MeHg exposure.

Environmental Origins of Methylmercury Accumulated in Subarctic Estuarine Fish Indicated by Mercury Stable Isotopes.

Methylmercury (MeHg) exposure can cause adverse reproductive and neurodevelopmental health effects. Estuarine fish may be exposed to MeHg produced in rivers and their watersheds, benthic sediment, and the marine water column, but the relative importance of each source is poorly understood. We measured stable isotopes of mercury (δ202Hg, Δ199Hg, and Δ201Hg), carbon (δ13C), and nitrogen (δ15N) in fish with contrasting habitats from a large subarctic coastal ecosystem to better understand MeHg exposure sources. We identify two distinct food chains exposed to predominantly freshwater and marine MeHg sources but do not find evidence for a benthic marine MeHg signature. This is consistent with our previous research showing benthic sediment is a net sink for MeHg in the estuary. Marine fish display lower and less variable Δ199Hg values (0.78‰ to 1.77‰) than freshwater fish (0.72‰ to 3.14‰) and higher δ202Hg values (marine: 0.1‰ to 0.57‰; freshwater: -0.76‰ to 0.15‰). We observe a shift in the Hg isotopic composition of juvenile and adult rainbow smelt (Osmerus mordax) when they transition between the freshwater and marine environment as their dominant foraging territory. The Hg isotopic composition of Atlantic salmon (Salmo salar) indicates they receive most of their MeHg from the marine environment despite a similar or longer duration spent in freshwater regions. We conclude that stable Hg isotopes effectively track fish MeHg exposure sources across different ontogenic stages.