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.

P10.06.A Expression of GDNF and its receptors in glioblastoma

Background

Neurotrophic factors are important for brain development, but their role in glioblastoma, the most aggressive primary brain cancer, is not fully understood. We focused on glial cell line-derived neurotrophic factor (GDNF), which has been shown to play a role in growth and migration in glioblastoma. The aim of this study was to investigate the expression of GDNF and its primary receptor GFRA1 as well as GDNF family receptors GFRA2-4 and RET.

Material and Methods

Tissue sections from 10 glioblastoma patients were stained with antibodies against GDNF (frozen tissue) and each of the receptors (formalin-fixed paraffin-embedded tissue). Moreover, the sections were stained with an RNA Scope assay for GDNF mRNA. The area fractions of positive receptor staining were quantified with a software-based classifier. Double immunofluorescence stainings were performed for GFRA1 and the astrocytic tumor cell marker GFAP, the microglia and macrophage marker IBA1, and the tumor stem cell markers OLIG2 and SOX2, respectively, for assessment of co-expression.

Results

GDNF staining in a varying number of cells was seen in 5 of the 10 samples. GDNF mRNA stainings were observed in a varying number of cells in all stained tissues, including in hypoxic areas and in microvascular proliferations. Mean area fractions of the receptors were 31 % (range 7-56) for GFRA1, 3 % (0,2-7) for GFRA2, 0,4 % (0,01-2) for GFRA3, 0,1 % (0,02-0,3) for GFRA4 and 1 % (0,1-2) for RET. Co-expression of GFRA1 and GFAP was widely present. Co-expression of GFRA1 and either OLIG2 or SOX2 was partially present. Co-expression of GFRA1 and IBA1 was limited.

Conclusion

Our results suggest that GDNF and GFRA1 are widely expressed in glioblastoma tissue, but GFRA2-4 and RET are also expressed and may play a role in glioblastoma tumor biology. Future experimental studies are needed to clarify the functional role of GDNF and its receptors in glioblastoma biology.

Exposure to Contaminated River Water is Associated with Early Hatching and Dysregulation of Gene Expression in Early Life Stages of the Endangered Copper Redhorse (Moxostoma hubbsi)

The copper redhorse (Moxostoma hubbsi) is an endangered fish that spawns exclusively in the Richelieu River (Quebec, Canada). Tributaries of the Richelieu are contaminated with high levels of current-use pesticides, which may impact early-life stage (ELS) copper redhorse and other native fishes. We assessed the effects of exposure to contaminated river water on ELS copper redhorse and river redhorse (Moxostoma carinatum), a related fish that shares the copper redhorse's spawning grounds and nursery habitat. A riverside flow-through system was used to expose copper and river redhorse embryos (1000 each) to Richelieu River water or laboratory water as a control. Fish were maintained until 14 days posthatch, and water samples were taken daily for chemical analysis. Following a heavy rain event, concentrations of two neonicotinoid pesticides, clothianidin and thiamethoxam, exceeded water quality guidelines for aquatic life (20 ng/L). Using nontargeted screening, we tentatively identified an additional 24 pharmaceutical and personal care products and 23 pesticides in river water. Effects of river water on ELS fish were observed in both species, but the copper redhorse appeared to be more sensitive. Fish exposed to river water hatched 10.7 (copper redhorse) and 2.4 (river redhorse) cumulative degree days earlier than controls. Copper redhorse survival was significantly lower in river water (73 ± 16%) compared to laboratory water (93 ± 3%), whereas river redhorse survival was similar between treatments (84 ± 6% and 89 ± 4%, respectively). Sequencing of copper redhorse larvae RNA revealed 18 differentially expressed genes (DEGs) following 14 days of exposure to river water. Eight up-regulated DEGs were linked to immune function and injury response, and seven down-regulated DEGs were involved with digestion and nutrient absorption. The present study provided valuable data on the effects of ELS exposure to a real-world mixture of contaminants in two fish species of concern. Environ Toxicol Chem 2022;41:1950-1966. © 2022 SETAC.

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 (Hg^II) 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 Hg^II and MeHg. We find that simple mixing of two distinct isotopic end-members: MeHg (1.4‰) and Hg^II (-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 Hg^II. We speculate that this results in a higher fraction of labile Hg^II 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.