Assessing gene network stability and individual variability in the fathead minnow (Pimephales promelas) transcriptome

Perspectives on transcriptomics in animal physiology studies

Reductionist approaches in physiology and biochemistry are essential for understanding how animals cope and adapt to their environments. Transcriptomics is no longer restricted to a select few, and accessibility and affordability continue to facilitate its rapid growth as a science. More than 6000 publications (a conservative estimate) over the past decade quantify the response of the transcriptome to a wide breadth of questions in animal physiology. Transcriptomes have been quantified under conditions of hypoxia, climate change, salinity, drought, environmental pollution, and ultraviolet radiation among others; these studies have greatly improved understanding of the molecular machinery required for organismal adaptation. These "snapshots in time" however are never complete as the transcriptome is exquisitely sensitive to an individual's current physiologic state. Animal physiologists new to the field must recognize limitations of transcriptome technologies and consider experimental designs that strengthen physiologic interpretation. Current estimates suggest that a sample size of 6 or more are required for RNA-seq experiments in order to capture the majority of differentially expressed genes confidently. "Outside-the-box" approaches for statistical analyses of data derived from RNA-seq should be explored, as studies continue to point out that high false discoveries rates are pervasive with RNA-seq studies, reminiscent of the early days of microarrays. Incorporating biological variability, rather than reducing it (i.e. pooling strategies), into experimental designs is essential. Moreover, real-time PCR must not be viewed as a "validation step" to justify low samples sizes, but rather an orthogonal method to strengthen biological interpretation. The use of proper experimental controls in transcriptomics studies (i.e. spike-in controls and technical replication) are recommended and there is a pressing need for inter-laboratory tests (round robin experiments) to quantify repeatability and to identify sources of transcriptome variation within the context of animal physiology. Testing the reproducibility of transcriptome experiments in light of physiology in non-model organisms would be a significant contribution to the community. Single cell transcriptomics and multiplexing barcoding strategies such as decode-seq are poised to further advance the reductionist view of animal physiology; researchers are encouraged to consult literature herein and elsewhere for guidance on best practices and limitations of transcriptome technologies when studying the physiology of animals.

Spotlight on environmental omics and toxicology: a long way in a short time

The applications for high throughput omics technologies in environmental science have increased dramatically in recent years. Transcriptomics, proteomics, and metabolomics have been used to study how chemicals in our environment affect both aquatic and terrestrial organisms, and the characterization of molecular initiating events is a significant goal in toxicology to better predict adverse responses to toxicants. This special journal edition demonstrates the scope of the science that leverages omics-based methods in both laboratory and wild populations within the context of environmental toxicology, ranging from fish to mammals. It is important to recognize that the environment comprises one axis of the One Health concept - the idea that human health is unequivocally intertwined to our environment and to the organisms that inhabit that environment. We have much to learn from a comparative approach, and studies that integrate the transcriptome, proteome, and the metabolome are expected to offer the most detailed mechanism-based adverse outcome pathways that are applicable for use in both environmental monitoring and risk assessment.

Defining the role of omics in assessing ecosystem health: Perspectives from the Canadian environmental monitoring program

Scientific reviews and studies continue to describe omics technologies as the next generation of tools for environmental monitoring, while cautioning that there are limitations and obstacles to overcome. However, omics has not yet transitioned into national environmental monitoring programs designed to assess ecosystem health. Using the example of the Canadian Environmental Effects Monitoring (EEM) program, the authors describe the steps that would be required for omics technologies to be included in such an established program. These steps include baseline collection of omics endpoints across different species and sites to generate a range of what is biologically normal within a particular ecosystem. Natural individual variability in the omes is not adequately characterized and is often not measured in the field, but is a key component to an environmental monitoring program, to determine the critical effect size or action threshold for management. Omics endpoints must develop a level of standardization, consistency, and rigor that will allow interpretation of the relevance of changes across broader scales. To date, population-level consequences of routinely measured endpoints such as reduced gonad size or intersex in fish is not entirely clear, and the significance of genome-wide molecular, proteome, or metabolic changes on organism or population health is further removed from the levels of ecological change traditionally managed. The present review is not intended to dismiss the idea that omics will play a future role in large-scale environmental monitoring studies, but rather outlines the necessary actions for its inclusion in regulatory monitoring programs focused on assessing ecosystem health.

Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio)

Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics. To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, better characterization and understanding are needed for natural variation in gene expression among fish individuals from lab cultures. Leveraging the transcriptomics data from a number of our toxicogenomics studies conducted over the years, we conducted a meta-analysis of nearly 600 microarrays generated from the ovary tissue of untreated, reproductively mature fathead minnow and zebrafish samples. As expected, there was considerable batch-to-batch transcriptomic variation; this “batch-effect” appeared to differentially impact subsets of fish transcriptomes in a nonsystematic way. Temporally more closely spaced batches tended to share a greater transcriptomic similarity among one another. The overall level of within-batch variation was quite low in fish ovary tissue, making it a suitable system for studying chemical stressors with subtle biological effects. The observed differences in the within-batch variability of gene expression, at the levels of both individual genes and pathways, were probably both technical and biological. This suggests that biological interpretation and prioritization of genes and pathways targeted by experimental conditions should take into account both their intrinsic variability and the size of induced transcriptional changes. There was significant conservation of both the genomes and transcriptomes between fathead minnow and zebrafish. The high degree of conservation offers promising opportunities in not only studying fish molecular responses to environmental stressors by a comparative biology approach, but also effective sharing of a large amount of existing public transcriptomics data for developing toxicogenomics applications.

Whole adult organism transcriptional profiling of acute metal exposures in male zebrafish

Background

A convergence of technological breakthroughs in the past decade has facilitated the development of rapid screening tools for biomarkers of toxicant exposure and effect. Platforms using the whole adult organism to evaluate the genome-wide response to toxicants are especially attractive. Recent work demonstrates the feasibility of this approach in vertebrates using the experimentally robust zebrafish model. In the present study, we evaluated gene expression changes in whole adult male zebrafish following an acute 24 hr high dose exposure to three metals with known human health risks. Male adult zebrafish were exposed to nickel chloride, cobalt chloride or sodium dichromate concentrations corresponding to their respective 96 hr LC₂₀, LC₄₀ and LC₆₀. Histopathology was performed on a subset of metal-exposed zebrafish to phenotypically anchor transcriptional changes associated with each metal.

Results

Comparative analysis identified subsets of differentially expressed transcripts both overlapping and unique to each metal. Application of gene ontology (GO) and transcription factor (TF) enrichment algorithms revealed a number of key biological processes perturbed by metal poisonings and the master transcriptional regulators mediating gene expression changes. Metal poisoning differentially activated biological processes associated with ribosome biogenesis, proteosomal degradation, and p53 signaling cascades, while repressing oxygen-generating pathways associated with amino acid and lipid metabolism. Despite appreciable effects on gene regulation, nickel poisoning did not induce any morphological alterations in male zebrafish organs and tissues. Histopathological effects of cobalt remained confined to the olfactory system, while chromium targeted the gills, pharynx, and intestinal mucosa. A number of enriched transcription factors mediated the observed gene response to metal poisoning, including known targets such as p53, HIF1α, and the myc oncogene, and novel regulatory factors such as XBP1, GATA6 and HNF3β.

Conclusions

This work uses an experimentally innovative approach to capture global responses to metal poisoning and provides mechanistic insights into metal toxicity.