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Martyniuk CJ. Perspectives on transcriptomics in animal physiology studies. Comp Biochem Physiol B Biochem Mol Biol 2020; 250:110490. [PMID: 32798690 DOI: 10.1016/j.cbpb.2020.110490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/05/2020] [Accepted: 08/10/2020] [Indexed: 12/31/2022]
Abstract
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.
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Affiliation(s)
- Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA.
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Zhang X, Xia P, Wang P, Yang J, Baird DJ. Omics Advances in Ecotoxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3842-3851. [PMID: 29481739 DOI: 10.1021/acs.est.7b06494] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Toxic substances in the environment generate adverse effects at all levels of biological organization from the molecular level to community and ecosystem. Given this complexity, it is not surprising that ecotoxicologists have struggled to address the full consequences of toxic substance release at ecosystem level, due to the limits of observational and experimental tools to reveal the changes in deep structure at different levels of organization. -Omics technologies, consisting of genomics and ecogenomics, have the power to reveal, in unprecedented detail, the cellular processes of an individual or biodiversity of a community in response to environmental change with high sample/observation throughput. This represents a historic opportunity to transform the way we study toxic substances in ecosystems, through direct linkage of ecological effects with the systems biology of organisms. Three recent examples of -omics advance in the assessment of toxic substances are explored here: (1) the use of functional genomics in the discovery of novel molecular mechanisms of toxicity of chemicals in the environment; (2) the development of laboratory pipelines of dose-dependent, reduced transcriptomics to support high-throughput chemical testing at the biological pathway level; and (3) the use of eDNA metabarcoding approaches for assessing chemical effects on biological communities in mesocosm experiments and through direct observation in field monitoring. -Omics advances in ecotoxicological studies not only generate new knowledge regarding mechanisms of toxicity and environmental effect, improving the relevance and immediacy of laboratory toxicological assessment, but can provide a wholly new paradigm for ecotoxicology by linking ecological models to mechanism-based, systems biology approaches.
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Affiliation(s)
- Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Pingping Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Jianghu Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Donald J Baird
- Environment & Climate Change Canada @ Canadian Rivers Institute, Department of Biology , University of New Brunswick , Fredericton , New Brunswick E3B 5A3 , Canada
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Martyniuk CJ. Are we closer to the vision? A proposed framework for incorporating omics into environmental assessments. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2018; 59:87-93. [PMID: 29549817 DOI: 10.1016/j.etap.2018.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/04/2018] [Indexed: 06/08/2023]
Abstract
Environmental science has benefited a great deal from omics-based technologies. High-throughput toxicology has defined adverse outcome pathways (AOPs), prioritized chemicals of concern, and identified novel actions of environmental chemicals. While many of these approaches are conducted under rigorous laboratory conditions, a significant challenge has been the interpretation of omics data in "real-world" exposure scenarios. Clarity in the interpretation of these data limits their use in environmental monitoring programs. In recent years, one overarching objective of many has been to address fundamental questions concerning experimental design and the robustness of data collected under the broad umbrella of environmental genomics. These questions include: (1) the likelihood that molecular profiles return to a predefined baseline level following remediation efforts, (2) how reference site selection in an urban environment influences interpretation of omics data and (3) what is the most appropriate species to monitor in the environment from an omics point of view. In addition, inter-genomics studies have been conducted to assess transcriptome reproducibility in toxicology studies. One lesson learned from inter-genomics studies is that there are core molecular networks that can be identified by multiple laboratories using the same platform. This supports the idea that "omics-networks" defined a priori may be a viable approach moving forward for evaluating environmental impacts over time. Both spatial and temporal variability in ecosystem structure is expected to influence molecular responses to environmental stressors, and it is important to recognize how these variables, as well as individual factor (i.e. sex, age, maturation), may confound interpretation of network responses to chemicals. This mini-review synthesizes the progress made towards adopting these tools into environmental monitoring and identifies future challenges to be addressed, as we move into the next era of high throughput sequencing. A conceptual framework for validating and incorporating molecular networks into environmental monitoring programs is proposed. As AOPs become more defined and their potential in environmental monitoring assessments becomes more recognized, the AOP framework may prove to be the conduit between omics and penultimate ecological responses for environmental risk assessments.
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Affiliation(s)
- Christopher J Martyniuk
- Canadian Rivers Institute and the Center for Environmental and Human Toxicology, Department of Physiological Sciences, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611 USA.
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Schüttler A, Reiche K, Altenburger R, Busch W. The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis. Toxicol Sci 2018; 157:291-304. [PMID: 28329862 PMCID: PMC5443304 DOI: 10.1093/toxsci/kfx045] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Numerous studies have been published in the past years investigating the transcriptome of the zebrafish embryo (ZFE) upon being subjected to chemical stress. Aiming at a more mechanistic understanding of the results of such studies, knowledge about commonalities of transcript regulation in response to chemical stress is needed. Thus, our goal in this study was to identify and interpret genes and gene sets constituting a general response to chemical exposure. Therefore, we aggregated and reanalyzed published toxicogenomics data obtained with the ZFE. We found that overlap of differentially transcribed genes in response to chemical stress across independent studies is generally low and the most commonly differentially transcribed genes appear in less than 50% of all treatments across studies. However, effect size analysis revealed several genes showing a common trend of differential expression, among which genes related to calcium homeostasis emerged as key, especially in exposure settings up to 24 h post-fertilization. Additionally, we found that these and other downregulated genes are often linked to anatomical regions developing during the respective exposure period. Genes showing a trend of increased expression were, among others, linked to signaling pathways (e.g., Wnt, Fgf) as well as lysosomal structures and apoptosis. The findings of this study help to increase the understanding of chemical stress responses in the developing zebrafish embryo and provide a starting point to improve experimental designs for this model system. In future, improved time- and concentration-resolved experiments should offer better understanding of stress response patterns and access to mechanistic information.
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Affiliation(s)
- Andreas Schüttler
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraβe 15, Leipig, Germany.,Institute for Environmental Research, RWTH Aachen, Worringerweg 1, Aachen, Germany
| | - Kristin Reiche
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraβe 15, Leipig, Germany.,Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraβe 1, Leipzig, Germany
| | - Rolf Altenburger
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraβe 15, Leipig, Germany.,Institute for Environmental Research, RWTH Aachen, Worringerweg 1, Aachen, Germany
| | - Wibke Busch
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, Leipig, Germany
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Huang C, Wang R, Zeng G, Huang D, Lai C, Zhang J, Xiao Z, Wan J, Xu P, Gong X, Xue W, Ren X. Transcriptome analysis reveals novel insights into the response to Pb exposure in Phanerochaete chrysosporium. CHEMOSPHERE 2018; 194:657-665. [PMID: 29245132 DOI: 10.1016/j.chemosphere.2017.12.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/30/2017] [Accepted: 12/08/2017] [Indexed: 06/07/2023]
Abstract
Metals released into the environment continue to be of concern for human health. Using white-rot fungi as biosorbents for heavy metals removal is an attractive alternative owing to its good performance and low cost. However, the molecular mechanism underlying heavy metal tolerance in white-rot fungi has not yet been fully elucidated. This study identified and analyzed the lead (Pb)-induced transcriptional changes in Phanerochaete chrysosporium, a well-known heavy metal hyperaccumulating white-rot fungus. The results confirmed its outstanding ability in Pb tolerance and effective defense system. By comparative analysis of gene expression profiles obtained from cDNA-amplified fragment length polymorphism (cDNA-AFLP), we isolated 43 transcript-derived fragments (TDFs) differentially regulated by Pb exposure in P. chrysosporium, and 23 TDFs presented significant similarities to genes encoding known or putative proteins which belong to different functional categories involving ion binding, energy and carbohydrate metabolism, and signal transduction. The detailed characterization of these Pb-responsive genes was presented and the expression patterns of some interesting genes were validated by quantitative RT-PCR. This work provides the first evidence of Pb-responsive genes along with their putatively functional annotations in P. chrysosporium, which may help to understand the mechanism underlying heavy metal accumulation and tolerance in P. chrysosporium.
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Affiliation(s)
- Chao Huang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Rongzhong Wang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Danlian Huang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Cui Lai
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, PR China
| | - Zhihua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, PR China
| | - Jia Wan
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Piao Xu
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xiaomin Gong
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Wenjing Xue
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xiaoya Ren
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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Revel M, Châtel A, Mouneyrac C. Omics tools: New challenges in aquatic nanotoxicology? AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 193:72-85. [PMID: 29049925 DOI: 10.1016/j.aquatox.2017.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 10/05/2017] [Accepted: 10/10/2017] [Indexed: 05/04/2023]
Abstract
In recent years, the implication of genomics into ecotoxicological studies has been studied closely to allow a better understanding of organism's responses to environmental contaminants including engineering nanomaterials (ENMs). ENMs are increasingly produced for various applications including cosmetics, electronics, sports equipment, biomedicine and agriculture. Because of their small size, ENMs possess chemical or physical characteristics improved compared to the corresponding macro-sized material. As their application expend, the release of manufactured ENMs into the environment is likely to increase and concern over impacts for the aquatic ecosystem is growing. Several studies reported deleterious effect of ENMs to aquatic organisms, but there is little information about the molecular mechanisms of toxicity. The development of ecotoxicogenomic approaches will improve the characterization of cellular and molecular modes of action of ENMs to aquatic organisms and allow a better prediction of contaminants toxicity. This paper presents an overview of transciptomic/proteomic studies in freshwater and marine organisms exposed to ENMs. Overall, induction of gene expression in relations to defense mechanisms, immune responses, growth and reproduction were measured after ENMs exposures of organisms, but with different patterns depending on exposure duration and concentrations used. In addition, some studies reported a positive correlation between gene expression and cellular modifications, but not at the individual level.
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Affiliation(s)
- Messika Revel
- Laboratoire Mer, Molécules, Santé (MMS, EA 2160), Université Catholique de l'Ouest, Angers F-49000, France.
| | - Amélie Châtel
- Laboratoire Mer, Molécules, Santé (MMS, EA 2160), Université Catholique de l'Ouest, Angers F-49000, France.
| | - Catherine Mouneyrac
- Laboratoire Mer, Molécules, Santé (MMS, EA 2160), Université Catholique de l'Ouest, Angers F-49000, France.
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7
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Feswick A, Munkittrick KR, Martyniuk CJ. Estrogen-responsive gene networks in the teleost liver: What are the key molecular indicators? ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2017; 56:366-374. [PMID: 29126055 DOI: 10.1016/j.etap.2017.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 10/28/2017] [Indexed: 06/07/2023]
Abstract
An overarching goal of environmental genomics is to leverage sensitive suites of markers that are robust and reliable to assess biological responses in a range of species inhabiting variable environments. The objective of this study was to identify core groups of transcripts and molecular signaling pathways that respond to 17alpha-ethylinestadiol (EE2), a ubiquitous estrogenic contaminant, using transcriptome datasets generated from six independent laboratories. We sought to determine which biomarkers and gene networks were those most robust and reliably detected in multiple laboratories. Six laboratories conducted microarray analysis in pieces of the same liver from male fathead minnows exposed to ∼15ng/L EE2 for 96h. There were common transcriptional networks identified in every dataset. These included down-regulation of gene networks associated with blood clotting, complement activation, triglyceride storage, and xenobiotic metabolism. Noteworthy was that more than ∼85% of the gene networks were suppressed by EE2. Leveraging both these data and those mined from the Comparative Toxicogenomics Database (CTD), we narrowed in on an EE2-responsive transcriptional network. All transcripts in this network responded ∼±5-fold or more to EE2, increasing reliability of detection. This network included estrogen receptor alpha, transferrin, myeloid cell leukemia 1, insulin like growth factor 1, insulin like growth factor binding protein 2, and methionine adenosyltransferase 2A. This estrogen-responsive interactome has the advantage over single markers (e.g. vitellogenin) in that these entities are directly connected to each other based upon evidence of expression regulation and protein binding. Thus, it represents an interacting functional suite of estrogenic markers. Vitellogenin, the gold standard for estrogenic exposures, can show high individual variability in its response to estrogens, and the use of a multi-gene approach for estrogenic chemicals is expected to improve sensitivity. In our case, the coefficient of variation was significantly lowered by the gene network (∼67%) compared to Vtg alone, supporting the use of this transcriptional network as a sensitive alternative for detecting estrogenic effluents and chemicals. We propose that screening chemicals for estrogenicity using interacting genes within a defined expression network will improve sensitivity, accuracy, and reduce the number of animals required for endocrine disruption assessments.
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Affiliation(s)
- April Feswick
- Department of Biology, University of New Brunswick, Saint John, New Brunswick E2L 4L5, Canada
| | - Kelly R Munkittrick
- Executive Director of Cold Regions and Water Initiatives, Wilfred Laurier University
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA; Department of Biology, University of New Brunswick, Saint John, New Brunswick E2L 4L5, Canada.
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8
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Feswick A, Isaacs M, Biales A, Flick RW, Bencic DC, Wang RL, Vulpe C, Brown-Augustine M, Loguinov A, Falciani F, Antczak P, Herbert J, Brown L, Denslow ND, Kroll KJ, Lavelle C, Dang V, Escalon L, Garcia-Reyero N, Martyniuk CJ, Munkittrick KR. How consistent are we? Interlaboratory comparison study in fathead minnows using the model estrogen 17α-ethinylestradiol to develop recommendations for environmental transcriptomics. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2017; 36:2614-2623. [PMID: 28316117 PMCID: PMC6145073 DOI: 10.1002/etc.3799] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/27/2016] [Accepted: 03/17/2017] [Indexed: 05/26/2023]
Abstract
Fundamental questions remain about the application of omics in environmental risk assessments, such as the consistency of data across laboratories. The objective of the present study was to determine the congruence of transcript data across 6 independent laboratories. Male fathead minnows were exposed to a measured concentration of 15.8 ng/L 17α-ethinylestradiol (EE2) for 96 h. Livers were divided equally and sent to the participating laboratories for transcriptomic analysis using the same fathead minnow microarray. Each laboratory was free to apply bioinformatics pipelines of its choice. There were 12 491 transcripts that were identified by one or more of the laboratories as responsive to EE2. Of these, 587 transcripts (4.7%) were detected by all laboratories. Mean overlap for differentially expressed genes among laboratories was approximately 50%, which improved to approximately 59.0% using a standardized analysis pipeline. The dynamic range of fold change estimates was variable between laboratories, but ranking transcripts by their relative fold difference resulted in a positive relationship for comparisons between any 2 laboratories (mean R2 > 0.9, p < 0.001). Ten estrogen-responsive genes encompassing a fold change range from dramatic (>20-fold; e.g., vitellogenin) to subtle (∼2-fold; i.e., block of proliferation 1) were identified as differentially expressed, suggesting that laboratories can consistently identify transcripts that are known a priori to be perturbed by a chemical stressor. Thus, attention should turn toward identifying core transcriptional networks using focused arrays for specific chemicals. In addition, agreed-on bioinformatics pipelines and the ranking of genes based on fold change (as opposed to p value) should be considered in environmental risk assessment. These recommendations are expected to improve comparisons across laboratories and advance the use of omics in regulations. Environ Toxicol Chem 2017;36:2593-2601. © 2017 SETAC.
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Affiliation(s)
- April Feswick
- Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Meghan Isaacs
- Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Adam Biales
- Molecular Indicators Research Branch, National Exposure Research Laboratory, Cincinnati, Ohio, USA
| | - Robert W Flick
- Molecular Indicators Research Branch, National Exposure Research Laboratory, Cincinnati, Ohio, USA
| | - David C Bencic
- Molecular Indicators Research Branch, National Exposure Research Laboratory, Cincinnati, Ohio, USA
| | - Rong-Lin Wang
- Molecular Indicators Research Branch, National Exposure Research Laboratory, Cincinnati, Ohio, USA
| | - Chris Vulpe
- Department of Nutritional Science and Toxicology, University of California-Berkeley, Berkeley, California, USA
| | - Marianna Brown-Augustine
- Department of Nutritional Science and Toxicology, University of California-Berkeley, Berkeley, California, USA
| | - Alex Loguinov
- Department of Nutritional Science and Toxicology, University of California-Berkeley, Berkeley, California, USA
| | - Francesco Falciani
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Philipp Antczak
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - John Herbert
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Lorraine Brown
- Pacific Environmental Science Centre, North Vancouver, British Columbia, Canada
| | - Nancy D Denslow
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Kevin J Kroll
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Candice Lavelle
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Viet Dang
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Lynn Escalon
- US Army Engineer Research & Development Center, Vicksburg, Mississippi
| | - Natàlia Garcia-Reyero
- US Army Engineer Research & Development Center, Vicksburg, Mississippi
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, Mississippi, USA
| | - Christopher J Martyniuk
- Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Kelly R Munkittrick
- Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
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Oziolor EM, Bickham JW, Matson CW. Evolutionary toxicology in an omics world. Evol Appl 2017; 10:752-761. [PMID: 29151868 PMCID: PMC5680431 DOI: 10.1111/eva.12462] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
Evolutionary toxicology is a young field that has grown rapidly in the past two decades. The potential of this field comes from the ability to link chemical contamination to multigenerational and population-wide effects in various species. The advancements and rapidly decreasing costs of -omic tools are improving the power and resolution of evolutionary toxicology studies. In this manuscript, we aim to address the trajectories and perspectives for conducting evolutionary toxicology studies with -omic approaches. We discuss the complementarity of using multiple -omic tools (genomics, eDNA, transcriptomics, proteomics, and metabolomics) for utility in understanding the toxicological relevance of adaptive responses in populations. In addition, we discuss phenotypic plasticity and its relevance to transcriptomic studies in toxicology. As evolutionary toxicology grows and expands its capacity to link toxicology with population-wide end points, we emphasize the applications of such studies in answering questions about ecological and population health, as well as future applicability to regulation. Thus, we aim to emphasize the enormous potential for evolutionary toxicology in an -omics world and give perspectives on the directions of future investigations.
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Affiliation(s)
- Elias M Oziolor
- Department of Environmental Science Center for Reservoir and Aquatic Systems Research (CRASR), and the Institute for Biomedical Studies Baylor University Waco TX USA
| | - John W Bickham
- Department of Wildlife and Fisheries Science Texas A&M University College Station TX USA
| | - Cole W Matson
- Department of Environmental Science Center for Reservoir and Aquatic Systems Research (CRASR), and the Institute for Biomedical Studies Baylor University Waco TX USA
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10
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Escher BI, Hackermüller J, Polte T, Scholz S, Aigner A, Altenburger R, Böhme A, Bopp SK, Brack W, Busch W, Chadeau-Hyam M, Covaci A, Eisenträger A, Galligan JJ, Garcia-Reyero N, Hartung T, Hein M, Herberth G, Jahnke A, Kleinjans J, Klüver N, Krauss M, Lamoree M, Lehmann I, Luckenbach T, Miller GW, Müller A, Phillips DH, Reemtsma T, Rolle-Kampczyk U, Schüürmann G, Schwikowski B, Tan YM, Trump S, Walter-Rohde S, Wambaugh JF. From the exposome to mechanistic understanding of chemical-induced adverse effects. ENVIRONMENT INTERNATIONAL 2017; 99:97-106. [PMID: 27939949 PMCID: PMC6116522 DOI: 10.1016/j.envint.2016.11.029] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/27/2016] [Accepted: 11/29/2016] [Indexed: 05/17/2023]
Abstract
The exposome encompasses an individual's exposure to exogenous chemicals, as well as endogenous chemicals that are produced or altered in response to external stressors. While the exposome concept has been established for human health, its principles can be extended to include broader ecological issues. The assessment of exposure is tightly interlinked with hazard assessment. Here, we explore if mechanistic understanding of the causal links between exposure and adverse effects on human health and the environment can be improved by integrating the exposome approach with the adverse outcome pathway (AOP) concept that structures and organizes the sequence of biological events from an initial molecular interaction of a chemical with a biological target to an adverse outcome. Complementing exposome research with the AOP concept may facilitate a mechanistic understanding of stress-induced adverse effects, examine the relative contributions from various components of the exposome, determine the primary risk drivers in complex mixtures, and promote an integrative assessment of chemical risks for both human and environmental health.
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Affiliation(s)
- Beate I Escher
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany.
| | - Jörg Hackermüller
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Tobias Polte
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Stefan Scholz
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Achim Aigner
- Leipzig University, Rudolf Boehm Institute for Pharmacology & Toxicology, Clinical Pharmacology, Haertelstr. 16-18, 04107 Leipzig, Germany
| | - Rolf Altenburger
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Alexander Böhme
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Stephanie K Bopp
- European Commission Joint Research Centre, Directorate F - Health, Consumers and Reference Materials, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Werner Brack
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Wibke Busch
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Marc Chadeau-Hyam
- University London, Imperial College, Department Epidemiology & Biostatistics, School of Public Health, St Marys Campus, Norfolk Place, London W2 1PG, England, United Kingdom
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk-Antwerp, Belgium
| | | | - James J Galligan
- Vanderbilt University, School of Medicine, A.B. Hancock Jr. Memorial Laboratory for Cancer Research, Department Biochemistry, Nashville, TN 37232, USA
| | - Natalia Garcia-Reyero
- US Army Engineer Research & Development Center, Vicksburg, MS, USA; Mississippi State University, Starkville, MS, USA
| | - Thomas Hartung
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA; University of Konstanz, Germany
| | - Michaela Hein
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Gunda Herberth
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Annika Jahnke
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Jos Kleinjans
- Maastricht University, Department Toxicogenomics, 6200 MD Maastricht, The Netherlands
| | - Nils Klüver
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Martin Krauss
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Marja Lamoree
- Vrije Universiteit, Faculty of Earth & Life Sciences, Institute for Environmental Studies, 1081 HV Amsterdam, The Netherlands
| | - Irina Lehmann
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Till Luckenbach
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Gary W Miller
- Dept of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Andrea Müller
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - David H Phillips
- King's College London, MRC-PHE Centre for Environment & Health, Analytical & Environmental Sciences Division, London SE1 9NH, England, United Kingdom
| | - Thorsten Reemtsma
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Gerrit Schüürmann
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany; Technical University Bergakademie Freiberg, Institute for Organic Chemistry, 09596 Freiberg, Germany
| | | | - Yu-Mei Tan
- US EPA, National Exposure Research Laboratory, Research Triangle Park, NC 27711, USA
| | - Saskia Trump
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | | | - John F Wambaugh
- US EPA, National Center for Computational Toxicology, Research Triangle Park, NC 27711, USA
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Martyniuk CJ, Simmons DB. Spotlight on environmental omics and toxicology: a long way in a short time. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 19:97-101. [PMID: 27398986 DOI: 10.1016/j.cbd.2016.06.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 06/17/2016] [Accepted: 06/23/2016] [Indexed: 01/08/2023]
Abstract
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.
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Affiliation(s)
- Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Denina B Simmons
- Water Science and Technology, Environment and Climate Change Canada, Burlington, ON, Canada
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