Toxicology Advances for 21st Century Chemical Pollution

Brooks, Bryan W.; Sabo‐Attwood, Tara; Choi, Kyungho; Kim, Sujin; Kostal, Jakub; LaLone, Carlie A.; Langan, Laura M.; Margiotta-Casaluci, Luigi; You, Jing; Zhang, Xiaowei

doi:10.1016/j.oneear.2020.04.007

Cited by 48 publications

(38 citation statements)

References 17 publications

(21 reference statements)

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“…Traditionally, studying single molecular biomarkers of exposure has proven very useful in toxicological studies 69 , 94 . Now, the recent advances in omics technologies enable a more holistic view of toxicological responses, including gene set enrichment analysis and pathway analysis approaches 95 – 98 . However, these analyses can be challenging when working with less studied and annotated species, such as marine teleosts.…”

Section: Summary and Perspectivesmentioning

confidence: 99%

The chemical defensome of five model teleost fish

Eide

Zhang

Karlsen

et al. 2021

Sci Rep

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How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Teleost fish is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes. We have previously shown that the xenosensing pregnane x receptor (pxr, nr1i2) is lost in many teleost species, including Atlantic cod (Gadus morhua) and three-spined stickleback (Gasterosteus aculeatus), but it is not known if compensatory mechanisms or signaling pathways have evolved in its absence. In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafish (Danio rerio), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus), Atlantic cod, and three-spined stickleback. Genome mining revealed evolved differences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants, but we did not observe any candidates of compensatory mechanisms or pathways in cod and stickleback in the absence of pxr. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies.

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Section: Summary and Perspectivesmentioning

confidence: 99%

The chemical defensome of five model teleost fish

Eide

Zhang

Karlsen

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Traditionally, studying single molecular biomarkers of exposure has proven very useful in toxicological studies 67,91 . Now, the recent advances in omics technologies enable a more holistic view of toxicological responses, including gene set enrichment analysis and pathway analysis approaches [92][93][94][95] . However, these analyses can be challenging when working with less studied and annotated species, such as marine teleosts.…”

Section: Summary and Perspectivesmentioning

confidence: 99%

The Chemical Defensome of Fish: Conservation and Divergence of Genes Involved in Sensing and Responding to Pollutants Among Five Model Teleosts

Eide

Zhang

Karlsen

et al. 2021

Preprint

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How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Although the types of defensome genes are generally conserved in animals, there are important differences in the complement and function of specific genes between species. Teleost fish is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes.In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafish (Danio rerio), Atlantic cod (Gadus morhua), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus) and three-spined stickleback (Gasterosteus aculeatus). Genome miningrevealed evolved differences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies.

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“…Although biomarkers mostly refer to physiological or physical phenotypes, at the molecular level, a biomarker can indicate diseaseassociated molecular changes and may be useful in disease diagnosis (1,2), various infections (3), neurological diseases (4), and for defining therapeutic targets (3). In toxicological studies, biomarkers are often used to define a set of differentially expressed genes or proteins in a toxic exposure or chemical risk assessment study (5)(6)(7)(8)(9)(10)(11). Data from various omics techniques, including transcriptomics, proteomics, and metabolomics, as well as epigenomics, are useful starting points for a biomarker discovery study (10,(12)(13)(14)(15).…”

Section: Introductionmentioning

confidence: 99%

“…In toxicological studies, biomarkers are often used to define a set of differentially expressed genes or proteins in a toxic exposure or chemical risk assessment study (5)(6)(7)(8)(9)(10)(11). Data from various omics techniques, including transcriptomics, proteomics, and metabolomics, as well as epigenomics, are useful starting points for a biomarker discovery study (10,(12)(13)(14)(15). In this chapter, we focus on the informative genes that can generally be used to distinguish samples from different groups, which can be normal or tumor tissues from human patients or tissues of animals that are exposed to toxic chemicals and their solvent controls, using gene expression data.…”

Section: Introductionmentioning

confidence: 99%

Machine Learning Approaches for Biomarker Discovery Using Gene Expression Data

2021

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Biomarkers are of great importance in many fields, such as cancer research, toxicology, diagnosis and treatment of diseases, and to better understand biological response mechanisms to internal or external intervention. Highthroughput gene expression profiling technologies, such as DNA microarrays and RNA sequencing, provide large gene expression data sets which enable datadriven biomarker discovery. Traditional statistical tests have been the mainstream for identifying differentially expressed genes as biomarkers. In recent years, machine learning techniques such as feature selection have gained more popularity. Given many options, picking the most appropriate method for a particular data becomes essential. Different evaluation metrics have therefore been proposed. Being evaluated on different aspects, a method' s varied performance across different datasets leads to the idea of integrating multiple methods. Many integration strategies are proposed and have shown great potential. This chapter gives an overview of the current research advances and existing issues in biomarker discovery using machine learning approaches on gene expression data.

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Toxicology Advances for 21st Century Chemical Pollution

Cited by 48 publications

References 17 publications

The chemical defensome of five model teleost fish

The chemical defensome of five model teleost fish

The Chemical Defensome of Fish: Conservation and Divergence of Genes Involved in Sensing and Responding to Pollutants Among Five Model Teleosts

Machine Learning Approaches for Biomarker Discovery Using Gene Expression Data

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