Coupling Environmental Whole Mixture Toxicity Screening with Unbiased RNA-Seq Reveals Site-Specific Biological Responses in Zebrafish
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chemicals
2.2. Sampling Methods
2.3. Chemical Analysis
2.4. Zebrafish Rearing, Exposure, and Morphological Assessment
2.5. RNA Isolation
2.6. Sequencing Data Pipeline
2.7. RNA-Seq Analysis
3. Results and Discussion
3.1. Chemical Characterization of PSD Extracts: Parallel PAH Contamination, Divergent Qualitative Screen
3.2. Developmental Toxicity: RM 6.5W Was More Toxic Than RM 7W
3.3. RNA-Seq: Direct Comparison of PHSS Extract Responses
3.3.1. RM 6.5W Elicits a More Robust Gene Expression Response than RM 7W
3.3.2. Distinct Themes Underly the Transcriptional Response to PHSS Extract Exposures
3.3.3. Xenobiotic Metabolism Glutathione Processes Are among the Expected GO Network Clusters
3.3.4. Visual System Development and Muscle Fiber Related Genes Are Disrupted
3.4. RNA-Seq: Comparison of Mixtures to Individual PAH and OPAH Exposure Responses
3.4.1. Principal Analysis Indicates AHR as Second Strongest Determinants of Variation
3.4.2. Differential Expression Heatmap Contains AHR Transcription and OPAH Related Clusters Yet PHSS Extract Exposure Remains Distinct
3.4.3. There Is Significant Overlap between Individual Constituent and Mixture GO Terms but Muscle Fiber Related Genes Are without a Match
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
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Detection | ||
---|---|---|
Chemical | RM 7W | RM 6.5W |
o,p’-DDD | X | X |
p,p’-DDE | X | X |
Hexachlorobenzene | X | X |
PCB65 | X | |
PCB118X | X | |
Tonalide | X | |
Benzoflourenone | X | |
benzanthrone | X |
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Rude, C.I.; Tidwell, L.G.; Tilton, S.C.; Waters, K.M.; Anderson, K.A.; Tanguay, R.L. Coupling Environmental Whole Mixture Toxicity Screening with Unbiased RNA-Seq Reveals Site-Specific Biological Responses in Zebrafish. Toxics 2023, 11, 201. https://doi.org/10.3390/toxics11030201
Rude CI, Tidwell LG, Tilton SC, Waters KM, Anderson KA, Tanguay RL. Coupling Environmental Whole Mixture Toxicity Screening with Unbiased RNA-Seq Reveals Site-Specific Biological Responses in Zebrafish. Toxics. 2023; 11(3):201. https://doi.org/10.3390/toxics11030201
Chicago/Turabian StyleRude, Christian I., Lane G. Tidwell, Susan C. Tilton, Katrina M. Waters, Kim A. Anderson, and Robyn L. Tanguay. 2023. "Coupling Environmental Whole Mixture Toxicity Screening with Unbiased RNA-Seq Reveals Site-Specific Biological Responses in Zebrafish" Toxics 11, no. 3: 201. https://doi.org/10.3390/toxics11030201
APA StyleRude, C. I., Tidwell, L. G., Tilton, S. C., Waters, K. M., Anderson, K. A., & Tanguay, R. L. (2023). Coupling Environmental Whole Mixture Toxicity Screening with Unbiased RNA-Seq Reveals Site-Specific Biological Responses in Zebrafish. Toxics, 11(3), 201. https://doi.org/10.3390/toxics11030201