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Vijayakumar S, Yesudhason BV, Anandharaj JL, Sathyaraj WV, Selvan Christyraj JRS. Impact of double-strand breaks induced by uv radiation on neuroinflammation and neurodegenerative disorders. Mol Biol Rep 2024; 51:725. [PMID: 38851636 DOI: 10.1007/s11033-024-09693-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
Exposure to UV affects the development and growth of a wide range of organisms. Nowadays, researchers are focusing on the impact of UV radiation and its underlying molecular mechanisms, as well as devising strategies to mitigate its harmful effects. Different forms of UV radiation, their typical exposure effects, the impact of UV on DNA integrity, and the deterioration of genetic material are discussed in this review; furthermore, we also review the effects of UV radiation that affect the biological functions of the organisms. Subsequently, we address the processes that aid organisms in navigating the damage in genetic material, neuroinflammation, and neurodegeneration brought on by UV-mediated double-strand breaks. To emphasize the molecular pathways, we conclude the review by going over the animal model studies that highlight the genes and proteins that are impacted by UV radiation.
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Affiliation(s)
- Srilakshmi Vijayakumar
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Beryl Vedha Yesudhason
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India.
| | - Jenif Leo Anandharaj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Weslen Vedakumari Sathyaraj
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamilnadu, India
| | - Johnson Retnaraj Samuel Selvan Christyraj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India.
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2
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McClure RS, Rericha Y, Waters KM, Tanguay RL. 3' RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism. FRONTIERS IN BIOINFORMATICS 2023; 3:1234218. [PMID: 37576716 PMCID: PMC10414111 DOI: 10.3389/fbinf.2023.1234218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction: The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Methods and results: Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. Conclusions: These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.
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Affiliation(s)
- Ryan S. McClure
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
| | - Yvonne Rericha
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
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Schwartz AV, Sant KE, George UZ. Development of a Dynamic Network Model to Identify Temporal Patterns of Structural Malformations in Zebrafish Embryos Exposed to a Model Toxicant, Tris(4-chlorophenyl)methanol. J Xenobiot 2023; 13:284-297. [PMID: 37367497 DOI: 10.3390/jox13020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Embryogenesis is a well-coordinated process relying on precise cues and environmental signals that direct spatiotemporal embryonic patterning. Quite often, when one error in this process occurs, others tend to co-occur. We posit that investigating the co-occurrence of these abnormalities over time would yield additional information about the mode of toxicity for chemicals. Here, we use the environmental contaminant tris(4-chlorophenyl)methanol (TCPMOH) as a model toxicant to assess the relationship between exposures and co-occurrence of developmental abnormalities in zebrafish embryos. We propose a dynamic network modeling approach to study the co-occurrence of abnormalities, including pericardial edema, yolk sac edema, cranial malformation, spinal deformity, delayed/failed swim bladder inflation, and mortality induced by TCPMOH exposure. TCPMOH-exposed samples revealed increased abnormality co-occurrence when compared to controls. The abnormalities were represented as nodes in the dynamic network model. Abnormalities with high co-occurrence over time were identified using network centrality scores. We found that the temporal patterns of abnormality co-occurrence varied between exposure groups. In particular, the high TCPMOH exposure group experienced abnormality co-occurrence earlier than the low exposure group. The network model also revealed that pericardial and yolk sac edema are the most common critical nodes among all TCPMOH exposure levels, preceding further abnormalities. Overall, this study introduces a dynamic network model as a tool for assessing developmental toxicology, integrating structural and temporal features with a concentration response.
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Affiliation(s)
- Ashley V Schwartz
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
| | - Karilyn E Sant
- School of Public Health, Division of Environmental Health, San Diego State University, San Diego, CA 92182, USA
| | - Uduak Z George
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
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Guillotin S, Delcourt N. Studying the Impact of Persistent Organic Pollutants Exposure on Human Health by Proteomic Analysis: A Systematic Review. Int J Mol Sci 2022; 23:ijms232214271. [PMID: 36430748 PMCID: PMC9692675 DOI: 10.3390/ijms232214271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Persistent organic pollutants (POPs) are organic chemical substances that are widely distributed in environments around the globe. POPs accumulate in living organisms and are found at high concentrations in the food chain. Humans are thus continuously exposed to these chemical substances, in which they exert hepatic, reproductive, developmental, behavioral, neurologic, endocrine, cardiovascular, and immunologic adverse health effects. However, considerable information is unknown regarding the mechanism by which POPs exert their adverse effects in humans, as well as the molecular and cellular responses involved. Data are notably lacking concerning the consequences of acute and chronic POP exposure on changes in gene expression, protein profile, and metabolic pathways. We conducted a systematic review to provide a synthesis of knowledge of POPs arising from proteomics-based research. The data source used for this review was PubMed. This study was carried out following the PRISMA guidelines. Of the 742 items originally identified, 89 were considered in the review. This review presents a comprehensive overview of the most recent research and available solutions to explore proteomics datasets to identify new features relevant to human health. Future perspectives in proteomics studies are discussed.
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Affiliation(s)
- Sophie Guillotin
- Poison Control Centre, Toulouse University Hospital, 31059 Toulouse, France
- INSERM UMR 1295, Centre d’Epidémiologie et de Recherche en Santé des Populations, 31000 Toulouse, France
| | - Nicolas Delcourt
- Poison Control Centre, Toulouse University Hospital, 31059 Toulouse, France
- INSERM UMR 1214, Toulouse NeuroImaging Center, 31024 Toulouse, France
- Correspondence: ; Tel.: +33-(0)-567691640
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Wilson LB, McClure RS, Waters KM, Simonich MT, Tanguay RL. Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene. FRONTIERS IN TOXICOLOGY 2022; 4:950503. [PMID: 36093370 PMCID: PMC9453431 DOI: 10.3389/ftox.2022.950503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants and are associated with human disease. Canonically, many PAHs induce toxicity via activation of the aryl hydrocarbon receptor (AHR) pathway. While the interaction between PAHs and the AHR is well-established, understanding which AHR-regulated transcriptional effects directly result in observable phenotypes and which are adaptive or benign is important to better understand PAH toxicity. Retene is a frequently detected PAH in environmental sampling and has been associated with AHR2-dependent developmental toxicity in zebrafish, though its mechanism of toxicity has not been fully elucidated. To interrogate transcriptional changes causally associated with retene toxicity, we conducted whole-animal RNA sequencing at 48 h post-fertilization after exposure to eight retene concentrations. We aimed to identify the most sensitive transcriptomic responses and to determine whether this approach could uncover gene sets uniquely differentially expressed at concentrations which induce a phenotype. We identified a concentration-response relationship for differential gene expression in both number of differentially expressed genes (DEGs) and magnitude of expression change. Elevated expression of cyp1a at retene concentrations below the threshold for teratogenicity suggested that while cyp1a expression is a sensitive biomarker of AHR activation, it may be too sensitive to serve as a biomarker of teratogenicity. Genes differentially expressed at only non-teratogenic concentrations were enriched for transforming growth factor-β (TGF-β) signaling pathway disruption while DEGs identified at only teratogenic concentrations were significantly enriched for response to xenobiotic stimulus and reduction-oxidation reaction activity. DEGs which spanned both non-teratogenic and teratogenic concentrations showed similar disrupted biological processes to those unique to teratogenic concentrations, indicating these processes were disrupted at low exposure concentrations. Gene co-expression network analysis identified several gene modules, including those associated with PAHs and AHR2 activation. One, Module 7, was strongly enriched for AHR2-associated genes and contained the strongest responses to retene. Benchmark concentration (BMC) of Module seven genes identified a median BMC of 7.5 µM, nearly the highest retene concentration with no associated teratogenicity, supporting the hypothesis that Module seven genes are largely responsible for retene toxicity.
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Affiliation(s)
- Lindsay B. Wilson
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
| | - Ryan S. McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Katrina M. Waters
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Michael T. Simonich
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
- *Correspondence: Robyn L. Tanguay,
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6
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Shankar P, Garcia GR, LaDu JK, Sullivan CM, Dunham CL, Goodale BC, Waters KM, Stanisheuski S, Maier CS, Thunga P, Reif DM, Tanguay RL. The Ahr2-Dependent wfikkn1 Gene Influences Zebrafish Transcriptome, Proteome, and Behavior. Toxicol Sci 2022; 187:325-344. [PMID: 35377459 DOI: 10.1093/toxsci/kfac037] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is required for vertebrate development and is also activated by exogenous chemicals, including polycyclic aromatic hydrocarbons (PAHs) and TCDD. AHR activation is well-understood, but roles of downstream molecular signaling events are largely unknown. From previous transcriptomics in 48-hours post fertilization (hpf) zebrafish exposed to several PAHs and TCDD, we found wfikkn1 was highly co-expressed with cyp1a (marker for AHR activation). Thus, we hypothesized wfikkn1's role in AHR signaling, and showed that wfikkn1 expression was Ahr2 (zebrafish ortholog of human AHR)-dependent in developing zebrafish exposed to TCDD. To functionally characterize wfikkn1, we made a CRISPR-Cas9 mutant line with a 16-bp deletion in wfikkn1's exon, and exposed wildtype and mutants to DMSO or TCDD. 48-hpf mRNA sequencing revealed over 700 genes that were differentially expressed (p < 0.05, log2FC > 1) between each pair of treatment combinations, suggesting an important role for wfikkn1 in altering both the 48-hpf transcriptome and TCDD-induced expression changes. Mass spectrometry-based proteomics of 48-hpf wildtype and mutants revealed 325 significant differentially expressed proteins. Functional enrichment demonstrated wfikkn1 was involved in skeletal muscle development and played a role in neurological pathways after TCDD exposure. Mutant zebrafish appeared morphologically normal but had significant behavior deficiencies at all life stages, and absence of Wfikkn1 did not significantly alter TCDD-induced behavior effects at all life stages. In conclusion, wfikkn1 did not appear to be significantly involved in TCDD's overt toxicity but is likely a necessary functional member of the AHR signaling cascade.
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Affiliation(s)
- Prarthana Shankar
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Gloria R Garcia
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Jane K LaDu
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Christopher M Sullivan
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Cheryl L Dunham
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Britton C Goodale
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756 USA
| | - Katrina M Waters
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331.,Biological Sciences Division, Pacific Northwest Laboratory, 902 Battelle Boulevard, Richland, P.O. Box 999, USA WA 99352
| | | | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, OR, 97330, USA
| | - Preethi Thunga
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - David M Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Robyn L Tanguay
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
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7
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Rericha Y, Cao D, Truong L, Simonich MT, Field JA, Tanguay RL. Sulfonamide functional head on short-chain perfluorinated substance drives developmental toxicity. iScience 2022; 25:103789. [PMID: 35146398 PMCID: PMC8819378 DOI: 10.1016/j.isci.2022.103789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/23/2021] [Accepted: 01/13/2022] [Indexed: 01/09/2023] Open
Abstract
Per- and polyfluoroalkyl substances (PFAS) are ubiquitously detected in environmental and biological samples and cause adverse health effects. Studies have predominately focused on long-chain PFAS, with far fewer addressing short-chain alternatives. This study leveraged embryonic zebrafish to investigate developmental toxicity of a short-chain series: perfluorobutane sulfonate (PFBS), perfluoropentanoic acid (PFPeA), perfluorobutane sulfonamide (FBSA), and 4:2 fluorotelomer sulfonic acid (4:2 FTS). Following static exposures at 8 h postfertilization (hpf) to each chemical (1-100 μM), morphological and behavioral endpoints were assessed at 24 and 120 hpf. Only FBSA induced abnormal morphology, while exposure to all chemicals caused aberrant larval behavior. RNA sequencing at 48 hpf following 47 μM exposures revealed only FBSA significantly disrupted normal gene expression. Measured tissue concentrations were FBSA > PFBS > 4:2 FTS > PFPeA. This study demonstrates functional head groups impact bioactivity and bioconcentration.
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Affiliation(s)
- Yvonne Rericha
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA.,Sinnhuber Aquatic Research Laboratory, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
| | - Dunping Cao
- Department of Chemistry, College of Science, Oregon State University, Corvallis, OR 97333, USA
| | - Lisa Truong
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA.,Sinnhuber Aquatic Research Laboratory, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
| | - Michael T Simonich
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA.,Sinnhuber Aquatic Research Laboratory, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
| | - Jennifer A Field
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
| | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA.,Sinnhuber Aquatic Research Laboratory, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
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