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Henke AN, Chilukuri S, Langan LM, Brooks BW. Reporting and reproducibility: Proteomics of fish models in environmental toxicology and ecotoxicology. Sci Total Environ 2024; 912:168455. [PMID: 37979845 DOI: 10.1016/j.scitotenv.2023.168455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Environmental toxicology and ecotoxicology research efforts are employing proteomics with fish models as New Approach Methodologies, along with in silico, in vitro and other omics techniques to elucidate hazards of toxicants and toxins. We performed a critical review of toxicology studies with fish models using proteomics and reported fundamental parameters across experimental design, sample preparation, mass spectrometry, and bioinformatics of fish, which represent alternative vertebrate models in environmental toxicology, and routinely studied animals in ecotoxicology. We observed inconsistencies in reporting and methodologies among experimental designs, sample preparations, data acquisitions and bioinformatics, which can affect reproducibility of experimental results. We identified a distinct need to develop reporting guidelines for proteomics use in environmental toxicology and ecotoxicology, increased QA/QC throughout studies, and method optimization with an emphasis on reducing inconsistencies among studies. Several recommendations are offered as logical steps to advance development and application of this emerging research area to understand chemical hazards to public health and the environment.
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Affiliation(s)
- Abigail N Henke
- Department of Biology, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA
| | | | - Laura M Langan
- Department of Environmental Science, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA.
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA.
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Abstract
Human health is determined by the interaction of our environment with the genome, epigenome, and microbiome, which shape the transcriptomic, proteomic, and metabolomic landscape of cells and tissues. Precision environmental health is an emerging field leveraging environmental and system-level ('omic) data to understand underlying environmental causes of disease, identify biomarkers of exposure and response, and develop new prevention and intervention strategies. In this article we provide real-life illustrations of the utility of precision environmental health approaches, identify current challenges in the field, and outline new opportunities to promote health through a precision environmental health framework.
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Affiliation(s)
- Andrea Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA.
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Cheryl Lyn Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
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Vitorino JD, Costa PM. After a Century of Research into Environmental Mutagens and Carcinogens, Where Do We Stand? Int J Environ Res Public Health 2023; 20:1040. [PMID: 36673796 PMCID: PMC9859577 DOI: 10.3390/ijerph20021040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Cancer is one of the longest-known human diseases, yet only in recent times have we begun to perceive that the percentage of neoplasms caused by environmental factors, lifestyle and chemicals, is likely underestimated. The first medical reports associating cancer with pollutants like tars appeared by the early 20th century, but despite initial evidence relating oncogenesis and chromosomal alterations, only after the structure of DNA had been elucidated in the 1950s have genetic disorders been fully perceived as cause. This led to a growing interest in genotoxic and mutagenic pollutants. Even though we are now familiar with a range of environmental carcinogens spanning between aromatic hydrocarbons and asbestos to radionuclides and forms of carbon nanomaterials, establishing causal networks between pollutants and cancer remains cumbersome. In most part, this is due to the complexity of toxicant matrices, unknown modes-of-action of chemicals or their mixtures, the widening array of novel pollutants plus difficulties in subtracting background effects from true aetiology of disease. Recent advances in analytical chemistry, high-throughput toxicology, next-generation sequencing, computational biology and databases that allocate whole normal and cancer genomes, all indicate that we are on the verge of a new age of research into mechanistic 'oncotoxicology', but how can it impact risk assessment and prevention?
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Affiliation(s)
| | - Pedro M. Costa
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
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Bittencourt LO, Damasceno-Silva RD, Aragão WAB, Eiró-Quirino L, Oliveira ACA, Fernandes RM, Freire MAM, Cartágenes SC, Dionizio A, Buzalaf MAR, Cassoli JS, Cirovic A, Cirovic A, Maia CDSF, Lima RR. Global Proteomic Profile of Aluminum-Induced Hippocampal Impairments in Rats: Are Low Doses of Aluminum Really Safe? Int J Mol Sci 2022; 23:ijms232012523. [PMID: 36293377 PMCID: PMC9603961 DOI: 10.3390/ijms232012523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
Hippocampus is the brain area where aluminum (Al) accumulates in abundance and is widely associated with learning and memory. In the present study, we evaluate behavioral, tissue, and proteomic changes in the hippocampus of Wistar rats caused by exposure to doses that mimic human consumption of aluminum chloride (AlCl3) in urban areas. For this, male Wistar rats were divided into two groups: Control (distilled water) and AlCl3 (8.3 mg/kg/day), both groups were exposed orally for 60 days. After the Al exposure protocol, cognitive functions were assessed by the Water maze test, followed by a collection for analysis of the global proteomic profile of the hippocampus by mass spectrometry. Aside from proteomic analysis, we performed a histological analysis of the hippocampus, to the determination of cell body density by cresyl violet staining in Cornu Ammonis fields (CA) 1 and 3, and hilus regions. Our results indicated that exposure to low doses of aluminum chloride triggered a decreased cognitive performance in learning and memory, being associated with the deregulation of proteins expression, mainly those related to the regulation of the cytoskeleton, cellular metabolism, mitochondrial activity, redox regulation, nervous system regulation, and synaptic signaling, reduced cell body density in CA1, CA3, and hilus.
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Affiliation(s)
- Leonardo Oliveira Bittencourt
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Rakhel Dayanne Damasceno-Silva
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Walessa Alana Bragança Aragão
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Luciana Eiró-Quirino
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Ana Carolina Alves Oliveira
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Rafael Monteiro Fernandes
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Marco Aurelio M. Freire
- Graduate Program in Health and Society, Faculty of Health Sciences, State University of Rio Grande do Norte (UERN), Mossoro 59610210, Brazil
| | - Sabrina Carvalho Cartágenes
- Laboratory of Pharmacology of Inflammation and Behavior, Institute of Health Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Aline Dionizio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 05508060, Brazil
| | | | - Juliana Silva Cassoli
- Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Ana Cirovic
- Faculty of Medicine, Institute of Anatomy, University of Belgrade, 11000 Belgrade, Serbia
| | - Aleksandar Cirovic
- Faculty of Medicine, Institute of Anatomy, University of Belgrade, 11000 Belgrade, Serbia
| | - Cristiane do Socorro Ferraz Maia
- Laboratory of Pharmacology of Inflammation and Behavior, Institute of Health Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Rafael Rodrigues Lima
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
- Correspondence:
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Cimbalo A, Frangiamone M, Lozano M, Escrivá L, Vila-Donat P, Manyes L. Protective role of fermented whey and pumpkin extract against aflatoxin B 1 and ochratoxin A toxicity in Jurkat T-cells. WORLD MYCOTOXIN J 2022. [DOI: 10.3920/wmj2022.2780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The beneficial effect of fermented whey and pumpkin extract rich in carotenoids was evaluated in Jurkat cells against aflatoxin B1 (AFB1) and ochratoxin A (OTA) cytotoxicity through a proteomic approach. The functional ingredients were added into mycotoxin contaminated bread formulation, which were digested in vitro in order to simulate human intestinal absorption. Cell cultures were exposed during 7 days to these mycotoxins dissolved in: (a) 0.1% organic solvent (DMSO), (b) an intestinal digest of bread with pumpkin individually (PID) and (c) an intestinal digest of bread with pumpkin mixed with fermented whey (PID+WF). Extracted proteins were subjected to reduction and alkylation and subsequently a tryptic digestion in order to be analysed by liquid chromatography coupled with quadrupole time of flight (LC/MS-Q-TOF). Results obtained highlighted the beneficial role of functional ingredients employed through the identification of proteins involved in several biological processes and metabolic pathways, mainly antioxidant activity, nucleosome assembly and secretory senescence phenotype. Among proteins involved in antioxidant activity, peroxiredoxin 1 and 2 stand out. Comparing the different conditions investigated, a remarkable change was observed in their expression, ranging from a repression using the standard (DMSO 0.1%), to an overexpression when treated with the functional ingredients. Similarly, after PID and PID+WF treatment, histones’ expression implicated in the metabolic pathway of nucleosome assembly, such as H2A, H2B, H2C, H3 and H4, was increased. Furthermore, the expression of protein cyclin A2, which downregulation is involved in limiting carcinogenic cells growth, was lower in presence of both functional ingredients. Based on these findings, functional ingredients can act as protectors against genomic stress caused by mycotoxins, preventing the loss of vital cell functions and paralysing the growth of carcinogenic cells.
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Affiliation(s)
- A. Cimbalo
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - M. Frangiamone
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - M. Lozano
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - L. Escrivá
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - P. Vila-Donat
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - L. Manyes
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
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Abstract
Our ability to predict and assess how environmental changes such as pollution and climate change affect components of the Earth's biome is of paramount importance. This need positioned the fields of ecotoxicology and stress ecology at the center of environmental monitoring efforts. Advances in these interdisciplinary fields depend not only on conceptual leaps but also on technological advances and data integration. High-throughput "omics" technologies enabled the measurement of molecular changes at virtually all levels of an organism's biological organization and thus continue to influence how the impacts of stressors are understood. This bibliometric review describes literature trends (2000-2020) that indicate that more different stressors than species are studied each year but that only a few stressors have been studied in more than two phyla. At the same time, the molecular responses of a diverse set of non-model species have been investigated, but cross-species comparisons are still rare. While transcriptomics studies dominated until 2016, a shift towards proteomics and multiomics studies is apparent. There is now a wealth of data at functional omics levels from many phylogenetically diverse species. This review, therefore, addresses the question of how to integrate omics information across species.
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Affiliation(s)
- Joshua Niklas Ebner
- Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
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