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Reddy Ramireddy VS, Kurakula R, Velayudhaperumal Chellam P, James A, van Hullebusch ED. Systematic computational toxicity analysis of the ozonolytic degraded compounds of azo dyes: Quantitative structure-activity relationship (QSAR) and adverse outcome pathway (AOP) based approach. ENVIRONMENTAL RESEARCH 2023; 231:116142. [PMID: 37217122 DOI: 10.1016/j.envres.2023.116142] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/27/2023] [Accepted: 05/13/2023] [Indexed: 05/24/2023]
Abstract
The present study identifies and analyses the degraded products of three azo dyes (Reactive Orange 16, Reactive Red 120, and Direct Red 80) and proffers their in silico toxicity predictions. In our previously published work, the synthetic dye effluents were degraded using an ozonolysis-based Advanced Oxidation Process. In the present study, the degraded products of the three dyes were analysed using GC-MS at endpoint strategy and further subjected to in silico toxicity analysis using Toxicity Estimation Software Tool (TEST), Prediction Of TOXicity of chemicals (ProTox-II), and Estimation Programs Interface Suite (EPI Suite). Several physiological toxicity endpoints, such as hepatotoxicity, carcinogenicity, mutagenicity, cellular and molecular interactions, were considered to assess the Quantitative Structure-Activity Relationships (QSAR) and adverse outcome pathways. The environmental fate of the by-products in terms of their biodegradability and possible bioaccumulation was also assessed. Results of ProTox-II suggested that the azo dye degradation products are carcinogenic, immunotoxic, and cytotoxic and displayed toxicity towards Androgen Receptor and Mitochondrial Membrane Potential. TEST results predicted LC50 and IGC50 values for three organisms Tetrahymena pyriformis, Daphnia magna, and Pimephales promelas. EPISUITE software via the BCFBAF module surmises that the degradation products' bioaccumulation (BAF) and bioconcentration factors (BCF) are high. The cumulative inference of the results suggests that most degradation by-products are toxic and need further remediation strategies. The study aims to complement existing tests to predict toxicity and prioritise the elimination/reduction of harmful degradation products of primary treatment procedures. The novelty of this study is that it streamlines in silico approaches to predict the nature of toxicity of degradation by-products of toxic industrial affluents like azo dyes. These approaches can assist the first phase of toxicology assessments for any pollutant for regulatory decision-making bodies to chalk out appropriate action plans for their remediation.
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Affiliation(s)
| | - Rakshitha Kurakula
- Department of Biotechnology, National Institute of Technology Andhra Pradesh, India
| | | | - Anina James
- Department of Zoology, Deen Dayal Upadhyaya College, New Delhi, India.
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Del Giudice G, Serra A, Saarimäki LA, Kotsis K, Rouse I, Colibaba SA, Jagiello K, Mikolajczyk A, Fratello M, Papadiamantis AG, Sanabria N, Annala ME, Morikka J, Kinaret PAS, Voyiatzis E, Melagraki G, Afantitis A, Tämm K, Puzyn T, Gulumian M, Lobaskin V, Lynch I, Federico A, Greco D. An ancestral molecular response to nanomaterial particulates. NATURE NANOTECHNOLOGY 2023; 18:957-966. [PMID: 37157020 PMCID: PMC10427433 DOI: 10.1038/s41565-023-01393-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 03/31/2023] [Indexed: 05/10/2023]
Abstract
The varied transcriptomic response to nanoparticles has hampered the understanding of the mechanism of action. Here, by performing a meta-analysis of a large collection of transcriptomics data from various engineered nanoparticle exposure studies, we identify common patterns of gene regulation that impact the transcriptomic response. Analysis identifies deregulation of immune functions as a prominent response across different exposure studies. Looking at the promoter regions of these genes, a set of binding sites for zinc finger transcription factors C2H2, involved in cell stress responses, protein misfolding and chromatin remodelling and immunomodulation, is identified. The model can be used to explain the outcomes of mechanism of action and is observed across a range of species indicating this is a conserved part of the innate immune system.
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Affiliation(s)
- G Del Giudice
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - A Serra
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere, Finland
| | - L A Saarimäki
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - K Kotsis
- School of Physics, University College Dublin, Dublin, Ireland
| | - I Rouse
- School of Physics, University College Dublin, Dublin, Ireland
| | - S A Colibaba
- School of Physics, University College Dublin, Dublin, Ireland
| | - K Jagiello
- Group of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | - A Mikolajczyk
- Group of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | - M Fratello
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - A G Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
- Novamechanics Ltd, Nicosia, Cyprus
| | - N Sanabria
- National Institute for Occupational Health, National Health Laboratory Services, Johannesburg, South Africa
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - M E Annala
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - J Morikka
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - P A S Kinaret
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland
| | | | - G Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece
| | | | - K Tämm
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - T Puzyn
- Group of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | - M Gulumian
- National Institute for Occupational Health, National Health Laboratory Services, Johannesburg, South Africa
- Haematology and Molecular Medicine Department, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Water Research Group, Unit for Environmental Sciences and Management, North West University, Potchefstroom, South Africa
| | - V Lobaskin
- School of Physics, University College Dublin, Dublin, Ireland
| | - I Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - A Federico
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere, Finland
| | - D Greco
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland.
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
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53
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Liang J, Wei HX, Zhou YY, Hao LL, Ning JY, Zhang L. Investigation on the potential adverse outcome pathway of the sensitive endpoint for nephrotoxicity induced by gardenia yellow based on an integrated strategy using bioinformatics analysis and in vitro testing validation. Food Chem Toxicol 2023:113930. [PMID: 37406755 DOI: 10.1016/j.fct.2023.113930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/17/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
To explore the potential the adverse outcome pathway of Gardenia Yellow (GY)-induced sensitive endpoint for nephrotoxicity, an integrated strategy was applied in the present study. Using bioinformatic analysis, based on the constructed Protein-protein interaction networks, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis on the core target network were performed to illustrate the potential gene targets and signal pathways. Then, the most enriched pathway was validated with Cell counting kit-8 assays and Western blot analysis in embryonic kidney epithelial 293 cell models. According to the findings, GY may interact with 321 targets related to the endpoint. The five targets on the top ranking in the PPI network were STAT3, SRC, HRAS, AKT1, EP300. Among them, PI3K/Akt was the most enriched pathway. In vitro testing showed that GY exerted a proliferative effect on the cell variability in a dose-dependent manner. GY at concentration of 1000 μg/ml and stimulation for 30 min can significantly enhance the expression of phosphorylated Akt. Thus, after the quantitative weight of evidence evaluation, Akt phosphorylation induced PI3K/Akt activation was speculated as a molecular initiating event leading to a proliferative and inflammatory response in renal tubular epithelial cells.
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Affiliation(s)
- Jiang Liang
- China National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Hong-Xin Wei
- Beijing Centers for Disease Prevention and Control /Beijing Research Center for Prevention Medicine, Beijing Key Laboratory of Diagnostic and Tracebility Technologies for Food Poisoning, Beijing, 100013, China
| | - Ying-Ying Zhou
- China National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Li-Li Hao
- China National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Jun-Yu Ning
- Beijing Centers for Disease Prevention and Control /Beijing Research Center for Prevention Medicine, Beijing Key Laboratory of Diagnostic and Tracebility Technologies for Food Poisoning, Beijing, 100013, China
| | - Lei Zhang
- China National Center for Food Safety Risk Assessment, Beijing, 100022, China.
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Lysak DH, Grisi M, Marable K, Conley GM, Michal CA, Moxley-Paquette V, Wolff WW, Downey K, Kock FVC, Costa PM, Ronda K, Moraes TB, Steiner K, Colnago LA, Simpson AJ. Exploring the Potential of Broadband Complementary Metal Oxide Semiconductor Micro-Coil Nuclear Magnetic Resonance for Environmental Research. Molecules 2023; 28:5080. [PMID: 37446742 PMCID: PMC10343494 DOI: 10.3390/molecules28135080] [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: 06/01/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
With sensitivity being the Achilles' heel of nuclear magnetic resonance (NMR), the superior mass sensitivity offered by micro-coils can be an excellent choice for tiny, mass limited samples such as eggs and small organisms. Recently, complementary metal oxide semiconductor (CMOS)-based micro-coil transceivers have been reported and demonstrate excellent mass sensitivity. However, the ability of broadband CMOS micro-coils to study heteronuclei has yet to be investigated, and here their potential is explored within the lens of environmental research. Eleven nuclei including 7Li, 19F, 31P and, 205Tl were studied and detection limits in the low to mid picomole range were found for an extended experiment. Further, two environmentally relevant samples (a sprouting broccoli seed and a D. magna egg) were successfully studied using the CMOS micro-coil system. 13C NMR was used to help resolve broad signals in the 1H spectrum of the 13C enriched broccoli seed, and steady state free precession was used to improve the signal-to-noise ratio by a factor of six. 19F NMR was used to track fluorinated contaminants in a single D. magna egg, showing potential for studying egg-pollutant interactions. Overall, CMOS micro-coil NMR demonstrates significant promise in environmental research, especially when the future potential to scale to multiple coil arrays (greatly improving throughput) is considered.
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Affiliation(s)
- Daniel H. Lysak
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Marco Grisi
- Annaida Technologies, Innovation Park, 1015 Lausanne, Switzerland
| | - Kathryn Marable
- Annaida Technologies, Innovation Park, 1015 Lausanne, Switzerland
| | | | - Carl A. Michal
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | | | - William W. Wolff
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Katelyn Downey
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Flavio V. C. Kock
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Peter M. Costa
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Kiera Ronda
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Tiago B. Moraes
- Departamento Engenharia de Biossistemas, Universidade de São Paulo/ESALQ, Av. Páduas Dias, 11, Piracicaba 13418-900, SP, Brazil
| | - Katrina Steiner
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Luiz A. Colnago
- Embrapa Instrumentação, Rua XV de Novembro 1452, São Carlos 13560-970, SP, Brazil
| | - Andre J. Simpson
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
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Obrecht M, Zurbruegg S, Accart N, Lambert C, Doelemeyer A, Ledermann B, Beckmann N. Magnetic resonance imaging and ultrasound elastography in the context of preclinical pharmacological research: significance for the 3R principles. Front Pharmacol 2023; 14:1177421. [PMID: 37448960 PMCID: PMC10337591 DOI: 10.3389/fphar.2023.1177421] [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: 03/21/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
The 3Rs principles-reduction, refinement, replacement-are at the core of preclinical research within drug discovery, which still relies to a great extent on the availability of models of disease in animals. Minimizing their distress, reducing their number as well as searching for means to replace them in experimental studies are constant objectives in this area. Due to its non-invasive character in vivo imaging supports these efforts by enabling repeated longitudinal assessments in each animal which serves as its own control, thereby enabling to reduce considerably the animal utilization in the experiments. The repetitive monitoring of pathology progression and the effects of therapy becomes feasible by assessment of quantitative biomarkers. Moreover, imaging has translational prospects by facilitating the comparison of studies performed in small rodents and humans. Also, learnings from the clinic may be potentially back-translated to preclinical settings and therefore contribute to refining animal investigations. By concentrating on activities around the application of magnetic resonance imaging (MRI) and ultrasound elastography to small rodent models of disease, we aim to illustrate how in vivo imaging contributes primarily to reduction and refinement in the context of pharmacological research.
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Affiliation(s)
- Michael Obrecht
- Diseases of Aging and Regenerative Medicines, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Stefan Zurbruegg
- Neurosciences Department, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Nathalie Accart
- Diseases of Aging and Regenerative Medicines, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Christian Lambert
- Diseases of Aging and Regenerative Medicines, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Arno Doelemeyer
- Diseases of Aging and Regenerative Medicines, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Birgit Ledermann
- 3Rs Leader, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Nicolau Beckmann
- Diseases of Aging and Regenerative Medicines, Novartis Institutes for BioMedical Research, Basel, Switzerland
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Zhang J, Li Y, Li H, Liu A, Cao J, Li X, Xia N, Zhang Z, Bai J, Zhang H. Aspirin ameliorates the neurotoxicity of benzo[a]pyrene in mice and HT22 cells: Possible role of miRNA-mRNA network. Food Chem Toxicol 2023:113919. [PMID: 37364758 DOI: 10.1016/j.fct.2023.113919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Benzo[a]pyrene (B[a]P) is neurotoxic, however, the mechanism and potential prevention are yet not clear. This study explored the miRNA-mRNA network in the B[a]P-induced neurotoxicity in mice and HT22 cells and the intervention of aspirin (ASP). HT22 cells were treated for 48 h with DMSO, B[a]P (20 μM), or both B[a]P (20 μM) and ASP (4 μM). Following B[a]P treatment, compared to the DMSO controls, HT22 cells showed injured cell morphology, reduced cell viability and neurotrophic factor concentrations, and increased LDH leakage, Aβ1-42, and inflammatory factor concentrations, which were improved by ASP. RNA sequencing and qPCR verified the significant differences of miRNA and mRNA profiles following B[a]P treatment, which were rescued by ASP. Bioinformatics analysis suggested the miRNA-mRNA network could be involved in the neurotoxicity of B[a]P and the intervention of ASP. The neurotoxicity and neuroinflammation were induced in mice's brains by B[a]P, and the target miRNA and mRNA were proved to be consistent with in vitro, which were ameliorated by ASP. The findings demonstrate a possible role of miRNA-mRNA network in the B[a]P-induced neurotoxicity. If this is confirmed by additional experiments, it will provide a promising pathway of intervention against B[a]P, using ASP or other agents with fewer toxic effects.
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Affiliation(s)
- Jinfeng Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China
| | - Yangyang Li
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China
| | - Huan Li
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China
| | - Aixiang Liu
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China
| | - Jingjing Cao
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China
| | - Xin Li
- Center of Disease Control and Prevention, Taiyuan Iron and Steel Company, Taiyuan, 030003, Shanxi, China
| | - Na Xia
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China
| | - Zhihong Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China
| | - Jianying Bai
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China
| | - Hongmei Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China; Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, Taiyuan, 030001, Shanxi, China; Key Laboratory of Cellular Physiology, Taiyuan, 030001, Shanxi, China; Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
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57
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Adegoke EO, Rahman MS, Amjad S, Pang WK, Ryu DY, Park YJ, Pang MG. Environmentally relevant doses of endocrine disrupting chemicals affect male fertility by interfering with sertoli cell glucose metabolism in mice. CHEMOSPHERE 2023; 337:139277. [PMID: 37364641 DOI: 10.1016/j.chemosphere.2023.139277] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/02/2023] [Accepted: 06/18/2023] [Indexed: 06/28/2023]
Abstract
The growing global deterioration in several aspects of human health has been partly attributed to hazardous effects of endocrine-disrupting chemicals (EDCs) exposure. Therefore, experts and government regulatory agencies have consistently advocated for studies on the combined effects of EDCs that model human exposure to multiple environmental chemicals in real life. Here, we investigated how low concentrations of bisphenol A (BPA), and phthalates compounds affect the Sertoli cell glucose uptake/lactate production in the testis and male fertility. An EDC mixture containing a detected amount of each chemical compound in humans, called daily exposure (DE), and DE increased in magnitude by 25 (DE25), 250 (DE250), and 2500 (DE2500), and corn oil (control) were administered for six weeks to male mice. We found that DE activated estrogen receptor beta (Erβ) and glucose-regulated protein 78 (Grp 78) and disrupted the estradiol (E2) balance. In addition, DE25, DE250, and DE2500 doses of the EDC mixture via binding with Sertoli cells' estrogen receptors (ERs) inhibited the glucose uptake and lactate production processes by downregulating glucose transporters (GLUTs) and glycolytic enzymes. As a result, endoplasmic reticulum stress (ERS), marked by unfolded protein response (UPR) activation, was induced. The accompanying upregulation of activating transcription factor 4 (ATF4), inositol requiring enzyme-1 (IRE1), C/EBP homologous protein (CHOP), and mitogen-activated protein kinase (MAPK) signaling promoted antioxidant depletion, testicular cell apoptosis, abnormal regulation of the blood-testis barrier, and decreased sperm count. Therefore, these findings suggest that human and wildlife exposure to multiple environmental chemicals can produce a wide range of reproductive health complications in male mammals.
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Affiliation(s)
- Elikanah Olusayo Adegoke
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Md Saidur Rahman
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Shehreen Amjad
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Won-Ki Pang
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Do-Yeal Ryu
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Yoo-Jin Park
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Mung-Geol Pang
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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58
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Ronda K, Downey K, Jenne A, Bastawrous M, Wolff WW, Steiner K, Lysak DH, Costa PM, Simpson MJ, Jobst KJ, Simpson AJ. Exploring Proton-Only NMR Experiments and Filters for Daphnia In Vivo: Potential and Limitations. Molecules 2023; 28:4863. [PMID: 37375418 DOI: 10.3390/molecules28124863] [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: 05/31/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Environmental metabolomics provides insight into how anthropogenic activities have an impact on the health of an organism at the molecular level. Within this field, in vivo NMR stands out as a powerful tool for monitoring real-time changes in an organism's metabolome. Typically, these studies use 2D 13C-1H experiments on 13C-enriched organisms. Daphnia are the most studied species, given their widespread use in toxicity testing. However, with COVID-19 and other geopolitical factors, the cost of isotope enrichment increased ~6-7 fold over the last two years, making 13C-enriched cultures difficult to maintain. Thus, it is essential to revisit proton-only in vivo NMR and ask, "Can any metabolic information be obtained from Daphnia using proton-only experiments?". Two samples are considered here: living and whole reswollen organisms. A range of filters are tested, including relaxation, lipid suppression, multiple-quantum, J-coupling suppression, 2D 1H-1H experiments, selective experiments, and those exploiting intermolecular single-quantum coherence. While most filters improve the ex vivo spectra, only the most complex filters succeed in vivo. If non-enriched organisms must be used, then, DREAMTIME is recommended for targeted monitoring, while IP-iSQC was the only experiment that allowed non-targeted metabolite identification in vivo. This paper is critically important as it documents not just the experiments that succeed in vivo but also those that fail and demonstrates first-hand the difficulties associated with proton-only in vivo NMR.
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Affiliation(s)
- Kiera Ronda
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Katelyn Downey
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Amy Jenne
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Monica Bastawrous
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - William W Wolff
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Katrina Steiner
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Daniel H Lysak
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Peter M Costa
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Myrna J Simpson
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Karl J Jobst
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, NL A1C 5S7, Canada
| | - Andre J Simpson
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
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Chen D, Huang H, Huang Y, Yang W, Shan W, Hao G, Wu J, Song B. Toxicity Tests for Chemical Pesticide Registration: Requirement Differences among the United States, the European Union, Japan, and China? JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7192-7200. [PMID: 37144888 DOI: 10.1021/acs.jafc.3c00410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Pesticide registration is a scientific, legal, and administrative process that checks if a pesticide is safe and effective for its intended use before it can be used. The toxicity test is a key part of pesticide registration, which includes human health and ecological effect testing. Different countries adopt their own toxicity test criteria for pesticide registration guidelines. However, these differences, which may help accelerate the progress of pesticide registration and reduce the number of animals used, are yet to be explored and compared. Herein, we outlined the details and compared the differences between the toxicity tests in the United States, the European Union, Japan, and China. Some differences lie in the types and waiver policy, while others are in new approach methodologies (NAMs). On the basis of these differences, there is great potential for the optimization of NAMs during the toxicity tests. It is expected that this perspective can contribute to developing and adopting NAMs.
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Affiliation(s)
- Dongyu Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Hui Huang
- Department of Planting Management, Ministry of Agriculture and Rural Affairs, Beijing 100125, People's Republic of China
| | - Yuanqin Huang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Weicheng Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Weili Shan
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing 100125, People's Republic of China
| | - Gefei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Jian Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Baoan Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
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Singh AV, Chandrasekar V, Paudel N, Laux P, Luch A, Gemmati D, Tissato V, Prabhu KS, Uddin S, Dakua SP. Integrative toxicogenomics: Advancing precision medicine and toxicology through artificial intelligence and OMICs technology. Biomed Pharmacother 2023; 163:114784. [PMID: 37121152 DOI: 10.1016/j.biopha.2023.114784] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/02/2023] Open
Abstract
More information about a person's genetic makeup, drug response, multi-omics response, and genomic response is now available leading to a gradual shift towards personalized treatment. Additionally, the promotion of non-animal testing has fueled the computational toxicogenomics as a pivotal part of the next-gen risk assessment paradigm. Artificial Intelligence (AI) has the potential to provid new ways analyzing the patient data and making predictions about treatment outcomes or toxicity. As personalized medicine and toxicogenomics involve huge data processing, AI can expedite this process by providing powerful data processing, analysis, and interpretation algorithms. AI can process and integrate a multitude of data including genome data, patient records, clinical data and identify patterns to derive predictive models anticipating clinical outcomes and assessing the risk of any personalized medicine approaches. In this article, we have studied the current trends and future perspectives in personalized medicine & toxicology, the role of toxicogenomics in connecting the two fields, and the impact of AI on personalized medicine & toxicology. In this work, we also study the key challenges and limitations in personalized medicine, toxicogenomics, and AI in order to fully realize their potential.
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Affiliation(s)
- Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany
| | | | - Namuna Paudel
- Department of Chemistry, Amrit Campus, Institute of Science and Technology, Tribhuvan University, Lainchaur, Kathmandu 44600 Nepal
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany
| | - Donato Gemmati
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; Centre Hemostasis & Thrombosis, University of Ferrara, 44121 Ferrara, Italy; Centre for Gender Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Veronica Tissato
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; Centre Hemostasis & Thrombosis, University of Ferrara, 44121 Ferrara, Italy; Centre for Gender Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
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61
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Zhang N, Zhang W, Wang M, Li G, Ning J, Nie Y, Xian B, Huang Z, Chen W, Gao S. An automatic recognition method of nematode survival rate based on bright field and dark field experimental images. Technol Health Care 2023; 31:199-208. [PMID: 37038792 DOI: 10.3233/thc-236017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
BACKGROUND The survival rate of experimental animals is a very important index in chemical toxicity evaluation experiments. The calculation of nematode survival rate is used in many experiments. OBJECTIVE Traditional survival rate quantification methods require manual counting. This is a time-consuming and laborious work when using 384-well plate for high-throughput chemical toxicity assessment experiments. At present, there is a great need for an automatic method to identify the survival rate of nematodes in the experiment of chemical toxicity evaluation. METHODS We designed an automatic nematode survival rate recognition method by combining the bright field experimental image of nematodes and the dark field image of nematodes which is captured after adding Propidium Iodide dye, and used it to calculate the nematode survival rate in different chemical environments. Experiment results show that the survival rate obtained by our automatic counting method is very similar to the survival rate obtained by manual counting. RESULTS Through several different chemical experiments, we can see that chemicals with different toxicity have different effects on the survival rate of nematodes. And the survival rate of nematodes under different chemical concentrations has an obvious gradient trend from high concentration to low concentration. In addition, our method can quantify the motility of nematodes. There are also significant differences in the motility of nematodes cultured in different chemical environments. Moreover, the nematode motility under different chemical concentrations showed an obvious gradient change trend from high concentration to low concentration. CONCLUSION Our study provides an accurate and efficient nematode survival rate recognition method for chemical toxicology research.
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Affiliation(s)
- Nan Zhang
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Wenjing Zhang
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Maoli Wang
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, Shandong, China
| | - Guojun Li
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Junyu Ning
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Yanmin Nie
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Bo Xian
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Zhihang Huang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Weiyang Chen
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, Shandong, China
| | - Shan Gao
- Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
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62
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Su R, He H, Sun C, Wang X, Liu X. Prediction of drug-induced hepatotoxicity based on histopathological whole slide images. Methods 2023; 212:31-38. [PMID: 36706825 DOI: 10.1016/j.ymeth.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/30/2022] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Liver is an important metabolic organ in human body and is sensitive to toxic chemicals or drugs. Adverse reactions caused by drug hepatotoxicity will damage the liver and hepatotoxicity is the leading cause of removal of approved drugs from the market. Therefore, it is of great significance to identify liver toxicity as early as possible in the drug development process. In this study, we developed a predictive model for drug hepatotoxicity based on histopathological whole slide images (WSI) which are the by-product of drug experiments and have received little attention. To better represent the WSIs, we constructed a graph representation for each WSI by dividing it into small patches, taking sampled patches as nodes and calculating the correlation coefficients between node features as the edges of the graph structure. Then a WSI-level graph convolutional network (GCN) was built to effectively extract the node information of the graph and predict the toxicity. In addition, we introduced a gated attention global context vector (gaGCV) to combine the global context to make node features to contain more comprehensive information. The results validated on rat liver in vivo data from the Open TG-GATES show that the use of WSI for the prediction of toxicity is feasible and effective.
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Affiliation(s)
- Ran Su
- School of Computer Software, College of Intelligence and Computing, Tianjin University, China
| | - Hao He
- School of Computer Software, College of Intelligence and Computing, Tianjin University, China
| | | | - Xiaomin Wang
- National Clinical Research Center for Infectious Diseases, Shenzhen, Guangdong, China.
| | - Xiaofeng Liu
- Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
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63
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Jenne A, von der Ecken S, Moxley-Paquette V, Soong R, Swyer I, Bastawrous M, Busse F, Bermel W, Schmidig D, Kuehn T, Kuemmerle R, Al Adwan-Stojilkovic D, Graf S, Frei T, Monette M, Wheeler AR, Simpson AJ. Integrated Digital Microfluidics NMR Spectroscopy: A Key Step toward Automated In Vivo Metabolomics. Anal Chem 2023; 95:5858-5866. [PMID: 36996326 DOI: 10.1021/acs.analchem.2c04201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Toxicity testing is currently undergoing a paradigm shift from examining apical end points such as death, to monitoring sub-lethal toxicity in vivo. In vivo nuclear magnetic resonance (NMR) spectroscopy is a key platform in this endeavor. A proof-of-principle study is presented which directly interfaces NMR with digital microfluidics (DMF). DMF is a "lab on a chip" method allowing for the movement, mixing, splitting, and dispensing of μL-sized droplets. The goal is for DMF to supply oxygenated water to keep the organisms alive while NMR detects metabolomic changes. Here, both vertical and horizontal NMR coil configurations are compared. While a horizontal configuration is ideal for DMF, NMR performance was found to be sub-par and instead, a vertical-optimized single-sided stripline showed most promise. In this configuration, three organisms were monitored in vivo using 1H-13C 2D NMR. Without support from DMF droplet exchange, the organisms quickly showed signs of anoxic stress; however, with droplet exchange, this was completely suppressed. The results demonstrate that DMF can be used to maintain living organisms and holds potential for automated exposures in future. However, due to numerous limitations of vertically orientated DMF, along with space limitations in standard bore NMR spectrometers, we recommend future development be performed using a horizontal (MRI style) magnet which would eliminate practically all the drawbacks identified here.
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Affiliation(s)
- Amy Jenne
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - Sebastian von der Ecken
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Nicoya, B-29 King Street East, Kitchener, Ontario N2G 2K4, Canada
| | - Vincent Moxley-Paquette
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - Ian Swyer
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Monica Bastawrous
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
| | - Falko Busse
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Daniel Schmidig
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Till Kuehn
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Rainer Kuemmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | | | - Stephan Graf
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Thomas Frei
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Martine Monette
- Bruker Canada Ltd., 2800 High Point Drive, Milton, Ontario L9T 6P4, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute for Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Andre J Simpson
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada
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Sharma B, Chenthamarakshan V, Dhurandhar A, Pereira S, Hendler JA, Dordick JS, Das P. Accurate clinical toxicity prediction using multi-task deep neural nets and contrastive molecular explanations. Sci Rep 2023; 13:4908. [PMID: 36966203 PMCID: PMC10039880 DOI: 10.1038/s41598-023-31169-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 03/07/2023] [Indexed: 03/27/2023] Open
Abstract
Explainable machine learning for molecular toxicity prediction is a promising approach for efficient drug development and chemical safety. A predictive ML model of toxicity can reduce experimental cost and time while mitigating ethical concerns by significantly reducing animal and clinical testing. Herein, we use a deep learning framework for simultaneously modeling in vitro, in vivo, and clinical toxicity data. Two different molecular input representations are used; Morgan fingerprints and pre-trained SMILES embeddings. A multi-task deep learning model accurately predicts toxicity for all endpoints, including clinical, as indicated by the area under the Receiver Operator Characteristic curve and balanced accuracy. In particular, pre-trained molecular SMILES embeddings as input to the multi-task model improved clinical toxicity predictions compared to existing models in MoleculeNet benchmark. Additionally, our multitask approach is comprehensive in the sense that it is comparable to state-of-the-art approaches for specific endpoints in in vitro, in vivo and clinical platforms. Through both the multi-task model and transfer learning, we were able to indicate the minimal need of in vivo data for clinical toxicity predictions. To provide confidence and explain the model's predictions, we adapt a post-hoc contrastive explanation method that returns pertinent positive and negative features, which correspond well to known mutagenic and reactive toxicophores, such as unsubstituted bonded heteroatoms, aromatic amines, and Michael receptors. Furthermore, toxicophore recovery by pertinent feature analysis captures more of the in vitro (53%) and in vivo (56%), rather than of the clinical (8%), endpoints, and indeed uncovers a preference in known toxicophore data towards in vitro and in vivo experimental data. To our knowledge, this is the first contrastive explanation, using both present and absent substructures, for predictions of clinical and in vivo molecular toxicity.
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Affiliation(s)
| | | | | | - Shiranee Pereira
- ICARE, International Center for Alternatives in Research and Education, Chennai, India
| | | | | | - Payel Das
- IBM Research, Yorktown Heights, NY, USA.
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Benfante V, Stefano A, Ali M, Laudicella R, Arancio W, Cucchiara A, Caruso F, Cammarata FP, Coronnello C, Russo G, Miele M, Vieni A, Tuttolomondo A, Yezzi A, Comelli A. An Overview of In Vitro Assays of 64Cu-, 68Ga-, 125I-, and 99mTc-Labelled Radiopharmaceuticals Using Radiometric Counters in the Era of Radiotheranostics. Diagnostics (Basel) 2023; 13:diagnostics13071210. [PMID: 37046428 PMCID: PMC10093267 DOI: 10.3390/diagnostics13071210] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/11/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Radionuclides are unstable isotopes that mainly emit alpha (α), beta (β) or gamma (γ) radiation through radiation decay. Therefore, they are used in the biomedical field to label biomolecules or drugs for diagnostic imaging applications, such as positron emission tomography (PET) and/or single-photon emission computed tomography (SPECT). A growing field of research is the development of new radiopharmaceuticals for use in cancer treatments. Preclinical studies are the gold standard for translational research. Specifically, in vitro radiopharmaceutical studies are based on the use of radiopharmaceuticals directly on cells. To date, radiometric β- and γ-counters are the only tools able to assess a preclinical in vitro assay with the aim of estimating uptake, retention, and release parameters, including time- and dose-dependent cytotoxicity and kinetic parameters. This review has been designed for researchers, such as biologists and biotechnologists, who would like to approach the radiobiology field and conduct in vitro assays for cellular radioactivity evaluations using radiometric counters. To demonstrate the importance of in vitro radiopharmaceutical assays using radiometric counters with a view to radiogenomics, many studies based on 64Cu-, 68Ga-, 125I-, and 99mTc-labeled radiopharmaceuticals have been revised and summarized in this manuscript.
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Affiliation(s)
- Viviana Benfante
- Ri.MED Foundation, Via Bandiera 11, 90133 Palermo, Italy
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, Molecular and Clinical Medicine, University of Palermo, 90127 Palermo, Italy
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), 90015 Cefalù, Italy
| | - Alessandro Stefano
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), 90015 Cefalù, Italy
| | - Muhammad Ali
- Ri.MED Foundation, Via Bandiera 11, 90133 Palermo, Italy
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, Molecular and Clinical Medicine, University of Palermo, 90127 Palermo, Italy
| | | | - Walter Arancio
- Ri.MED Foundation, Via Bandiera 11, 90133 Palermo, Italy
| | - Antonino Cucchiara
- Department of Diagnostic and Therapeutic Services, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Via Tricomi 5, 90127 Palermo, Italy
| | - Fabio Caruso
- Department of Diagnostic and Therapeutic Services, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Via Tricomi 5, 90127 Palermo, Italy
| | - Francesco Paolo Cammarata
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), 90015 Cefalù, Italy
| | - Claudia Coronnello
- Ri.MED Foundation, Via Bandiera 11, 90133 Palermo, Italy
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Giorgio Russo
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), 90015 Cefalù, Italy
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Monica Miele
- Ri.MED Foundation, Via Bandiera 11, 90133 Palermo, Italy
| | - Alessandra Vieni
- Department of Diagnostic and Therapeutic Services, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Via Tricomi 5, 90127 Palermo, Italy
| | - Antonino Tuttolomondo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, Molecular and Clinical Medicine, University of Palermo, 90127 Palermo, Italy
| | - Anthony Yezzi
- Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Albert Comelli
- Ri.MED Foundation, Via Bandiera 11, 90133 Palermo, Italy
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
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Chauhan V, Yu J, Vuong N, Haber LT, Williams A, Auerbach SS, Beaton D, Wang Y, Stainforth R, Wilkins RC, Azzam EI, Richardson RB, Khan MGM, Jadhav A, Burtt JJ, Leblanc J, Randhawa K, Tollefsen KE, Yauk CL. Considerations for application of benchmark dose modeling in radiation research: workshop highlights. Int J Radiat Biol 2023; 99:1320-1331. [PMID: 36881459 DOI: 10.1080/09553002.2023.2181998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND Exposure to different forms of ionizing radiation occurs in diverse occupational, medical, and environmental settings. Improving the accuracy of the estimated health risks associated with exposure is therefore, essential for protecting the public, particularly as it relates to chronic low dose exposures. A key aspect to understanding health risks is precise and accurate modeling of the dose-response relationship. Toward this vision, benchmark dose (BMD) modeling may be a suitable approach for consideration in the radiation field. BMD modeling is already extensively used for chemical hazard assessments and is considered statistically preferable to identifying low and no observed adverse effects levels. BMD modeling involves fitting mathematical models to dose-response data for a relevant biological endpoint and identifying a point of departure (the BMD, or its lower bound). Recent examples in chemical toxicology show that when applied to molecular endpoints (e.g. genotoxic and transcriptional endpoints), BMDs correlate to points of departure for more apical endpoints such as phenotypic changes (e.g. adverse effects) of interest to regulatory decisions. This use of BMD modeling may be valuable to explore in the radiation field, specifically in combination with adverse outcome pathways, and may facilitate better interpretation of relevant in vivo and in vitro dose-response data. To advance this application, a workshop was organized on June 3rd, 2022, in Ottawa, Ontario that brought together BMD experts in chemical toxicology and the radiation scientific community of researchers, regulators, and policy-makers. The workshop's objective was to introduce radiation scientists to BMD modeling and its practical application using case examples from the chemical toxicity field and demonstrate the BMDExpress software using a radiation dataset. Discussions focused on the BMD approach, the importance of experimental design, regulatory applications, its use in supporting the development of adverse outcome pathways, and specific radiation-relevant examples. CONCLUSIONS Although further deliberations are needed to advance the use of BMD modeling in the radiation field, these initial discussions and partnerships highlight some key steps to guide future undertakings related to new experimental work.
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Affiliation(s)
- Vinita Chauhan
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Canada
| | - Jihang Yu
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
| | - Ngoc Vuong
- Radiation Protection Bureau, Health Canada, Ottawa, Canada
| | - Lynne T Haber
- Department of Environmental and Public Health Sciences, Risk Science Center, University of Cincinnati, Cincinnati, OH, USA
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Scott S Auerbach
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Danielle Beaton
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
| | - Yi Wang
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | | | - Ruth C Wilkins
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Canada
| | - Edouard I Azzam
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
- Department of Radiology, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Richard B Richardson
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
- Medical Physics Unit, McGill University, Montreal, QC, Canada
| | | | - Ashok Jadhav
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
| | - Julie J Burtt
- Directorate of Environmental and Radiation Protection and Assessment, Canadian Nuclear Safety Commission, Ottawa, Canada
| | - Julie Leblanc
- Directorate of Environmental and Radiation Protection and Assessment, Canadian Nuclear Safety Commission, Ottawa, Canada
| | - Kristi Randhawa
- Directorate of Environmental and Radiation Protection and Assessment, Canadian Nuclear Safety Commission, Ottawa, Canada
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Oslo, Norway
- Norwegian University of Life Sciences (NMBU), Ås, Norway
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Canada
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Marshall LJ, Bailey J, Cassotta M, Herrmann K, Pistollato F. Poor Translatability of Biomedical Research Using Animals - A Narrative Review. Altern Lab Anim 2023; 51:102-135. [PMID: 36883244 DOI: 10.1177/02611929231157756] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The failure rate for the translation of drugs from animal testing to human treatments remains at over 92%, where it has been for the past few decades. The majority of these failures are due to unexpected toxicity - that is, safety issues revealed in human trials that were not apparent in animal tests - or lack of efficacy. However, the use of more innovative tools, such as organs-on-chips, in the preclinical pipeline for drug testing, has revealed that these tools are more able to predict unexpected safety events prior to clinical trials and so can be used for this, as well as for efficacy testing. Here, we review several disease areas, and consider how the use of animal models has failed to offer effective new treatments. We also make some suggestions as to how the more human-relevant new approach methodologies might be applied to address this.
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Affiliation(s)
- Lindsay J Marshall
- Animal Research Issues, 94219The Humane Society of the United States, Gaithersburg, MD, USA
| | - Jarrod Bailey
- 380235Cruelty Free International, London, UK; 542332Animal Free Research UK, London, UK
| | | | - Kathrin Herrmann
- Johns Hopkins Bloomberg School of Public Health, 457389Center for Alternatives to Animal Testing, Baltimore, MD, USA; Senate Department for the Environment, Urban Mobility, Consumer Protection and Climate Action, Berlin, Germany
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Hill BN, Britton KN, Hunter DL, Olin JK, Lowery M, Hedge JM, Knapp BR, Jarema KA, Rowson Z, Padilla S. Inconsistencies in variable reporting and methods in larval zebrafish behavioral assays. Neurotoxicol Teratol 2023; 96:107163. [PMID: 36758822 PMCID: PMC10337341 DOI: 10.1016/j.ntt.2023.107163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/06/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
New approaches in developmental neurotoxicity (DNT) screening are needed due to the tens of thousands of chemicals requiring hazard assessments. Zebrafish (Danio rerio) are an alternative vertebrate model for DNT testing, but without a standardized protocol for larval behavioral assays, comparison of results among laboratories is challenging. To evaluate the congruence of protocols across laboratories, we conducted a literature review of DNT studies focusing on larval zebrafish behavior assays and cataloged experimental design consistencies. Our review focused on 51 unique method variables in publications where chemical exposure occurred in early development and subsequent larval locomotor evaluation focused on assays that included a light/dark photoperiod transition. We initially identified 94 publications, but only 31 exclusively met our inclusion criteria which focused on parameters that are important to an assay employed by our laboratory. No publication reported 100% of the targeted variables; only 51 to 86% of those variables were reported in the reviewed publications, with some aspects of the experimental design consistent among laboratories. However, no protocol was exactly the same for any two publications. Many of these variables had more than one parameter/design reported, highlighting the inconsistencies among methods. Overall, there is not only a strong need for the development of a standardized testing protocol for larval zebrafish locomotor assays, but there is also a need for a standardized protocol for reporting experimental variables in the literature. Here we include an extensive guideline checklist for conducting larval zebrafish developmental behavior assays.
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Affiliation(s)
- Bridgett N Hill
- ORISE Research Participation Program hosted by EPA, Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Rapid Assay Development Branch, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Katy N Britton
- ORAU Research Participation Program hosted by EPA, Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Rapid Assay Development Branch, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Deborah L Hunter
- Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Rapid Assay Development Branch, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Jeanene K Olin
- Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Rapid Assay Development Branch, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Morgan Lowery
- Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Rapid Assay Development Branch, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Joan M Hedge
- Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Advanced Experimental Toxicology Models Branch, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Bridget R Knapp
- ORISE Research Participation Program hosted by EPA, Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Rapid Assay Development Branch, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Kimberly A Jarema
- Center for Public Health and Environmental Assessment, Immediate Office, Program Operations Staff, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Zachary Rowson
- ORISE Research Participation Program hosted by EPA, Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Rapid Assay Development Branch, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Stephanie Padilla
- Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Rapid Assay Development Branch, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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Puty B, Bittencourt LO, Plaça JR, de Oliveira EHC, Lima RR. Astrocyte-Like Cells Transcriptome Changes After Exposure to a Low and Non-cytotoxic MeHg Concentration. Biol Trace Elem Res 2023; 201:1151-1162. [PMID: 35378667 DOI: 10.1007/s12011-022-03225-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023]
Abstract
The central nervous system is the main target of MeHg toxicity and glial cells are the first line of defense; however, their true role remains unclear. This study aimed to identify the global map of human glial-like (U87) cells transcriptome after exposure to a non-toxic and non-lethal MeHg concentration and to investigate the related molecular changes. U87 cells were exposed upon 0.1, 0.5, and 1 µM MeHg for 4 and 24 h. Although no changes were observed in the percentage of viable cells, the metabolic viability was significantly decreased after exposure to 1 µM MeHg for 24 h; thus, the non-toxic concentration of 0.1 µM MeHg was chosen to perform microarray analysis. Significant changes in U87 cells transcriptome were observed only after 24 h. The expression of 392 genes was down regulated while 431 genes were up-regulated. Gene ontology showed alterations in biological processes (75%), cellular components (21%), and molecular functions (4%). The main pathways showed by KEGG and Reactome were cell cycle regulation and Rho GTPase signaling. The complex mechanism of U87 cells response against MeHg exposure indicates that even a low and non-toxic concentration is able to alter the gene expression profile.
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Affiliation(s)
- Bruna Puty
- Laboratory of Functional and Structural Biology, Institute of Biological Science, Federal University of Pará, Belém, Brazil
- Laboratory of Tissue Culture and Cytogenetics, Environmental Section, Evandro Chagas Institute, Ananindeua, Brazil
| | - Leonardo Oliveira Bittencourt
- Laboratory of Functional and Structural Biology, Institute of Biological Science, Federal University of Pará, Belém, Brazil
| | - Jéssica Rodrigues Plaça
- National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | | | - Rafael Rodrigues Lima
- Laboratory of Functional and Structural Biology, Institute of Biological Science, Federal University of Pará, Belém, Brazil.
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70
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Vliet SMF, Hazemi M, Blatz D, Jensen M, Mayasich S, Transue TR, Simmons C, Wilkinson A, LaLone CA. Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation. J Vis Exp 2023:10.3791/63970. [PMID: 36847398 PMCID: PMC10758989 DOI: 10.3791/63970] [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] [Indexed: 02/12/2023] Open
Abstract
The US Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool is a fast, freely available, online screening application that allows researchers and regulators to extrapolate toxicity information across species. For biological targets in model systems such as human cells, mice, rats, and zebrafish, toxicity data are available for a variety of chemicals. Through the evaluation of protein target conservation, this tool can be used to extrapolate data generated from such model systems to thousands of other species lacking toxicity data, yielding predictions of relative intrinsic chemical susceptibility. The latest releases of the tool (versions 2.0-6.1) have incorporated new features that allow for the rapid synthesis, interpretation, and use of the data for publication plus presentation-quality graphics. Among these features are customizable data visualizations and a comprehensive summary report designed to summarize SeqAPASS data for ease of interpretation. This paper describes the protocol to guide users through submitting jobs, navigating the various levels of protein sequence comparisons, and interpreting and displaying the resulting data. New features of SeqAPASS v2.0-6.0 are highlighted. Furthermore, two use-cases focused on transthyretin and opioid receptor protein conservation using this tool are described. Finally, SeqAPASS' strengths and limitations are discussed to define the domain of applicability for the tool and highlight different applications for cross-species extrapolation.
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Affiliation(s)
- Sara M F Vliet
- Office of Research and Development, Center for Computational Toxicology and Exposure, Scientific Computing and Data Curation Division, U.S. Environmental Protection Agency;
| | | | | | - Marissa Jensen
- Swenson College of Science and Engineering, Department of Biology, University of Minnesota Duluth
| | | | | | - Cody Simmons
- General Dynamics Information Technology, Research Triangle Park
| | | | - Carlie A LaLone
- Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, U.S. Environmental Protection Agency
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71
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Lysak DH, Kock FVC, Mamone S, Soong R, Glöggler S, Simpson AJ. In vivo singlet state filtered nuclear magnetic resonance: towards monitoring toxic responses inside living organisms. Chem Sci 2023; 14:1413-1418. [PMID: 36794179 PMCID: PMC9906653 DOI: 10.1039/d2sc06624f] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
In line with recent paradigm shifts in toxicity testing, in vivo nuclear magnetic resonance (NMR) is a powerful tool for studying the biological impacts and perturbations caused by toxicants in living organisms. However, despite the excellent molecular insights that can be obtained through this technique, in vivo NMR applications are hampered by considerable experimental challenges such as poor line shape and spectral overlap. Here, we demonstrate the application of singlet-filtered NMR to target specific metabolites and facilitate the study of metabolite fluxes in living Daphnia magna, an aquatic keystone species and model organism. Informed by mathematical simulations and experiments on ex vivo organisms, singlet state NMR is used to monitor the flux of metabolites such as d-glucose and serine in living D. magna, during the environmentally relevant processes of anoxic stress and reduced food availability. Overall, singlet state NMR is shown to have significant future potential for studying metabolic processes in vivo.
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Affiliation(s)
- Daniel H. Lysak
- Environmental NMR Centre, University of Toronto Scarborough1265 Military TrailScarboroughOntarioCanada
| | - Flavio V. C. Kock
- Environmental NMR Centre, University of Toronto Scarborough1265 Military TrailScarboroughOntarioCanada,Department of Chemistry, Federal University of São Carlos (UFSCar)Rod. Washington Luís, MonjolinhoSão Carlos–SP13565-905Brazil
| | - Salvatore Mamone
- NMR Signal Enhancement Group, Max Planck Institute for Multidisciplinary Sciences Am Fassberg 11 37077 Göttingen Germany
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto Scarborough1265 Military TrailScarboroughOntarioCanada
| | - Stefan Glöggler
- NMR Signal Enhancement Group, Max Planck Institute for Multidisciplinary Sciences Am Fassberg 11 37077 Göttingen Germany
| | - Andre J. Simpson
- NMR Signal Enhancement Group, Max Planck Institute for Multidisciplinary SciencesAm Fassberg11 37077GöttingenGermany
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72
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Zhang Y, Liu Z, Wang Z, Gao H, Wang Y, Cui M, Peng H, Xiao Y, Jin Y, Yu D, Chen W, Wang Q. Health risk assessment of cadmium exposure by integration of an in silico physiologically based toxicokinetic model and in vitro tests. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130191. [PMID: 36272375 DOI: 10.1016/j.jhazmat.2022.130191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Cadmium (Cd) is a common environmental pollutant that can damage multiple organs, including the kidney. To prevent renal effects, international authorities have set health-based guidance values of Cd from epidemiological studies. To explore the health risk of Cd exposure and whether human equivalent doses (HEDs) derived from in vitro tests match the current guidance values, we integrated renal tubular epithelial cell-based assays with a physiologically based toxicokinetic model combined with the Monte Carlo method. For females, the HEDs (μg/kg/week) derived from KE2 (DNA damage), KE3 (cell cycle arrest), and KE4 (apoptosis) were 0.20 (2.5th-97.5th percentiles: 0.09-0.48), 0.52 (0.24-1.26), and 2.73 (1.27-6.57), respectively; for males the respective HEDs were 0.23 (0.10-0.49), 0.60 (0.27-1.30), and 3.11 (1.39-6.78). Among them, HEDKE4 (female) was close to the tolerable weekly intake (2.5 μg/kg/week) set by the European Food Safety Authority. The margin of exposure (MOE) derived from HEDKE4 (female) indicated that risks of renal toxicity for populations living in cadmium-contaminated regions should be of concern. This study provided a new approach methodology (NAM) for environmental chemical risk assessment using in silico and in vitro methods.
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Affiliation(s)
- Yangchun Zhang
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Ziqi Liu
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Ziwei Wang
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Huan Gao
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuqing Wang
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Mengxing Cui
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Honghao Peng
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yongmei Xiao
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuan Jin
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China
| | - Wen Chen
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Qing Wang
- Department of Toxicology, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou 510080, China.
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73
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Everson JL, Tseng YC, Eberhart JK. High-throughput detection of craniofacial defects in fluorescent zebrafish. Birth Defects Res 2023; 115:371-389. [PMID: 36369674 PMCID: PMC9898129 DOI: 10.1002/bdr2.2127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/14/2022]
Abstract
Losses and malformations of cranial neural crest cell (cNCC) derivatives are a hallmark of several common brain and face malformations. Nevertheless, the etiology of these cNCC defects remains unknown for many cases, suggesting a complex basis involving interactions between genetic and/or environmental factors. However, the sheer number of possible factors (thousands of genes and hundreds of thousands of toxicants) has hindered identification of specific interactions. Here, we develop a high-throughput analysis that will enable faster identification of multifactorial interactions in the genesis of craniofacial defects. Zebrafish embryos expressing a fluorescent marker of cNCCs (fli1:EGFP) were exposed to a pathway inhibitor standard or environmental toxicant, and resulting changes in fluorescence were measured in high-throughput using a fluorescent microplate reader to approximate cNCC losses. Embryos exposed to the environmental Hedgehog pathway inhibitor piperonyl butoxide (PBO), a Hedgehog pathway inhibitor standard, or alcohol (ethanol) exhibited reduced fli1:EGFP fluorescence at one day post fertilization, which corresponded with craniofacial defects at five days post fertilization. Combining PBO and alcohol in a co-exposure paradigm synergistically reduced fluorescence, demonstrating a multifactorial interaction. Using pathway reporter transgenics, we show that the plate reader assay is sensitive at detecting alterations in Hedgehog signaling, a critical regulator of craniofacial development. We go on to demonstrate that this technique readily detects defects in other important cell types, namely neurons. Together, these findings demonstrate this novel in vivo platform can predict developmental abnormalities and multifactorial interactions in high-throughput.
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Affiliation(s)
- Joshua L. Everson
- Department of Molecular Biosciences, School of Natural Sciences, University of Texas at Austin, Austin, Texas, USA,Waggoner Center for Alcohol and Addiction Research, School of Pharmacy, University of Texas at Austin, Austin, Texas, USA
| | - Yung-Chia Tseng
- Department of Molecular Biosciences, School of Natural Sciences, University of Texas at Austin, Austin, Texas, USA
| | - Johann K. Eberhart
- Department of Molecular Biosciences, School of Natural Sciences, University of Texas at Austin, Austin, Texas, USA,Waggoner Center for Alcohol and Addiction Research, School of Pharmacy, University of Texas at Austin, Austin, Texas, USA
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74
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Wang H, Zhang Q, Pi J. Advances in research strategies and approaches for toxicity testing of environmental exposures. Toxicol Appl Pharmacol 2023; 460:116363. [PMID: 36623737 DOI: 10.1016/j.taap.2023.116363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Huihui Wang
- Group of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China; The Key Laboratory of Liaoning Province on Toxic and Biological Effects of Arsenic, Shenyang 110122, China.
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
| | - Jingbo Pi
- The Key Laboratory of Liaoning Province on Toxic and Biological Effects of Arsenic, Shenyang 110122, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China..
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75
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Lu H, Yang D, Shi Y, Chen K, Li P, Huang S, Cui D, Feng Y, Wang T, Yang J, Zhu X, Xia D, Wu Y. Toxicogenomics scoring system: TGSS, a novel integrated risk assessment model for chemical carcinogenicity prediction. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 250:114466. [PMID: 36587411 DOI: 10.1016/j.ecoenv.2022.114466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Given the increasing exposure of humans to environmental chemicals and the limitations of conventional toxicity test, there is an urgent need to develop next-generation risk assessment methods. OBJECTIVES This study aims to establish a novel computational system named Toxicogenomics Scoring System (TGSS) to predict the carcinogenicity of chemicals coupling chemical-gene interactions with multiple cancer transcriptomic datasets. METHODS Chemical-related gene signatures were derived from chemical-gene interaction data from the Comparative Toxicogenomics Database (CTD). For each cancer type in TCGA, genes were ranked by their effects on tumorigenesis, which is based on the differential expression between tumor and normal samples. Next, we developed carcinogenicity scores (C-scores) using pre-ranked GSEA to quantify the correlation between chemical-related gene signatures and ranked gene lists. Then we established TGSS by systematically evaluating the C-scores in multiple chemical-tumor pairs. Furthermore, we examined the performance of our approach by ROC curves or prognostic analyses in TCGA and multiple independent cancer cohorts. RESULTS Forty-six environmental chemicals were finally included in the study. C-score was calculated for each chemical-tumor pair. The C-scores of IARC Group 3 chemicals were significantly lower than those of chemicals in Group 1 (P-value = 0.02) and Group 2 (P-values = 7.49 ×10-5). ROC curves analysis indicated that C-score could distinguish "high-risk chemicals" from the other compounds (AUC = 0.67) with a specificity and sensitivity of 0.86 and 0.57. The results of survival analysis were also in line with the assessed carcinogenicity in TGSS for the chemicals in Group 1. Finally, consistent results were further validated in independent cancer cohorts. CONCLUSION TGSS highlighted the great potential of integrating chemical-gene interactions with gene-cancer relationships to predict the carcinogenic risk of chemicals, which would be valuable for systems toxicology.
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Affiliation(s)
- Haohua Lu
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dexin Yang
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Shi
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kelie Chen
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Peiwei Li
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sisi Huang
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dongyu Cui
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuqin Feng
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tianru Wang
- Epidemiology Stream, Dalla Lana School of Public Health, University of Toronto, M5T 3M7 ON, Canada
| | - Jun Yang
- Department of Public Health, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China; Zhejiang Provincial Center for Uterine Cancer Diagnosis and Therapy Research of Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinqiang Zhu
- Central Laboratory of the Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang, China
| | - Dajing Xia
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Yihua Wu
- Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou, Zhejiang, China.
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76
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Yang H, Obrezanova O, Pointon A, Stebbeds W, Francis J, Beattie KA, Clements P, Harvey JS, Smith GF, Bender A. Prediction of inotropic effect based on calcium transients in human iPSC-derived cardiomyocytes and machine learning. Toxicol Appl Pharmacol 2023; 459:116342. [PMID: 36502871 DOI: 10.1016/j.taap.2022.116342] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/23/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Functional changes to cardiomyocytes are undesirable during drug discovery and identifying the inotropic effects of compounds is hence necessary to decrease the risk of cardiovascular adverse effects in the clinic. Recently, approaches leveraging calcium transients in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have been developed to detect contractility changes, induced by a variety of mechanisms early during drug discovery projects. Although these approaches have been able to provide some predictive ability, we hypothesised that using additional waveform parameters could offer improved insights, as well as predictivity. In this study, we derived 25 parameters from each calcium transient waveform and developed a modified Random Forest method to predict the inotropic effects of the compounds. In total annotated data for 48 compounds were available for modelling, out of which 31 were inotropes. The results show that the Random Forest model with a modified purity criterion performed slightly better than an unmodified algorithm in terms of the Area Under the Curve, giving values of 0.84 vs 0.81 in a cross-validation, and outperformed the ToxCast Pipeline model, for which the highest value was 0.76 when using the best-performing parameter, PW10. Our study hence demonstrates that more advanced parameters derived from waveforms, in combination with additional machine learning methods, provide improved predictivity of cardiovascular risk associated with inotropic effects.
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Affiliation(s)
- Hongbin Yang
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, UK
| | - Olga Obrezanova
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Amy Pointon
- Functional and Mechanistic Safety, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Will Stebbeds
- Screening Profiling and Mechanistic Biology, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, UK
| | - Jo Francis
- Mechanistic & Structural Biology, AstraZeneca, Cambridge, UK
| | - Kylie A Beattie
- Target and Systems Safety, Non-Clinical Safety, In Vivo/In Vitro Translation, GlaxoSmithKline, Ware, UK
| | - Peter Clements
- Pathology UK, Non-Clinical Safety, In Vivo/In Vitro Translation, GlaxoSmithKline, Ware, UK
| | - James S Harvey
- Target and Systems Safety, Non-Clinical Safety, In Vivo/In Vitro Translation, GlaxoSmithKline, Ware, UK
| | - Graham F Smith
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, UK.
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77
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Smeltz MG, Clifton MS, Henderson WM, McMillan L, Wetmore BA. Targeted Per- and Polyfluoroalkyl substances (PFAS) assessments for high throughput screening: Analytical and testing considerations to inform a PFAS stock quality evaluation framework. Toxicol Appl Pharmacol 2023; 459:116355. [PMID: 36535553 PMCID: PMC10367912 DOI: 10.1016/j.taap.2022.116355] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/25/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Per- and polyfluoroalkyl substances (PFAS) represent a large chemical class lacking hazard, toxicokinetic, and exposure information. To accelerate PFAS hazard evaluation, new approach methodologies (NAMs) comprised of in vitro high-throughput toxicity screening, toxicokinetic data, and computational modeling are being employed in read across strategies to evaluate the larger PFAS landscape. A critical consideration to ensure robust evaluations is a parallel assessment of the quality of the screening stock solutions, where dimethyl sulfoxide (DMSO) is often the diluent of choice. Challenged by the lack of commercially available reference standards for many of the selected PFAS and reliance on mass spectrometry approaches for such an evaluation, we developed a high-throughput framework to evaluate the quality of screening stocks for 205 PFAS selected for these NAM efforts. Using mass spectrometry coupled with either liquid or gas chromatography, a quality scoring system was developed that incorporated observations during mass spectral examination to provide a simple pass or fail notation. Informational flags were used to further describe findings regarding parent analyte presence through accurate mass identification, evidence of contaminants and/or degradation, or further describe characteristics such as isomer presence. Across the PFAS-DMSO stocks tested, 148 unique PFAS received passing quality scores to allow for further in vitro testing whereas 57 received a failing score primarily due to detection issues or confounding effects of DMSO. Principle component analysis indicated vapor pressure and Henry's Law Constant as top indicators for a failed quality score for those analyzed by gas chromatography. Three PFAS in the hexafluoropropylene oxide family failed due to degradation in DMSO. As the PFAS evaluated spanned over 20 different structural categories, additional commentary describes analytical observations across specific groups related to PFAS stock composition, detection, stability, and methodologic considerations that will be useful for informing future analytical assessment and downstream HTS efforts. The high-throughput stock quality scoring workflow presented holds value as a tool to evaluate chemical presence and quality efficiently and for informing data inclusion in PFAS or other NAM screening efforts.
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Affiliation(s)
- Marci G Smeltz
- Center for Computational Toxicology and Exposure, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, NC 27711, United States of America
| | - M Scott Clifton
- Center for Environmental Measurement and Modeling, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, NC 27711, United States of America
| | - W Matthew Henderson
- Center for Environmental Measurement and Modeling, Office of Research and Development, United States Environmental Protection Agency, Athens, GA 23605, United States of America
| | - Larry McMillan
- National Caucus and Center on Black Aged, Inc, Durham, NC, United States of America
| | - Barbara A Wetmore
- Center for Computational Toxicology and Exposure, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, NC 27711, United States of America.
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78
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Bouwmeester MC, Tao Y, Proença S, van Steenbeek FG, Samsom RA, Nijmeijer SM, Sinnige T, van der Laan LJW, Legler J, Schneeberger K, Kramer NI, Spee B. Drug Metabolism of Hepatocyte-like Organoids and Their Applicability in In Vitro Toxicity Testing. Molecules 2023; 28:molecules28020621. [PMID: 36677681 PMCID: PMC9867526 DOI: 10.3390/molecules28020621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Emerging advances in the field of in vitro toxicity testing attempt to meet the need for reliable human-based safety assessment in drug development. Intrahepatic cholangiocyte organoids (ICOs) are described as a donor-derived in vitro model for disease modelling and regenerative medicine. Here, we explored the potential of hepatocyte-like ICOs (HL-ICOs) in in vitro toxicity testing by exploring the expression and activity of genes involved in drug metabolism, a key determinant in drug-induced toxicity, and the exposure of HL-ICOs to well-known hepatotoxicants. The current state of drug metabolism in HL-ICOs showed levels comparable to those of PHHs and HepaRGs for CYP3A4; however, other enzymes, such as CYP2B6 and CYP2D6, were expressed at lower levels. Additionally, EC50 values were determined in HL-ICOs for acetaminophen (24.0−26.8 mM), diclofenac (475.5−>500 µM), perhexiline (9.7−>31.5 µM), troglitazone (23.1−90.8 µM), and valproic acid (>10 mM). Exposure to the hepatotoxicants showed EC50s in HL-ICOs comparable to those in PHHs and HepaRGs; however, for acetaminophen exposure, HL-ICOs were less sensitive. Further elucidation of enzyme and transporter activity in drug metabolism in HL-ICOs and exposure to a more extensive compound set are needed to accurately define the potential of HL-ICOs in in vitro toxicity testing.
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Affiliation(s)
- Manon C. Bouwmeester
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Regenerative Medicine Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Yu Tao
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Regenerative Medicine Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Susana Proença
- Division of Toxicology, Wageningen University, 6700 EA Wageningen, The Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Frank G. van Steenbeek
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Regenerative Medicine Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Roos-Anne Samsom
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Regenerative Medicine Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Sandra M. Nijmeijer
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Theo Sinnige
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Luc J. W. van der Laan
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
| | - Juliette Legler
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Kerstin Schneeberger
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Regenerative Medicine Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Nynke I. Kramer
- Division of Toxicology, Wageningen University, 6700 EA Wageningen, The Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Bart Spee
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Regenerative Medicine Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
- Correspondence:
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79
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Chapman F, Pour SJ, Wieczorek R, Trelles Sticken E, Budde J, Röwer K, Otte S, Mason E, Czekala L, Nahde T, O'Connell G, Simms L, Stevenson M. Twenty-eight day repeated exposure of human 3D bronchial epithelial model to heated tobacco aerosols indicates decreased toxicological responses compared to cigarette smoke. FRONTIERS IN TOXICOLOGY 2023; 5:1076752. [PMID: 36875887 PMCID: PMC9979258 DOI: 10.3389/ftox.2023.1076752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/09/2023] [Indexed: 02/18/2023] Open
Abstract
Tobacco harm reduction (THR) involves providing adult smokers with potentially reduced harm modes of nicotine delivery as alternatives to smoking combustible cigarettes. Heated tobacco products (HTPs) form a category with THR potential due to their ability to deliver nicotine and flavours through heating, not burning, tobacco. By eliminating burning, heated tobacco does not produce smoke but an aerosol which contains fewer and lower levels of harmful chemicals compared to cigarette smoke. In this study we assessed the in vitro toxicological profiles of two prototype HTPs' aerosols compared to the 1R6F reference cigarette using the 3D human (bronchial) MucilAir™ model. To increase consumer relevance, whole aerosol/smoke exposures were delivered repeatedly across a 28 day period (16, 32, or 48 puffs per exposure). Cytotoxicity (LDH secretion), histology (Alcian Blue/H&E; Muc5AC; FoxJ1 staining), cilia active area and beat frequency and inflammatory marker (IL-6; IL-8; MMP-1; MMP-3; MMP-9; TNFα) levels were assessed. Diluted 1R6F smoke consistently induced greater and earlier effects compared to the prototype HTP aerosols across the endpoints, and in a puff dependent manner. Although some significant changes across the endpoints were induced by exposure to the HTPs, these were substantially less pronounced and less frequently observed, with apparent adaptive responses occurring over the experimental period. Furthermore, these differences between the two product categories were observed at a greater dilution (and generally lower nicotine delivery range) for 1R6F (1R6F smoke diluted 1/14, HTP aerosols diluted 1/2, with air). Overall, the findings demonstrate the THR potential of the prototype HTPs through demonstrated substantial reductions in toxicological outcomes in in vitro 3D human lung models.
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Affiliation(s)
| | | | | | | | | | - Karin Röwer
- Reemtsma Cigarettenfabriken GmbH, Hamburg, Germany
| | - Sandra Otte
- Reemtsma Cigarettenfabriken GmbH, Hamburg, Germany
| | | | | | - Thomas Nahde
- Reemtsma Cigarettenfabriken GmbH, Hamburg, Germany
| | | | - Liam Simms
- Imperial Brands PLC, Bristol, United Kingdom
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80
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Villeneuve DL, Blackwell BR, Blanksma CA, Cavallin JE, Cheng WY, Conolly RB, Conrow K, Feifarek DJ, Heinis LJ, Jensen KM, Kahl MD, Milsk RY, Poole ST, Randolph EC, Saari TW, Watanabe KH, Ankley GT. Case Study in 21st-Century Ecotoxicology: Using In Vitro Aromatase Inhibition Data to Predict Reproductive Outcomes in Fish In Vivo. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:100-116. [PMID: 36282016 PMCID: PMC10782516 DOI: 10.1002/etc.5504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/24/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
To reduce the use of intact animals for chemical safety testing, while ensuring protection of ecosystems and human health, there is a demand for new approach methodologies (NAMs) that provide relevant scientific information at a quality equivalent to or better than traditional approaches. The present case study examined whether bioactivity and associated potency measured in an in vitro screening assay for aromatase inhibition could be used together with an adverse outcome pathway (AOP) and mechanistically based computational models to predict previously uncharacterized in vivo effects. Model simulations were used to inform designs of 60-h and 10-21-day in vivo exposures of adult fathead minnows (Pimephales promelas) to three or four test concentrations of the in vitro aromatase inhibitor imazalil ranging from 0.12 to 260 µg/L water. Consistent with an AOP linking aromatase inhibition to reproductive impairment in fish, exposure to the fungicide resulted in significant reductions in ex vivo production of 17β-estradiol (E2) by ovary tissue (≥165 µg imazalil/L), plasma E2 concentrations (≥74 µg imazalil/L), vitellogenin (Vtg) messenger RNA expression (≥165 µg imazalil/L), Vtg plasma concentrations (≥74 µg imazalil/L), uptake of Vtg into oocytes (≥260 µg imazalil/L), and overall reproductive output in terms of cumulative fecundity, number of spawning events, and eggs per spawning event (≥24 µg imazalil/L). Despite many potential sources of uncertainty in potency and efficacy estimates based on model simulations, observed magnitudes of apical effects were quite consistent with model predictions, and in vivo potency was within an order of magnitude of that predicted based on in vitro relative potency. Overall, our study suggests that NAMs and AOP-based approaches can support meaningful reduction and refinement of animal testing. Environ Toxicol Chem 2023;42:100-116. © 2022 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Daniel L. Villeneuve
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Brett R. Blackwell
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | | | - Jenna E. Cavallin
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Wan-Yun Cheng
- US Environmental Protection Agency, Integrated Systems Toxicology Division, Research Triangle Park, NC, USA
| | - Rory B. Conolly
- US Environmental Protection Agency, Integrated Systems Toxicology Division, Research Triangle Park, NC, USA
| | - Kendra Conrow
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306-4908
| | - David J. Feifarek
- Student Services Contractor, US EPA Mid-Continent Ecology Division, Duluth, MN, USA
| | - Larry J. Heinis
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Kathleen M. Jensen
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Michael D. Kahl
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Rebecca Y. Milsk
- ORISE Participant, US EPA Mid-Continent Ecology Division, Duluth, MN, USA
| | - Shane T. Poole
- Student Services Contractor, US EPA Mid-Continent Ecology Division, Duluth, MN, USA
| | - Eric C. Randolph
- ORISE Participant, US EPA Mid-Continent Ecology Division, Duluth, MN, USA
| | - Travis W. Saari
- Student Services Contractor, US EPA Mid-Continent Ecology Division, Duluth, MN, USA
| | - Karen H. Watanabe
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306-4908
| | - Gerald T. Ankley
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
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81
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Saarimäki LA, Morikka J, Pavel A, Korpilähde S, del Giudice G, Federico A, Fratello M, Serra A, Greco D. Toxicogenomics Data for Chemical Safety Assessment and Development of New Approach Methodologies: An Adverse Outcome Pathway-Based Approach. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203984. [PMID: 36479815 PMCID: PMC9839874 DOI: 10.1002/advs.202203984] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/09/2022] [Indexed: 05/25/2023]
Abstract
Mechanistic toxicology provides a powerful approach to inform on the safety of chemicals and the development of safe-by-design compounds. Although toxicogenomics supports mechanistic evaluation of chemical exposures, its implementation into the regulatory framework is hindered by uncertainties in the analysis and interpretation of such data. The use of mechanistic evidence through the adverse outcome pathway (AOP) concept is promoted for the development of new approach methodologies (NAMs) that can reduce animal experimentation. However, to unleash the full potential of AOPs and build confidence into toxicogenomics, robust associations between AOPs and patterns of molecular alteration need to be established. Systematic curation of molecular events to AOPs will create the much-needed link between toxicogenomics and systemic mechanisms depicted by the AOPs. This, in turn, will introduce novel ways of benefitting from the AOPs, including predictive models and targeted assays, while also reducing the need for multiple testing strategies. Hence, a multi-step strategy to annotate AOPs is developed, and the resulting associations are applied to successfully highlight relevant adverse outcomes for chemical exposures with strong in vitro and in vivo convergence, supporting chemical grouping and other data-driven approaches. Finally, a panel of AOP-derived in vitro biomarkers for pulmonary fibrosis (PF) is identified and experimentally validated.
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Affiliation(s)
- Laura Aliisa Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Jack Morikka
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Alisa Pavel
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Seela Korpilähde
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Giusy del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Antonio Federico
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Michele Fratello
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Angela Serra
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
- Tampere Institute for Advanced StudyTampere UniversityKalevantie 4Tampere33100Finland
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
- Institute of BiotechnologyUniversity of HelsinkiP.O.Box 56HelsinkiUusimaa00014Finland
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82
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Marx-Stoelting P, Rivière G, Luijten M, Aiello-Holden K, Bandow N, Baken K, Cañas A, Castano A, Denys S, Fillol C, Herzler M, Iavicoli I, Karakitsios S, Klanova J, Kolossa-Gehring M, Koutsodimou A, Vicente JL, Lynch I, Namorado S, Norager S, Pittman A, Rotter S, Sarigiannis D, Silva MJ, Theunis J, Tralau T, Uhl M, van Klaveren J, Wendt-Rasch L, Westerholm E, Rousselle C, Sanders P. A walk in the PARC: developing and implementing 21st century chemical risk assessment in Europe. Arch Toxicol 2023; 97:893-908. [PMID: 36645448 PMCID: PMC9968685 DOI: 10.1007/s00204-022-03435-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 01/17/2023]
Abstract
Current approaches for the assessment of environmental and human health risks due to exposure to chemical substances have served their purpose reasonably well. Nevertheless, the systems in place for different uses of chemicals are faced with various challenges, ranging from a growing number of chemicals to changes in the types of chemicals and materials produced. This has triggered global awareness of the need for a paradigm shift, which in turn has led to the publication of new concepts for chemical risk assessment and explorations of how to translate these concepts into pragmatic approaches. As a result, next-generation risk assessment (NGRA) is generally seen as the way forward. However, incorporating new scientific insights and innovative approaches into hazard and exposure assessments in such a way that regulatory needs are adequately met has appeared to be challenging. The European Partnership for the Assessment of Risks from Chemicals (PARC) has been designed to address various challenges associated with innovating chemical risk assessment. Its overall goal is to consolidate and strengthen the European research and innovation capacity for chemical risk assessment to protect human health and the environment. With around 200 participating organisations from all over Europe, including three European agencies, and a total budget of over 400 million euro, PARC is one of the largest projects of its kind. It has a duration of seven years and is coordinated by ANSES, the French Agency for Food, Environmental and Occupational Health & Safety.
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Affiliation(s)
- P. Marx-Stoelting
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - G. Rivière
- grid.15540.350000 0001 0584 7022French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 94701 Maisons-Alfort, France
| | - M. Luijten
- National Institute for Health and Environment (RIVM), Bilthoven, The Netherlands
| | - K. Aiello-Holden
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - N. Bandow
- grid.425100.20000 0004 0554 9748German Environment Agency (UBA), Wörlitzer Platz 1, 06844 Dessau, Germany
| | - K. Baken
- grid.6717.70000000120341548VITO (Flemish Institute for Technological Research), Boeretang 200, 2400 Mol, Belgium
| | - A. Cañas
- grid.413448.e0000 0000 9314 1427National Centre for Environmental Health, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - A. Castano
- grid.413448.e0000 0000 9314 1427National Centre for Environmental Health, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - S. Denys
- grid.493975.50000 0004 5948 8741Santé Publique France (SpFrance), 12, Rue du Val D’Osne, 94415 St. Maurice, France
| | - C. Fillol
- grid.493975.50000 0004 5948 8741Santé Publique France (SpFrance), 12, Rue du Val D’Osne, 94415 St. Maurice, France
| | - M. Herzler
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - I. Iavicoli
- grid.4691.a0000 0001 0790 385XDepartment of Public Health, University of Naples Federico II (UNINA), Naples, Italy
| | - S. Karakitsios
- grid.4793.90000000109457005Aristoteles University Thessaloniki (AUTH), Thessaloniki, Greece
| | - J. Klanova
- Masaryk Uinversity, Recetox, Kotlarska 2, 61137 Brno, Czechia
| | - M. Kolossa-Gehring
- grid.425100.20000 0004 0554 9748German Environment Agency (UBA), Wörlitzer Platz 1, 06844 Dessau, Germany
| | - A. Koutsodimou
- General Chemical State Laboratory of Greece, Athens, Greece
| | - J. Lobo Vicente
- grid.453985.60000 0004 0619 3405European Environment Agency, Kongens Nytorv 6, 1050 Copenhagen K, Denmark
| | - I. Lynch
- grid.6572.60000 0004 1936 7486School of Geography, Earth and Environmental Sciences, University of Birmingham (UoB), Edgbaston, Birmingham, B15 2TT UK
| | - S. Namorado
- grid.422270.10000 0001 2287 695XNational Institute of Health Dr. Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - S. Norager
- grid.270680.bEuropean Commission, DG Research and Innovation, Orban 09/199, 1049 Brussels, Belgium
| | - A. Pittman
- grid.15540.350000 0001 0584 7022French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 94701 Maisons-Alfort, France
| | - S. Rotter
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - D. Sarigiannis
- grid.4793.90000000109457005Aristoteles University Thessaloniki (AUTH), Thessaloniki, Greece
| | - M. J. Silva
- grid.422270.10000 0001 2287 695XNational Institute of Health Dr. Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - J. Theunis
- grid.6717.70000000120341548VITO (Flemish Institute for Technological Research), Boeretang 200, 2400 Mol, Belgium
| | - T. Tralau
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - M. Uhl
- Austrian Federal Environments Agency, Vienna, Austria
| | - J. van Klaveren
- National Institute for Health and Environment (RIVM), Bilthoven, The Netherlands
| | - L. Wendt-Rasch
- grid.437386.d0000 0001 1523 2072Swedish Chemicals Agency (KemI), Vasagatan 12D, 172 67 Sundbyberg, Sweden
| | - E. Westerholm
- grid.437386.d0000 0001 1523 2072Swedish Chemicals Agency (KemI), Vasagatan 12D, 172 67 Sundbyberg, Sweden
| | - C. Rousselle
- grid.15540.350000 0001 0584 7022French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 94701 Maisons-Alfort, France
| | - P. Sanders
- grid.15540.350000 0001 0584 7022French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 94701 Maisons-Alfort, France
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83
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Khalid A, Yi W, Yoo S, Abbas S, Si J, Hou X, Hou J. Single-chirality of single-walled carbon nanotubes (SWCNTs) through chromatography and its potential biological applications. NEW J CHEM 2023. [DOI: 10.1039/d2nj04056e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Gel chromatography is used to separate single-chirality and selective-diameter SWCNTs. We also explore the use of photothermal therapy and biosensor applications based on single-chirality, selected-diameter, and unique geometric shape.
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Affiliation(s)
- Asif Khalid
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Wenhui Yi
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Sweejiang Yoo
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Shakeel Abbas
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Jinhai Si
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Xun Hou
- Key Laboratory for Information Photonic Technology of Shaanxi & Key Laboratory for Physical Electronics and Devices of the Ministry of Education, School of Electronics Science and Engineering, Faculty of Electronics and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China
| | - Jin Hou
- Department of Pharmacology, School of Basic Medical Science, Xi’an Medical University, Xi’an, Shaanxi, 710021, China
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84
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Bhalla D, Steijaert MN, Poppelaars ES, Teunis M, van der Voet M, Corradi M, Dévière E, Noothout L, Tomassen W, Rooseboom M, Currie RA, Krul C, Pieters R, van Noort V, Wildwater M. DARTpaths, an in silico platform to investigate molecular mechanisms of compounds. Bioinformatics 2023; 39:6883905. [PMID: 36477801 PMCID: PMC9825785 DOI: 10.1093/bioinformatics/btac767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/11/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
SUMMARY Xpaths is a collection of algorithms that allow for the prediction of compound-induced molecular mechanisms of action by integrating phenotypic endpoints of different species; and proposes follow-up tests for model organisms to validate these pathway predictions. The Xpaths algorithms are applied to predict developmental and reproductive toxicity (DART) and implemented into an in silico platform, called DARTpaths. AVAILABILITY AND IMPLEMENTATION All code is available on GitHub https://github.com/Xpaths/dartpaths-app under Apache license 2.0, detailed overview with demo is available at https://www.vivaltes.com/dartpaths/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | | | | | - Marie Corradi
- Innovative Testing in Life Sciences & Chemistry, Utrecht University of Applied Sciences, Utrecht 3584 CH, The Netherlands
| | | | | | | | - Martijn Rooseboom
- Toxicology Group, Shell Global Solutions International B.V., The Hague 2596 HR, the Netherlands
| | - Richard A Currie
- Predictive and Computational Toxicology, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Cyrille Krul
- Innovative Testing in Life Sciences & Chemistry, Utrecht University of Applied Sciences, Utrecht 3584 CH, The Netherlands
| | - Raymond Pieters
- Innovative Testing in Life Sciences & Chemistry, Utrecht University of Applied Sciences, Utrecht 3584 CH, The Netherlands
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht 3584 CM, The Netherlands
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85
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Cavasotto CN, Scardino V. Machine Learning Toxicity Prediction: Latest Advances by Toxicity End Point. ACS OMEGA 2022; 7:47536-47546. [PMID: 36591139 PMCID: PMC9798519 DOI: 10.1021/acsomega.2c05693] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/28/2022] [Indexed: 05/29/2023]
Abstract
Machine learning (ML) models to predict the toxicity of small molecules have garnered great attention and have become widely used in recent years. Computational toxicity prediction is particularly advantageous in the early stages of drug discovery in order to filter out molecules with high probability of failing in clinical trials. This has been helped by the increase in the number of large toxicology databases available. However, being an area of recent application, a greater understanding of the scope and applicability of ML methods is still necessary. There are various kinds of toxic end points that have been predicted in silico. Acute oral toxicity, hepatotoxicity, cardiotoxicity, mutagenicity, and the 12 Tox21 data end points are among the most commonly investigated. Machine learning methods exhibit different performances on different data sets due to dissimilar complexity, class distributions, or chemical space covered, which makes it hard to compare the performance of algorithms over different toxic end points. The general pipeline to predict toxicity using ML has already been analyzed in various reviews. In this contribution, we focus on the recent progress in the area and the outstanding challenges, making a detailed description of the state-of-the-art models implemented for each toxic end point. The type of molecular representation, the algorithm, and the evaluation metric used in each research work are explained and analyzed. A detailed description of end points that are usually predicted, their clinical relevance, the available databases, and the challenges they bring to the field are also highlighted.
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Affiliation(s)
- Claudio N. Cavasotto
- Computational
Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones
en Medicina Traslacional (IIMT), CONICET-Universidad
Austral, Pilar, B1629AHJ Buenos Aires, Argentina
- Austral
Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, B1629AHJ Buenos Aires, Argentina
- Facultad
de Ciencias Biomédicas, Facultad de Ingenierá, Universidad Austral, Pilar, B1630FHB Buenos
Aires, Argentina
| | - Valeria Scardino
- Austral
Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, B1629AHJ Buenos Aires, Argentina
- Meton
AI, Inc., Wilmington, Delaware 19801, United
States
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86
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Villeneuve DL, Le M, Hazemi M, Biales A, Bencic DC, Bush K, Flick R, Martinson J, Morshead M, Rodriguez KS, Vitense K, Flynn K. Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay. Curr Res Toxicol 2022; 4:100099. [PMID: 36619288 PMCID: PMC9816907 DOI: 10.1016/j.crtox.2022.100099] [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: 08/17/2022] [Revised: 11/03/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Concentrations at which global gene expression profiles in cells or animals exposed to a test substance start to differ significantly from those of controls have been proposed as an alternative point of departure for use in screening level hazard assessment. The present study describes pilot testing of a high throughput compatible transcriptomics assay with larval fathead minnows. One day post hatch fathead minnows were exposed to eleven different concentrations of three metals, three selective serotonin reuptake inhibitors, and four neonicotinoid-like compounds for 24 h and concentration response modeling was applied to whole body gene expression data. Transcriptomics-based points of departure (tPODs) were consistently lower than effect concentrations reported in apical endpoint studies in fish. However, larval fathead minnow-based tPODs were not always lower than concentrations reported to elicit apical toxicity in other aquatic organisms like crustaceans or insects. Random in silico subsampling of data from the pilot assays was used to evaluate various assay design and acceptance considerations such as transcriptome coverage, number of replicate individuals to sequence per treatment, and minimum number of differentially expressed genes to produce a reliable tPOD estimate. Results showed a strong association between the total number of genes for which a concentration response relationship could be derived and the overall variability in the resulting tPOD estimates. We conclude that, for our current assay design and analysis pipeline, tPODs based on fewer than 15 differentially expressed genes are likely to be unreliable for screening and that interindividual variability in gene expression profiles appears to be a more significant driver of tPOD variability than sample size alone. Results represent initial steps toward developing high throughput transcriptomics assays for use in ecological hazard screening.
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Key Words
- BMD, Benchmark dose
- Benchmark dose
- Computational toxicology
- DEGs, Differentially expressed genes
- ECOTOX knowledgebase
- Fish
- HTTr, High throughput transcriptomics
- RIN, RNA integrity number
- RNA sequencing
- RNAseq, RNA sequencing
- SSRI, Selective serotonin reuptake inhibitor
- ToxCast, US EPA Toxicity Forecaster
- Transcriptomics-based point of departure
- cDNA, Complementary DNA
- eco-HTTr, Ecological high throughput transcriptomics
- tPOD, Transcriptomics-based point of departure
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Affiliation(s)
- Daniel L. Villeneuve
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA,Corresponding author at: U.S. EPA Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd., Duluth, MN 55804-2595, USA.
| | - Michelle Le
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Monique Hazemi
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Adam Biales
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Cincinnati, OH 45220, USA
| | - David C. Bencic
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Cincinnati, OH 45220, USA
| | - Kendra Bush
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Robert Flick
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Cincinnati, OH 45220, USA
| | - John Martinson
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Cincinnati, OH 45220, USA
| | - Mackenzie Morshead
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Kelvin Santana Rodriguez
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Kelsey Vitense
- US Environmental Protection Agency, Scientific Computing and Data Curation Division, Duluth, MN 55804, USA
| | - Kevin Flynn
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
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87
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Oliveira-Filho EC, Grisolia CK. The Ecotoxicology of Microbial Insecticides and Their Toxins in Genetically Modified Crops: An Overview. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16495. [PMID: 36554372 PMCID: PMC9778766 DOI: 10.3390/ijerph192416495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
The use of microbial insecticides and their toxins in biological control and transgenic plants has increased their presence in the environment. Although they are natural products, the main concerns are related to the potential impacts on the environment and human health. Several assays have been performed worldwide to investigate the toxicity or adverse effects of these microbial products or their individual toxins. This overview examines the published data concerning the knowledge obtained about the ecotoxicity and environmental risks of these natural pesticides. The data presented show that many results are difficult to compare due to the diversity of measurement units used in the different research data. Even so, the products and toxins tested present low toxicity and low risk when compared to the concentrations used for pesticide purposes. Complementary studies should be carried out to assess possible effects on human health.
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Affiliation(s)
| | - Cesar K. Grisolia
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília 70910-900, DF, Brazil
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88
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Development of a novel ex vivo model for chemical ocular toxicity assessment and its applicability for hair straightening products. Food Chem Toxicol 2022; 170:113457. [DOI: 10.1016/j.fct.2022.113457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/09/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
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89
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Saha S, Chukwuka AV, Mukherjee D, Dhara K, Saha NC, Faggio C. Behavioral and physiological toxicity thresholds of a freshwater vertebrate (Heteropneustes fossilis) and invertebrate (Branchiura sowerbyi), exposed to zinc oxide nanoparticles (nZnO): A General Unified Threshold model of Survival (GUTS). Comp Biochem Physiol C Toxicol Pharmacol 2022; 262:109450. [PMID: 36058464 DOI: 10.1016/j.cbpc.2022.109450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/10/2022] [Accepted: 08/29/2022] [Indexed: 11/26/2022]
Abstract
The toxic effects of Zinc oxide nanoparticles (nZnO) on Branchiura sowerbyi and Heteropneustes fossilis, was assessed in a 96-hour acute exposure regime using behavioral (including loss-of balance and clumping tendencies) and physiological (mucus secretion and oxygen consumption) endpoints. While the relationship between behavioral, physiological biomarkers, and exposure concentrations was assessed using correlation analysis, nZnO toxicity was further predicted using the General Unified Threshold model for Survival (GUTS). The time-dependent lethal limits for acute nZnO toxicity (LC50) on B. sowerbyi were estimated to be 0.668, 0.588, 0.448, and 0.400 mg/l, respectively, at 24, 48, 72, and 96 h whereas for H. fossilis the LC50 values are 0.954, 0.905, 0.874 and 0.838 mg/l. Threshold effect values i.e., LOEC (Lowest Observed Effect Concentration), NOEC (No Observed Effect Concentration), and MATC (Maximum Acceptable Toxicant Concentration) threshold effect values at 96 h were higher for fish compared to the oligochaete. For B. sowerbyi, the GUTS-SD (stochastic death) model is a better predictor of nanoparticle exposure effects compared to the GUTS-IT (individual tolerance) model, however in the case of H. fossilis, the reverse pattern was observed. Oxygen consumption rate was negatively correlated to mortality under acute exposure duration. The strong negative correlation between mortality and oxygen consumption strongly suggests a metabolic-toxicity pathway for nZnO exposure effects. The higher toxicity threshold values i.e., LOEC, NOEC, and MATC for fish compared to the oligochaete invertebrate indicates greater risks for invertebrates compared to vertebrates, with resultant implications for local habitat trophic relationships.
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Affiliation(s)
- Shubhajit Saha
- Department of Zoology, Sundarban Hazi Desarat College, South 24, Parganas 743 611, West Bengal, India. https://twitter.com/@DrShubhajitS
| | - Azubuike V Chukwuka
- National Environmental Standards and Regulations Enforcement Agency (NESREA), Nigeria
| | - Dip Mukherjee
- Department of Zoology, S.B.S. Government College, Hili, Dakshin Dinajpur 733126, India
| | - Kishore Dhara
- Freshwater Fisheries Research & Training Centre, Directorate of Fisheries, Kalyani, Nadia 741 251, India
| | - Nimai Chandra Saha
- Department of Zoology, University of Burdwan, Purba Barddhaman 713 104, India.
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy.
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90
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Brockmeier EK, Basili D, Herbert J, Rendal C, Boakes L, Grauslys A, Taylor NS, Danby EB, Gutsell S, Kanda R, Cronin M, Barclay J, Antczak P, Viant MR, Hodges G, Falciani F. Data-driven learning of narcosis mode of action identifies a CNS transcriptional signature shared between whole organism Caenorhabditis elegans and a fish gill cell line. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157666. [PMID: 35908689 DOI: 10.1016/j.scitotenv.2022.157666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/27/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
With the large numbers of man-made chemicals produced and released in the environment, there is a need to provide assessments on their potential effects on environmental safety and human health. Current regulatory frameworks rely on a mix of both hazard and risk-based approaches to make safety decisions, but the large number of chemicals in commerce combined with an increased need to conduct assessments in the absence of animal testing makes this increasingly challenging. This challenge is catalysing the use of more mechanistic knowledge in safety assessment from both in silico and in vitro approaches in the hope that this will increase confidence in being able to identify modes of action (MoA) for the chemicals in question. Here we approach this challenge by testing whether a functional genomics approach in C. elegans and in a fish cell line can identify molecular mechanisms underlying the effects of narcotics, and the effects of more specific acting toxicants. We show that narcosis affects the expression of neuronal genes associated with CNS function in C. elegans and in a fish cell line. Overall, we believe that our study provides an important step in developing mechanistically relevant biomarkers which can be used to screen for hazards, and which prevent the need for repeated animal or cross-species comparisons for each new chemical.
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Affiliation(s)
- Erica K Brockmeier
- Department of Biochemistry & System Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Danilo Basili
- Department of Biochemistry & System Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; Safety and Environmental Assurance Centre (SEAC), Unilever, Colworth Park, Sharnbrook, UK
| | - John Herbert
- Department of Biochemistry & System Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Cecilie Rendal
- Safety and Environmental Assurance Centre (SEAC), Unilever, Colworth Park, Sharnbrook, UK
| | - Leigh Boakes
- Department of Biochemistry & System Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; Christeyns Food Hygiene, Warrington, UK
| | - Arturas Grauslys
- Department of Biochemistry & System Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; Computational Biology Facility (CBF), University of Liverpool, Liverpool, UK
| | - Nadine S Taylor
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Emma Butler Danby
- Safety and Environmental Assurance Centre (SEAC), Unilever, Colworth Park, Sharnbrook, UK
| | - Steve Gutsell
- Safety and Environmental Assurance Centre (SEAC), Unilever, Colworth Park, Sharnbrook, UK
| | - Rakesh Kanda
- Institute of Environment, Health and Societies, Brunel University, London, UK
| | - Mark Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Jeff Barclay
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Philipp Antczak
- Department of Biochemistry & System Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; Computational Biology Facility (CBF), University of Liverpool, Liverpool, UK
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Geoff Hodges
- Safety and Environmental Assurance Centre (SEAC), Unilever, Colworth Park, Sharnbrook, UK
| | - Francesco Falciani
- Department of Biochemistry & System Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; Computational Biology Facility (CBF), University of Liverpool, Liverpool, UK.
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91
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Everson JL, Eberhart JK. Gene-alcohol interactions in birth defects. Curr Top Dev Biol 2022; 152:77-113. [PMID: 36707215 PMCID: PMC9897481 DOI: 10.1016/bs.ctdb.2022.10.003] [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] [Indexed: 11/16/2022]
Abstract
Most human birth defects are thought to result from complex interactions between combinations of genetic and environmental factors. This is true even for conditions that, at face value, may appear simple and straightforward, like fetal alcohol spectrum disorders (FASD). FASD describe the full range of structural and neurological disruptions that result from prenatal alcohol exposure. While FASD require alcohol exposure, evidence from human and animal model studies demonstrate that additional genetic and/or environmental factors can influence the embryo's susceptibility to alcohol. Only a limited number of alcohol interactions in birth defects have been identified, with many sensitizing genetic and environmental factors likely yet to be identified. Because of this, while unsatisfying, there is no definitively "safe" dose of alcohol for all pregnancies. Determining these other factors, as well as mechanistically characterizing known interactions, is critical for better understanding and preventing FASD and requires combined scrutiny of human and model organism studies.
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Affiliation(s)
- Joshua L Everson
- Department of Molecular Biosciences, School of Natural Sciences, University of Texas at Austin, Austin, TX, United States; Waggoner Center for Alcohol and Addiction Research, School of Pharmacy, University of Texas at Austin, Austin, TX, United States.
| | - Johann K Eberhart
- Department of Molecular Biosciences, School of Natural Sciences, University of Texas at Austin, Austin, TX, United States; Waggoner Center for Alcohol and Addiction Research, School of Pharmacy, University of Texas at Austin, Austin, TX, United States.
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92
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Chen Q, Riviere JE, Lin Z. Toxicokinetics, dose-response, and risk assessment of nanomaterials: Methodology, challenges, and future perspectives. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1808. [PMID: 36416026 PMCID: PMC9699155 DOI: 10.1002/wnan.1808] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/24/2022]
Abstract
The rapid growth of nanomaterial applications has raised safety concerns for human health. A number of studies have been conducted to assess the toxicokinetics, toxicology, dose-response, and risk assessment of different nanomaterials using in vitro and in vivo animal and human models. However, current studies cannot meet the demand for efficient assessment of toxicokinetics, dose-response relationships, or the toxicological risk arising from the rapidly increasing number of newly synthesized nanomaterials. In this article, we review the methods for conducting toxicokinetics, hazard identification, dose-response, exposure, and risk assessment studies of nanomaterials, identify the knowledge gaps, and discuss the challenges remaining. We provide the rationale behind the appropriate design of nanomaterial plasma toxicokinetic and tissue distribution studies, including caveats on the interpretation and correlation of in vitro and in vivo toxicology studies. The potential of using physiologically based pharmacokinetic (PBPK) models to extrapolate toxicokinetic and toxicity findings from in vitro to in vivo and from animals to humans is discussed, and the knowledge gaps of PBPK modeling for nanomaterials are identified. While challenges still exist, there has been progress in the toxicokinetics, hazard identification, and risk assessment of nanomaterials in the past two decades. Recent advancements in the field are highlighted with relevant examples. We also share latest guidelines as well as our perspectives on future studies needed to characterize the toxicokinetics, toxicity, and dose-response relationship in support of nanomaterial risk assessment. This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials Toxicology and Regulatory Issues in Nanomedicine > Regulatory and Policy Issues in Nanomedicine.
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Affiliation(s)
- Qiran Chen
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, USA
| | - Jim E. Riviere
- 1Data Consortium, Kansas State University, Olathe, Kansas, USA
- Center for Chemical Toxicology Research and Pharmacokinetics, Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Zhoumeng Lin
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, USA
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93
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Confirmation of high-throughput screening data and novel mechanistic insights into FXR-xenobiotic interactions by orthogonal assays. Curr Res Toxicol 2022; 3:100092. [PMID: 36353521 PMCID: PMC9637864 DOI: 10.1016/j.crtox.2022.100092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/05/2022] Open
Abstract
Toxicology in the 21st Century (Tox21) is a federal collaboration employing a high-throughput robotic screening system to test 10,000 environmental chemicals. One of the primary goals of the program is prioritizing toxicity evaluations through in vitro high-throughput screening (HTS) assays for large numbers of chemicals already in commercial use for which little or no toxicity data is available. Within the Tox21 screening program, disruption in nuclear receptor (NR) signaling represents a particular area of interest. Given the role of NR's in modulating a wide range of biological processes, alterations of their activity can have profound biological impacts. Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily that has demonstrated importance in bile acid homeostasis, glucose metabolism, lipid homeostasis and hepatic regeneration. In this study, we re-evaluated 24 FXR agonists and antagonists identified through Tox21 using select orthogonal assays. In transient transactivation assays, 7/8 putative agonists and 4/4 putative inactive compounds were confirmed. Likewise, we confirmed 9/12 antagonists tested. Using a mammalian two hybrid approach we demonstrate that both FXR agonists and antagonists facilitate FXRα-coregulator interactions suggesting that differential coregulator recruitment may mediate activation/repression of FXRα mediated transcription. Additionally, we tested the ability of select FXR agonists and antagonists to facilitate hepatic transcription of FXR gene targets Shp and Bsep in a teleost (Medaka) model. Through application of in vitro cell-based assays, in silico modeling and in vivo gene expressions, we demonstrated the molecular complexity of FXR:ligand interactions and confirmed the ability of diverse ligands to modulate FXRα, facilitate differential coregulator recruitment and activate/repress receptor-mediated transcription. Overall, we suggest a multiplicative approach to assessment of nuclear receptor function may facilitate a greater understanding of the biological and mechanistic complexities of nuclear receptor activities and further our ability to interpret broad HTS outcomes.
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Key Words
- Bsep, bile salt export pump
- CDCA, chenodeoxycholic acid
- DMSO, dimethyl sulfoxide
- EPA, U.S. Environmental Protection Agency
- FXR, Farnesoid X receptor
- Farnesoid X receptor
- High-throughput screening
- M2H, mammalian two-hybrid
- Medaka
- RXR, retinoid X receptor
- Shp, small heterodimer partner
- Teleost models
- Tox21, Toxicology in the 21st Century
- ToxCast
- qHTS, quantitative high-throughput screening
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94
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Valdiviezo A, Kato Y, Baker ES, Chiu WA, Rusyn I. Evaluation of Metabolism of a Defined Pesticide Mixture through Multiple In Vitro Liver Models. TOXICS 2022; 10:566. [PMID: 36287846 PMCID: PMC9609317 DOI: 10.3390/toxics10100566] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
The evaluation of exposure to multiple contaminants in a mixture presents a number of challenges. For example, the characterization of chemical metabolism in a mixture setting remains a research area with critical knowledge gaps. Studies of chemical metabolism typically utilize suspension cultures of primary human hepatocytes; however, this model is not suitable for studies of more extended exposures and donor-to-donor variability in a metabolic capacity is unavoidable. To address this issue, we utilized several in vitro models based on human-induced pluripotent stem cell (iPSC)-derived hepatocytes (iHep) to characterize the metabolism of an equimolar (1 or 5 µM) mixture of 20 pesticides. We used iHep suspensions and 2D sandwich cultures, and a microphysiological system OrganoPlate® 2-lane 96 (MimetasTM) that also included endothelial cells and THP-1 cell-derived macrophages. When cell culture media were evaluated using gas and liquid chromatography coupled to tandem mass spectrometry methods, we found that the parent molecule concentrations diminished, consistent with metabolic activity. This effect was most pronounced in iHep suspensions with a 1 µM mixture, and was lowest in OrganoPlate® 2-lane 96 for both mixtures. Additionally, we used ion mobility spectrometry-mass spectrometry (IMS-MS) to screen for metabolite formation in these cultures. These analyses revealed the presence of five primary metabolites that allowed for a more comprehensive evaluation of chemical metabolism in vitro. These findings suggest that iHep-based suspension assays maintain higher metabolic activity compared to 2D sandwich and OrganoPlate® 2-lane 96 model. Moreover, this study illustrates that IMS-MS can characterize in vitro metabolite formation following exposure to mixtures of environmental contaminants.
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Affiliation(s)
- Alan Valdiviezo
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Yuki Kato
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Laboratory for Drug Discovery and Development, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Erin S. Baker
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Weihsueh A. Chiu
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
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95
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Deng T, Xu X, Fu J, Xu Y, Qu W, Pi J, Wang H. Application of ARE-reporter systems in drug discovery and safety assessment. Toxicol Appl Pharmacol 2022; 454:116243. [PMID: 36115658 DOI: 10.1016/j.taap.2022.116243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 11/28/2022]
Abstract
The human body is continuously exposed to xenobiotics and internal or external oxidants. The health risk assessment of exogenous chemicals remains a complex and challenging issue. Alternative toxicological test methods have become an essential strategy for health risk assessment. As a core regulator of constitutive and inducible expression of antioxidant response element (ARE)-dependent genes, nuclear factor erythroid 2-related factor 2 (Nrf2) plays a critical role in maintaining cellular redox homeostasis. Consistent with the properties of Nrf2-mediated antioxidant response, Nrf2-ARE activity is a direct indicator of oxidative stress and thus has been used to identify and characterize oxidative stressors and redox modulators. To screen and distinguish chemicals or environmental insults that affect the cellular antioxidant activity and/or induce oxidative stress, various in vitro cell models expressing distinct ARE reporters with high-throughput and high-content properties have been developed. These ARE-reporter systems are currently widely applied in drug discovery and safety assessment. In the present review, we provide an overview of the basic structures and applications of various ARE-reporter systems employed for discovering Nrf2-ARE modulators and characterizing oxidative stressors.
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Affiliation(s)
- Tianqi Deng
- Laboratory of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China
| | - Xiaoge Xu
- Laboratory of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China
| | - Jingqi Fu
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Yuanyuan Xu
- Laboratory of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China
| | - Weidong Qu
- Key Laboratory of Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Jingbo Pi
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China.
| | - Huihui Wang
- Laboratory of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China.
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96
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Baldassari S, Cervetto C, Amato S, Fruscione F, Balagura G, Pelassa S, Musante I, Iacomino M, Traverso M, Corradi A, Scudieri P, Maura G, Marcoli M, Zara F. Vesicular Glutamate Release from Feeder-FreehiPSC-Derived Neurons. Int J Mol Sci 2022; 23:ijms231810545. [PMID: 36142455 PMCID: PMC9501332 DOI: 10.3390/ijms231810545] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Human-induced pluripotent stem cells (hiPSCs) represent one of the main and powerful tools for the in vitro modeling of neurological diseases. Standard hiPSC-based protocols make use of animal-derived feeder systems to better support the neuronal differentiation process. Despite their efficiency, such protocols may not be appropriate to dissect neuronal specific properties or to avoid interspecies contaminations, hindering their future translation into clinical and drug discovery approaches. In this work, we focused on the optimization of a reproducible protocol in feeder-free conditions able to generate functional glutamatergic neurons. This protocol is based on a generation of neuroprecursor cells differentiated into human neurons with the administration in the culture medium of specific neurotrophins in a Geltrex-coated substrate. We confirmed the efficiency of this protocol through molecular analysis (upregulation of neuronal markers and neurotransmitter receptors assessed by gene expression profiling and expression of the neuronal markers at the protein level), morphological analysis, and immunfluorescence detection of pre-synaptic and post-synaptic markers at synaptic boutons. The hiPSC-derived neurons acquired Ca2+-dependent glutamate release properties as a hallmark of neuronal maturation. In conclusion, our study describes a new methodological approach to achieve feeder-free neuronal differentiation from hiPSC and adds a new tool for functional characterization of hiPSC-derived neurons.
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Affiliation(s)
- Simona Baldassari
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
| | - Chiara Cervetto
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
- Interuniversity Center for the Promotion of the 3Rs Principles in Teaching and Research (Centro 3R), 56100 Pisa, Italy
- Correspondence: (C.C.); (M.M.)
| | - Sarah Amato
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
| | - Floriana Fruscione
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
| | - Ganna Balagura
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Largo Paolo Daneo 3, 16132 Genova, Italy
| | - Simone Pelassa
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
| | - Ilaria Musante
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Largo Paolo Daneo 3, 16132 Genova, Italy
| | - Michele Iacomino
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
| | - Monica Traverso
- Paediatric Neurology and Neuromuscular Disorders Unit, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
| | - Anna Corradi
- Department of Experimental Medicine, University of Genoa, Viale Benedetto XV 3, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Paolo Scudieri
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Largo Paolo Daneo 3, 16132 Genova, Italy
| | - Guido Maura
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
| | - Manuela Marcoli
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
- Interuniversity Center for the Promotion of the 3Rs Principles in Teaching and Research (Centro 3R), 56100 Pisa, Italy
- Center of Excellence for Biomedical Research, Viale Benedetto XV, 16132 Genova, Italy
- Correspondence: (C.C.); (M.M.)
| | - Federico Zara
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Largo Paolo Daneo 3, 16132 Genova, Italy
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97
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van der Zalm AJ, Barroso J, Browne P, Casey W, Gordon J, Henry TR, Kleinstreuer NC, Lowit AB, Perron M, Clippinger AJ. A framework for establishing scientific confidence in new approach methodologies. Arch Toxicol 2022; 96:2865-2879. [PMID: 35987941 PMCID: PMC9525335 DOI: 10.1007/s00204-022-03365-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/11/2022] [Indexed: 12/28/2022]
Abstract
Robust and efficient processes are needed to establish scientific confidence in new approach methodologies (NAMs) if they are to be considered for regulatory applications. NAMs need to be fit for purpose, reliable and, for the assessment of human health effects, provide information relevant to human biology. They must also be independently reviewed and transparently communicated. Ideally, NAM developers should communicate with stakeholders such as regulators and industry to identify the question(s), and specified purpose that the NAM is intended to address, and the context in which it will be used. Assessment of the biological relevance of the NAM should focus on its alignment with human biology, mechanistic understanding, and ability to provide information that leads to health protective decisions, rather than solely comparing NAM-based chemical testing results with those from traditional animal test methods. However, when NAM results are compared to historical animal test results, the variability observed within animal test method results should be used to inform performance benchmarks. Building on previous efforts, this paper proposes a framework comprising five essential elements to establish scientific confidence in NAMs for regulatory use: fitness for purpose, human biological relevance, technical characterization, data integrity and transparency, and independent review. Universal uptake of this framework would facilitate the timely development and use of NAMs by the international community. While this paper focuses on NAMs for assessing human health effects of pesticides and industrial chemicals, many of the suggested elements are expected to apply to other types of chemicals and to ecotoxicological effect assessments.
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Affiliation(s)
| | - João Barroso
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Patience Browne
- Organisation for Economic Co-Operation and Development, Hazard Assessment and Pesticides Programmes, Environmental Directorate, Paris, France
| | - Warren Casey
- National Institutes of Health, Division of the National Toxicology Program, National Institutes of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John Gordon
- U.S. Consumer Product Safety Commission, Directorate for Health Sciences, Rockville, MD, USA
| | - Tala R Henry
- U.S. Environmental Protection Agency, Office of Pollution Prevention and Toxics, Washington, DC, USA
| | - Nicole C Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Research Triangle Park, NC, USA
| | - Anna B Lowit
- U.S. Environmental Protection Agency, Office of Pollution Prevention and Toxics, Washington, DC, USA
| | - Monique Perron
- U.S. Environmental Protection Agency, Office of Pesticide Programs, Washington, DC, USA
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98
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Alvarez-Mora I, Mijangos L, Lopez-Herguedas N, Amigo JM, Eguiraun H, Salvoch M, Monperrus M, Etxebarria N. SETApp: A machine learning and image analysis based application to automate the sea urchin embryo test. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113728. [PMID: 35689888 DOI: 10.1016/j.ecoenv.2022.113728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Since countless xenobiotic compounds are being found in the environment, ecotoxicology faces an astounding challenge in identifying toxicants. The combination of high-throughput in vivo/in vitro bioassays with high-resolution chemical analysis is an effective way to elucidate the cause-effect relationship. However, these combined strategies imply an enormous workload that can hinder their implementation in routine analysis. The purpose of this study was to develop a new high throughput screening method that could be used as a predictive expert system that automatically quantifies the size increase and malformation of the larvae and, thus, eases the application of the sea urchin embryo test in complex toxicant identification pipelines such as effect-directed analysis. For this task, a training set of 242 images was used to calibrate the size-increase and malformation level of the larvae. Two classification models based on partial least squares discriminant analysis (PLS-DA) were built and compared. Moreover, Hierarchical PLS-DA shows a high proficiency in classifying the larvae, achieving a prediction accuracy of 84 % in validation. The scripts built along the work were compiled in a user-friendly standalone app (SETApp) freely accessible at https://github.com/UPV-EHU-IBeA/SETApp. The SETApp was tested in a real case scenario to fulfill the tedious requirements of a WWTP effect-directed analysis.
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Affiliation(s)
- Iker Alvarez-Mora
- Department of Analytical Chemistry, University of the Basque Country, Leioa, Biscay, Basque Country 48080, Spain; Plentzia Marine Station, University of the Basque Country, Plentzia, Biscay, Basque Country 48620, Spain.
| | - Leire Mijangos
- Department of Analytical Chemistry, University of the Basque Country, Leioa, Biscay, Basque Country 48080, Spain; Plentzia Marine Station, University of the Basque Country, Plentzia, Biscay, Basque Country 48620, Spain.
| | - Naroa Lopez-Herguedas
- Department of Analytical Chemistry, University of the Basque Country, Leioa, Biscay, Basque Country 48080, Spain; Plentzia Marine Station, University of the Basque Country, Plentzia, Biscay, Basque Country 48620, Spain.
| | - Jose M Amigo
- Department of Analytical Chemistry, University of the Basque Country, Leioa, Biscay, Basque Country 48080, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Biscay, Basque Country 48009, Spain.
| | - Harkaitz Eguiraun
- Plentzia Marine Station, University of the Basque Country, Plentzia, Biscay, Basque Country 48620, Spain; Department of Graphic Design and Engineering Projects, University of the Basque Country, Bilbao, Biscay, Basque Country 48013, Spain.
| | - Maddi Salvoch
- Department of Analytical Chemistry, University of the Basque Country, Leioa, Biscay, Basque Country 48080, Spain; Plentzia Marine Station, University of the Basque Country, Plentzia, Biscay, Basque Country 48620, Spain.
| | - Mathilde Monperrus
- Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Université de Pau et des Pays de l'Adour, Angelu, Basque Country 64000, France.
| | - Nestor Etxebarria
- Department of Analytical Chemistry, University of the Basque Country, Leioa, Biscay, Basque Country 48080, Spain; Plentzia Marine Station, University of the Basque Country, Plentzia, Biscay, Basque Country 48620, Spain.
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99
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Thá EL, Gagosian VSC, Canavez ADPM, Schuck DC, Brohem CA, Gradia DF, de Freitas RA, Prado KB, Cestari MM, Lorencini M, Leme DM. In vitro evaluation of the inhalation toxicity of the cosmetic ingredient aluminum chlorohydrate. J Appl Toxicol 2022; 42:2016-2029. [PMID: 35883269 DOI: 10.1002/jat.4371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 11/08/2022]
Abstract
Aluminum chlorohydrate (ACH) is a major aerosol component frequently used as the active ingredient in antiperspirants, and in vivo studies have raised a concern about its inhalation toxicity. Still, few studies have addressed its effects on the human respiratory tract. Therefore, we developed a study on ACH inhalation toxicity using an in vitro human alveolar cell model (A549 cells) with molecular and cellular markers of oxidative stress, immunotoxicity, and epigenetic changes. The chemical characterization of ACH suspensions indicated particle instability and aggregation; however, side-scatter analysis demonstrated significant particle uptake in cells exposed to ACH. Exposure of A549 cells to non-cytotoxic concentrations of ACH (0.25, 0.5, and 1 mg/ml) showed that ACH induced reactive oxygen species. Moreover, ACH upregulated TNF, IL6, IL8, and IL1A genes, but not the lncRNAs NEAT1 and MALAT1. Finally, no alterations on the global DNA methylation pattern (5-methylcytosine and 5-hydroxymethylcytosine) or the phosphorylation of histone H2AX (γ-H2AX) were observed. Our data suggest that ACH may induce oxidative stress and inflammation on alveolar cells, and A549 cells may be useful to identify cellular and molecular events that may be associated with adverse effects on the lungs. Still, further research is needed to ensure the inhalation safety of ACH.
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Affiliation(s)
- Emanoela Lundgren Thá
- Graduate Program in Genetics, Department of Genetics-Federal University of Paraná (UFPR), Curitiba, Brazil
| | | | | | | | - Carla Abdo Brohem
- Product Safety Management-Q&PP, Grupo Boticário, São José dos Pinhais, Brazil
| | | | | | - Karin Braun Prado
- Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | | | - Márcio Lorencini
- Product Safety Management-Q&PP, Grupo Boticário, São José dos Pinhais, Brazil
| | - Daniela Morais Leme
- Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
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100
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Mandal M, Levy J, Ives C, Hwang S, Zhou YH, Motsinger-Reif A, Pan H, Huggins W, Hamilton C, Wright F, Edwards S. Correlation Analysis of Variables From the Atherosclerosis Risk in Communities Study. Front Pharmacol 2022; 13:883433. [PMID: 35899108 PMCID: PMC9310100 DOI: 10.3389/fphar.2022.883433] [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: 02/25/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
The need to test chemicals in a timely and cost-effective manner has driven the development of new alternative methods (NAMs) that utilize in silico and in vitro approaches for toxicity prediction. There is a wealth of existing data from human studies that can aid in understanding the ability of NAMs to support chemical safety assessment. This study aims to streamline the integration of data from existing human cohorts by programmatically identifying related variables within each study. Study variables from the Atherosclerosis Risk in Communities (ARIC) study were clustered based on their correlation within the study. The quality of the clusters was evaluated via a combination of manual review and natural language processing (NLP). We identified 391 clusters including 3,285 variables. Manual review of the clusters containing more than one variable determined that human reviewers considered 95% of the clusters related to some degree. To evaluate potential bias in the human reviewers, clusters were also scored via NLP, which showed a high concordance with the human classification. Clusters were further consolidated into cluster groups using the Louvain community finding algorithm. Manual review of the cluster groups confirmed that clusters within a group were more related than clusters from different groups. Our data-driven approach can facilitate data harmonization and curation efforts by providing human annotators with groups of related variables reflecting the themes present in the data. Reviewing groups of related variables should increase efficiency of the human review, and the number of variables reviewed can be reduced by focusing curator attention on variable groups whose theme is relevant for the topic being studied.
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Affiliation(s)
- Meisha Mandal
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Josh Levy
- Levy Informatics, Chapel Hill, NC, United States
| | - Cataia Ives
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Stephen Hwang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Yi-Hui Zhou
- Department of Statistics, North Carolina State University, Raleigh, NC, United States
- Bioinformatics Research Center and Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Huaqin Pan
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Wayne Huggins
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Carol Hamilton
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Fred Wright
- Department of Statistics, North Carolina State University, Raleigh, NC, United States
- Bioinformatics Research Center and Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Stephen Edwards
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
- *Correspondence: Stephen Edwards,
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