Shaofei Zhang, Barbara L Parsons, Devon Fitzgerald, Anne Ashford, James Todd Auman, Tao Chen, Annette Dodge, Azeddine Elhajouji, Lena Pfaller, Shawn Harris, Jake Higgins, Cheryl A Hobbs, Francesco Marchetti, Matthew J Meier, Meagan B Myers, Jesse Salk, Rebecca Sahroui, David Schuster, Raja Settivari, Stephanie L Smith-Roe, Carole L Yauk, Jian Yan, Andrew Williams, Connie L Chen
{"title":"Transferability, Reproducibility and Sensitivity of Mutation Quantification by Duplex Sequencing.","authors":"Shaofei Zhang, Barbara L Parsons, Devon Fitzgerald, Anne Ashford, James Todd Auman, Tao Chen, Annette Dodge, Azeddine Elhajouji, Lena Pfaller, Shawn Harris, Jake Higgins, Cheryl A Hobbs, Francesco Marchetti, Matthew J Meier, Meagan B Myers, Jesse Salk, Rebecca Sahroui, David Schuster, Raja Settivari, Stephanie L Smith-Roe, Carole L Yauk, Jian Yan, Andrew Williams, Connie L Chen","doi":"10.1002/em.70020","DOIUrl":"https://doi.org/10.1002/em.70020","url":null,"abstract":"<p><p>Duplex Sequencing (DS) is an ultra-accurate, error-corrected next generation sequencing (ecNGS) technology for mutation analysis. A working group (WG) within Health and Environmental Sciences Institute's Genetic Toxicology Technical Committee is investigating the suitability of ecNGS for regulatory mutagenicity testing, using DS as a model. Initial steps to promote acceptance require demonstrating technical reproducibility across DS-experienced and inexperienced laboratories and establishing the method's sensitivity relative to conventional tests. Thus, the WG conducted a 'reconstruction experiment' to evaluate the transferability, reproducibility, and sensitivity of DS. TwinStrand Biosciences first applied DS to establish mutation frequency (MF) in DNA samples extracted from the livers of an untreated Sprague Dawley rat, or rats treated with either 100 mg/kg/day benzo[a]pyrene (B[a]P) for ten days or 40 mg/kg/day N-ethyl-N-nitrosourea (ENU) for three days. Using the measured MF in these original samples, mixtures were then constructed using the B[a]P- and ENU-treated samples to create \"MF standards\" with target MFs 1.2-, 1.5-, and 2-fold greater than the untreated control. Aliquots of these standards were distributed to seven laboratories in North America and Europe. DS libraries were prepared by each laboratory and TwinStrand. All eight laboratories met library preparation and assay performance metrics to yield high quality sequencing data with MF in the expected 'MF standard' range. The measured MF and mutation spectra were nearly identical across the laboratories and a 2-fold increase in MF could readily be identified in all labs relative to the untreated controls. The results confirm the high reproducibility and sensitivity of DS for mutagenicity assessment.</p>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Katherine Douglas, Dana Sorensen, Arnav Saud, Ananya Sridharan, Mallika Mathew, Jyotsna Hiranandani, Ava Gonick, Courtney Young, Kelly Nguyen, Nhu Phi, Jeffrey H Miller
{"title":"Identification of Hot and Cold Regions for Mutagenesis in the Escherichia coli tdk Gene: A Catalog of Mutational Sites.","authors":"Katherine Douglas, Dana Sorensen, Arnav Saud, Ananya Sridharan, Mallika Mathew, Jyotsna Hiranandani, Ava Gonick, Courtney Young, Kelly Nguyen, Nhu Phi, Jeffrey H Miller","doi":"10.1002/em.70021","DOIUrl":"https://doi.org/10.1002/em.70021","url":null,"abstract":"<p><p>We constructed a catalog of mutational sites in the tdk gene of Escherichia coli that consists of 378 different base pair substitutions at 245 different sites (base pairs). This allows us to examine the tendency of different sub-regions of the gene to be more or less prone to mutations when compared with other sub-regions. We do this by recording the number of occurrences of close to 1100 mutations resulting from 9 different mutagens or mutators at each site within a rolling 20-site interval. We can define 5 mutationally prone regions (MPRs). Aligning the profile of MPRs in tdk next to those we previously described in the thyA gene results in a linear map with 8 MPR regions, reinforcing the concept that certain sub-regions of genes are more mutable than others, even when other variables are accounted for. The catalog should prove useful for future studies.</p>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144368715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Miguel Pinto, Joana Sacadura, Pedro M Costa, Sandra Caeiro, Henriqueta Louro, Maria J Silva
{"title":"Assessment of the Genotoxic Hazard of Estuarine Sediments Using an Integrative Approach With LacZ Plasmid-Based Transgenic Mice.","authors":"Miguel Pinto, Joana Sacadura, Pedro M Costa, Sandra Caeiro, Henriqueta Louro, Maria J Silva","doi":"10.1002/em.70019","DOIUrl":"https://doi.org/10.1002/em.70019","url":null,"abstract":"<p><p>Under the influence of multiple anthropogenic pressures, from industrial to agricultural activities, estuaries have long been regarded as particularly sensitive ecosystems to contamination. The present study aimed at investigating the genotoxic potential of a contaminated sediment sample from an urban and industrial area of the Sado Estuary, by combining the analysis of multiple endpoints in the LacZ plasmid-based transgenic mouse model exposed for 28 days to contaminated estuarine sediment extracts through drinking water. The DNA and chromosome damaging effects were monitored in peripheral blood at 7-day intervals using the standard and enzyme-modified Comet assay, as well as the micronucleus assays in peripheral blood cells. After euthanasia, DNA damage was analyzed in several mouse tissues, and LacZ mutant frequencies were determined in the liver. Livers were also surveyed for histopathological analysis. A time-dependent increase in micronuclei frequency was seen at all tested doses, in spite of no induction of DNA damage in any organ or mutation induction in the liver of exposed mice. The liver from mice exposed to sediment extracts did not reveal major alterations besides evidence of inflammation. Overall, the integration of the endpoints analyzed in the mice is suggestive of potential chronic, rather than acute, adverse effects in vivo, and points to the need for further research in the resident human population in the area. This experimental design can be used to assess the genotoxicity of complex environmental mixtures, understand how they work, and reduce costs and resources while speeding up data collection and interpretation.</p>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rushikesh M. Shukla, Darshan T. Valani, Chetan K. Kajavadara, Satyam N. Patel, Rajesh J. Patel, Laxit K. Bhatt, Rajesh Sundar, Mukul R. Jain
{"title":"Comparative Analysis of TA102 and WP2 uvrA(pKM101) Strains in Detecting Nitrosamine Mutagens in the Enhanced Ames Test","authors":"Rushikesh M. Shukla, Darshan T. Valani, Chetan K. Kajavadara, Satyam N. Patel, Rajesh J. Patel, Laxit K. Bhatt, Rajesh Sundar, Mukul R. Jain","doi":"10.1002/em.70018","DOIUrl":"10.1002/em.70018","url":null,"abstract":"<div>\u0000 \u0000 <p>The Ames test is a fundamental assay for evaluating chemical mutagenicity, particularly for nitrosamines, which are widespread environmental and pharmaceutical contaminants. To improve sensitivity, regulatory agencies have endorsed the enhanced Ames test (EAT), which incorporates five tester strains, a 30-min pre-incubation step, and metabolic activation using both rat and hamster liver S9 fractions. While <i>Salmonella typhimurium</i> TA102 is known for its sensitivity to oxidative mutagens, its performance under EAT conditions has not been fully characterized. This study evaluated the mutagenic response of TA102 using two nitrosamine positive controls: <i>N</i>-nitrosodimethylamine (NDMA) and 1-cyclopentyl-4-nitrosopiperazine (CPNP). <i>E. coli</i> WP2 <i>uvr</i>A(pKM101) showed consistent mutagenic responses to both NDMA and CPNP, consistent with existing EAT data. TA102 demonstrated a robust response to NDMA but not to CPNP, suggesting limited sensitivity to certain nitrosamines. These findings support the continued use of WP2 <i>uvr</i>A(pKM101) in EAT protocols and highlight the limited utility of TA102 for comprehensive nitrosamine mutagenicity assessment.</p>\u0000 </div>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":"66 5","pages":"291-297"},"PeriodicalIF":2.3,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mitochondria-Nuclear Crosstalk: Orchestrating mtDNA Maintenance","authors":"Ghazal Darfarin, Janice Pluth","doi":"10.1002/em.70013","DOIUrl":"10.1002/em.70013","url":null,"abstract":"<p>The mitochondria (mt) and nucleus engage in a dynamic bidirectional communication to maintain cellular homeostasis, regulating energy production, stress response, and cell fate. Anterograde signaling directs mt function, while retrograde signaling conveys metabolic and stress-related changes from mt to the nucleus. Central to this crosstalk is mitochondrial DNA (mtDNA), which encodes key oxidative phosphorylation components. MtDNA integrity is preserved through quality control mechanisms, including fusion and fission dynamics, mitophagy, and nuclear-encoded DNA repair. Disruption in these pathways contributes to mt dysfunction, oxidative stress, and genetic instability—hallmarks of aging and diseases. Additionally, redox signaling and NAD+ homeostasis integrate mt and nuclear responses, modulating transcriptional programs that support mt biogenesis and stress adaptation. This review explores the molecular mechanisms coordinating mito-nuclear interactions, emphasizing their role in maintaining mtDNA integrity and cellular equilibrium. Understanding these processes provides insights into how mt dysfunction drives aging and disease, paving the way for targeted therapeutic strategies.</p>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":"66 5","pages":"222-242"},"PeriodicalIF":2.3,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/em.70013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Steven M. Bryce, Svetlana L. Avlasevich, Adam Conrad, Nikki E. Hall, Kyle Tichenor, Erica Briggs, Stephen D. Dertinger, Jeffrey C. Bemis
{"title":"Application of Biological Modifiers to a Multiplexed, Human Cell-Based DNA Damage Assay Provides Mechanistic Information on Genotoxicity and Molecular Targets","authors":"Steven M. Bryce, Svetlana L. Avlasevich, Adam Conrad, Nikki E. Hall, Kyle Tichenor, Erica Briggs, Stephen D. Dertinger, Jeffrey C. Bemis","doi":"10.1002/em.70017","DOIUrl":"10.1002/em.70017","url":null,"abstract":"<div>\u0000 \u0000 <p>This laboratory has reported that the combined use of In Vitro MicroFlow and MultiFlow assays provides information regarding chemicals' genotoxic mode of action (MoA). In an effort to go beyond MoA assessments, we incorporated a panel of biological response modifiers that elicit specific effects on the assays' biomarker response profiles. This was done to pursue our hypothesis that such perturbation signatures would reveal information on clastogenic mechanisms and molecular targets. For this proof-of-concept study, we exposed TK6 cells to 20 known clastogens. Cells were exposed in 96-well plates in the presence and absence of each of four modifying agents at one optimized concentration: talazoparib (PARP inhibitor), MK-8776 (CHK1 inhibitor), AZD-7648 (DNA-PK inhibitor), or a cocktail of reactive oxygen species scavengers. In parallel, cells were also exposed to each of the test chemicals for 4 h, at which time cells were washed and allowed to recover for an additional 20 h. For each of these treatment conditions, sample processing and flow cytometric analyses were performed using standard In Vitro MicroFlow and MultiFlow procedures to measure micronuclei, γH2AX, phosphohistone-H3 (p-H3), p53 activation, and relative nuclei counts. The resulting biomarker response data were processed with PROAST benchmark dose (BMD) software, with modifying agent as a covariate. Unsupervised hierarchical clustering of the collective potency metrics for various combinations of biomarkers showed that clastogens with similar genotoxic mechanisms grouped together. Overall, this study shows that in combination with biological response modifiers, MultiFlow and In Vitro MicroFlow biomarkers can provide mechanistic insights into chemical-induced genotoxicity.</p>\u0000 </div>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":"66 5","pages":"280-290"},"PeriodicalIF":2.3,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/em.70017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Fertilized Avian Egg Fetal Liver Assays for Assessing DNA Damaging Potential of Chemicals: A Comparative Analysis With In Vitro and In Vivo Genotoxicity Assays and Rodent Carcinogenicity","authors":"Tetyana Kobets, Gary M. Williams","doi":"10.1002/em.70016","DOIUrl":"10.1002/em.70016","url":null,"abstract":"<div>\u0000 \u0000 <p>The ability to produce direct DNA damage (genotoxicity), which underlies the carcinogenicity of various chemicals, is typically evaluated in a regulatory-approved battery of in vitro tests with potential in vivo follow-up. Growing concerns for animal welfare and implementation of regulations restricting the use of animal testing necessitate the introduction of New Approach Methodologies (NAMs). The avian egg-based (<i>in ovo</i>) models were developed as metabolically competent NAMs capable of bioactivation, detoxication, and elimination of xenobiotics to potentially replace short-term in vivo genotoxicity assays for chemicals that are genotoxic in vitro. These models utilize avian (chicken or turkey) fetal livers for the evaluation of endpoints indicative of DNA damage produced by either direct or indirect mechanisms, the formation of nuclear DNA adducts and strand breaks. Avian embryos have genetic and morphologic resemblance to mammals and can be used for the evaluation of other endpoints including histopathology and genomic profiling. A concordance analysis of 87 and 59 chemicals assessed in the chicken and turkey models, respectively, revealed a stronger correlation with the results from in vivo genotoxicity assays (76% and 67% sensitivity, 79% and 72% specificity for chicken and turkey, respectively) compared to in vitro assays (58% and 56% sensitivity, 45% and 63% specificity for chicken and turkey, respectively). These results demonstrate that <i>in ovo</i> models detect the genotoxic potential of a broader range of compounds compared to in vitro assays with S9 supplementation. In conclusion, fertilized avian egg fetal liver assays offer a promising alternative to traditional in vivo genotoxicity assays.</p>\u0000 </div>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":"66 5","pages":"258-279"},"PeriodicalIF":2.3,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/em.70016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Prachi Pradeep, Stefanie Seifert, Ajay Vikram Singh, Peter Laux, Ralph Pirow
{"title":"Applicability of In Silico New Approach Methods for the Risk Assessment of Tattoo Ink Ingredients","authors":"Prachi Pradeep, Stefanie Seifert, Ajay Vikram Singh, Peter Laux, Ralph Pirow","doi":"10.1002/em.70010","DOIUrl":"https://doi.org/10.1002/em.70010","url":null,"abstract":"<p>Tattoo inks contain several substances, including organic and inorganic pigments, additives, and solvents, which may pose a health risk to not only the tattooed skin but also to other parts of the human body due to intradermal exposure. Substances in tattoo inks are regulated by entry 75 in Annex XVII of REACH Regulation (EC) No. 1907/2006. However, despite these legal requirements, a well-defined criterion for the safety assessment of tattoo inks remains lacking. In this context, 2021 BfR opinion titled “Tattoo inks: minimum requirements and test methods” proposed a comprehensive risk assessment of pigments using in vitro/in-chemico data in accordance with OECD Guidelines and CLP Regulations. In the absence of experimental data, new approach methodologies (NAMs) may be used for data-gap filling. Therefore, this work evaluates the applicability of in silico NAMs for data-gap filling for a list of tattoo ink ingredients identified by the Joint Research Centre (JRC) and BfR for genotoxicity assessment. Experimental in vitro genotoxicity data were acquired from the International Uniform Chemical Information Database (IUCLID) which makes non-confidential REACH Study Results publicly accessible. The specific aims of this analysis were the evaluation of in silico genotoxicity predictions from publicly available QSAR tools and structural alerts, the development and validation of new QSAR models specific to tattoo ink ingredients, and the application of in silico models for categorization and prioritization of data-poor ingredients for further screening. Based on the workflow developed in this study, 4 high priority, 18 medium priority, and 2 low priority substances were identified for further assessment.</p>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":"66 4","pages":"199-209"},"PeriodicalIF":2.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/em.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144091823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yax Thakkar, T. Kobets, Anne Marie Api, J. D. Duan, G. M. Williams
{"title":"The Chicken Egg Genotoxicity Assay (CEGA): Assessing Target Tissue Exposure and Metabolism in the Embryo-Fetal Chicken Livers","authors":"Yax Thakkar, T. Kobets, Anne Marie Api, J. D. Duan, G. M. Williams","doi":"10.1002/em.70015","DOIUrl":"10.1002/em.70015","url":null,"abstract":"<p>The Chicken Egg Genotoxicity Assay (CEGA) is an avian egg-based model that utilizes the livers of developing chicken embryo-fetuses to assess the ability of chemicals to produce direct DNA damage. The main goal of the study was to evaluate target tissue exposure and metabolism in the CEGA to assess its suitability as a biologically relevant new approach methodology (NAM) for detecting the genotoxic potential of chemicals. An imaging study using two-photon excitation microscopy after the administration of a fluorescent dye (acridine orange) verified that chemicals following administration into the air sac of the fertilized chicken egg reach the target organ, liver. A metabolism study using liquid chromatography with high resolution mass spectrometry (LC/MS), conducted after the administration of benzo(a)pyrene (B(a)P) according to the CEGA protocol, confirmed the formation of sufficient amounts of reactive metabolite(s) responsible for the genotoxic effects of a parent compound upon reaching the target tissue. Moreover, an RNA sequencing study revealed that B(a)P in embryo-fetal chicken livers significantly upregulated several genes responsible for the activity of the CYP1A1 enzyme, which is critical for the bioactivation of B(a)P. These findings, along with the previously reported DNA damage (i.e., DNA adducts and single-strand breaks) produced by B(a)P in CEGA, support sufficient target tissue exposure to B(a)P and the ability of avian fetal livers to bioactivate B(a)P to a reactive intermediate. Overall, the findings in the study support the conclusion that the CEGA can be considered a robust potential alternative to the animal testing strategy for assessing the genotoxic potential of chemicals.</p>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":"66 5","pages":"243-257"},"PeriodicalIF":2.3,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/em.70015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143970973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Elizabeth Huliganga, Eunnara Cho, Carol D. Swartz, Andrew Williams, Leslie Recio, Jesse J. Salk, Francesco Marchetti, Carole L. Yauk
{"title":"Adverse Outcome Pathway-Informed Integrated Testing to Identify Chemicals Causing Genotoxicity Through Oxidative DNA Damage: Case Study on 4-Nitroquinoline 1-Oxide","authors":"Elizabeth Huliganga, Eunnara Cho, Carol D. Swartz, Andrew Williams, Leslie Recio, Jesse J. Salk, Francesco Marchetti, Carole L. Yauk","doi":"10.1002/em.70011","DOIUrl":"10.1002/em.70011","url":null,"abstract":"<p>Adverse outcome pathways (AOPs) provide a framework to organize and weigh evidence linking molecular interactions of toxicants in cells to adverse outcomes relevant to risk assessment or regulatory decision-making. Applying this framework facilitates the interpretation of data produced using new test methods. We used an existing AOP (AOP #296) that describes how oxidative DNA damage leads to mutations and chromosomal aberrations to develop an integrated testing strategy to evaluate whether a chemical operates through this pathway. We exposed human TK6 cells to increasing concentrations of 4-nitroquinoline 1-oxide (4NQO), a tobacco mimetic that causes oxidative DNA damage, in a time-series design. We measured oxidative DNA damage and strand breaks using the high-throughput CometChip assay with and without formamidopyrimidine DNA glycosylase (Fpg), alongside analyses of micronucleus (MN) frequency by flow cytometry, and mutations by error-corrected sequencing (duplex sequencing—DS). Our analysis shows how these methods can be combined to quantify 4NQO-induced, concentration- and time-dependent increases in: (a) oxidative DNA damage (occurred early and at low concentrations); (b) strand breaks (remained elevated to 6 h post-exposure); (c) MN frequency (at 24 h); (d) mutation frequency (at 48 h); and (e) C > A transversions consistent with expected substitutions induced by oxidative DNA lesions. The time series shows the repair of oxidative DNA damage with persistent strand breaks remaining at 6 h. Overall, we provide an example of an AOP-informed testing strategy and contribute to the quantitative understanding of AOP #296. We also demonstrate the value of DS as an effective approach for mutagenicity assessment.</p>","PeriodicalId":11791,"journal":{"name":"Environmental and Molecular Mutagenesis","volume":"66 4","pages":"185-198"},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/em.70011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143970486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}