Mutagenesis[JOURNAL]
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200 papers
The Buccal Micronucleus (BMN) Cytome assay: enhancing its applications by addressing challenges and exploring new opportunities.
Volpi EV, Fenech M
Mutagenesis · 2026 Mar · PMID 41649162 · Publisher ↗
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Assessment of mutagenic potential of puberulic acid contaminated in red yeast rice (beni-koji) health food supplements.
Sugiyama KI, Furuhama A, Horibata K … +9 more , Tsuda M, Izawa K, Tsuji G, Demizu Y, Matsushita K, Toyoda T, Hirabayashi Y, Saito Y, Honma M
Mutagenesis · 2026 Apr · PMID 41641978 · Full text
In March 2024, a food poisoning incident in Japan was traced to red yeast rice (beni-koji) supplements contaminated with puberulic acid (PA), a mycotoxin produced by Penicillium adametzioides. Although PA was implicated...
In March 2024, a food poisoning incident in Japan was traced to red yeast rice (beni-koji) supplements contaminated with puberulic acid (PA), a mycotoxin produced by Penicillium adametzioides. Although PA was implicated in renal dysfunction in both humans and rats, its mutagenic potential had not been clarified. Here, we comprehensively assessed the mutagenicity of PA using a tiered approach that combined in silico, in vitro, and in vivo methods. In silico quantitative structure-activity relationship analyses predicted PA to be mutagenic, and in vitro Ames tests confirmed the positive finding. In contrast, in vivo assays, including the transgenic rodent gene mutation assay in mice and the Pig-a assay in rats, demonstrated no induction of mutations in kidney, glandular stomach, and blood cells, even at high exposure levels. Collectively, these findings indicate that PA is mutagenic in vitro bacterial tests, but not in mammalian in vivo systems, suggesting that the overall concern for mutagenicity in humans is low.
Mutagenicity of 5-hydroxycytosine in human cells.
Suzuki T, Hirota A, Iwai S … +1 more , Kamiya H
Mutagenesis · 2026 Apr · PMID 41626744 · Publisher ↗
Base damage in DNA constitutes a major source of mutations, and consequently leads to cancers. In human cells, 8-oxo-7,8-dihydroguanine (8-hydroxyguanine) induces targeted G → T transversions, and untargeted base substit...
Base damage in DNA constitutes a major source of mutations, and consequently leads to cancers. In human cells, 8-oxo-7,8-dihydroguanine (8-hydroxyguanine) induces targeted G → T transversions, and untargeted base substitution mutations at positions distant from the damaged site (action-at-a-distance mutations). OGG1 is a base excision repair enzyme and suppresses the former mutations, but is involved in the latter mutations' process. In this study, 5-hydroxycytosine (CO), another oxidized base removed by base excision repair, was incorporated into the inside and outside regions of the supF gene, and the CO-plasmid DNAs were transfected into human U2OS cells. The damaged cytosine base caused base substitution mutations at the lesion site, and seemed to induce the action-at-a-distance mutations at a lower frequency than the oxidized guanine base. These results indicated that CO is mutagenic in human cells. In addition, the (6-4) photoproduct of 5'-TpT-3', the lesion repaired by another type of DNA repair pathway, nucleotide excision repair, did not cause the action-at-a-distance mutations.
Using error-corrected sequencing for evaluating mutagenicity of molnupiravir in humans.
McKinzie PB, Valapil RR, Heil EL … +4 more , Polli JE, Myers MB, Pearce MG, Dobrovolsky VN
Mutagenesis · 2026 Jan · PMID 41510958 · Publisher ↗
Molnupiravir (MOV) is a prodrug of N-hydroxycytidine (NHC), an analog of the endogenous ribonucleoside cytidine that can be administered orally. MOV is used for treating patients infected by SARS-CoV-2, the coronavirus r...
Molnupiravir (MOV) is a prodrug of N-hydroxycytidine (NHC), an analog of the endogenous ribonucleoside cytidine that can be administered orally. MOV is used for treating patients infected by SARS-CoV-2, the coronavirus responsible for COVID-19. MOV and NHC are mutagenic in bacterial and in mammalian cell cultures, yet both chemicals have been negative or equivocal in nonclinical in vivo models of mutagenesis. We designed and validated a novel error-corrected sequencing (ECS) method for detecting single basepair substitutions in tissue samples obtained from genetically heterogeneous humans. The software used for this ECS method is available for free from a public on-line repository and it is suitable for analysis of in vivo and in vitro derived samples collected in various experimental scenarios. We recruited two groups of patients having COVID-19 one to three years ago, one group that received a full course of MOV therapy and the other group (matched for age and COVID-19 diagnosis date) that did not receive MOV. Using the ECS method, we determined the frequencies of basepair substitutions in nucleated cells isolated from peripheral blood of the patients. There was no observed difference in the frequency of mutations, the types of mutations, or mutational spectra between the MOV and the control groups. Also, the spectra of mutations in the MOV group did not show any evidence of the mutational signature expected from exposures to MOV or NHC based on data from mammalian cell culture models. Within the limits of this study, the dose of MOV authorized for the treatment of COVID-19 under emergency use authorization appears to have no mutational consequences for treated patients.
Evaluating DNA damage in peripheral blood lymphocytes: a promising biomarker for diagnosis, prognosis, and treatment monitoring in colorectal cancer.
Guedes AR, Cunha R, Silva AM … +1 more , Gaivão I
Mutagenesis · 2026 Apr · PMID 41510948 · Publisher ↗
Colorectal cancer (CRC) remains a major health challenge due to its late-stage diagnosis and the variability in patient prognosis. This study explores the potential of DNA damage in peripheral blood lymphocytes (PBLs) as...
Colorectal cancer (CRC) remains a major health challenge due to its late-stage diagnosis and the variability in patient prognosis. This study explores the potential of DNA damage in peripheral blood lymphocytes (PBLs) as a biomarker for CRC, comparing it with standard clinical parameters. We assessed DNA strand breaks using the alkaline comet assay in 27 CRC patients at diagnosis and posttreatment, comparing these levels with 31 healthy controls. Patients received 5-fluorouracil (5-FU)-based chemotherapy (with irinotecan or oxaliplatin), radiotherapy, or combined chemoradiotherapy. At diagnosis (t0), DNA damage in PBLs was significantly higher in CRC compared to healthy controls (mean ± SD %DNA in tail: CRC 27.9 ± 14.0%; controls 6.5 ± 3.8%; P = .001), and independently of common confounding factors (sex, age, smoking, and alcohol consumption). Crucially, the prognostic signal came from baseline (t0): 6 of 27 patients relapsed/metastasized within 8-10 months, and high-DNA-damage basal levels were the only significant prognostic predictor (P = .0137), yielding an infinitely elevated odds ratio (95% CI: ≥2.203) and 100% sensitivity. In stark contrast, carcinoembryonic antigen (CEA) and cancer antigen 19-9 (CA19-9) showed limited performance. At t0, among patients with available serum data (n = 23), most values were below clinical cut-offs: CEA 3 ng/ml (14/23, 61%); CA19-9 37 U/ml (19/23, 83%). Prognostic sensitivities were 50.0% (CEA) and 16.7% (CA19-9). Posttreatment (t1) increases in DNA damage are pharmacodynamically expected with DNA-damaging therapy. t1 values were higher in patients who relapsed (P < .001), whereas the within-patient change (Δ = t1 - t0) was not associated with outcome (P = .148); these posttreatment findings are exploratory. Evaluating DNA damage in PBLs, therefore, offers a valuable noninvasive biomarker for early detection, treatment monitoring, and short-term risk stratification in CRC, warranting validation in larger, stage-balanced cohorts.
Deep learning and object detection methods for scoring cell types within the human buccal cell micronucleus and cytome assays for human biomonitoring.
Smith E, Wagman J, Barnes C … +2 more , Rees P, Johnson G
Mutagenesis · 2026 Mar · PMID 41236179 · Full text
Micronuclei (MN) are critical biomarkers for pathological conditions, yet their manual scoring is inherently laborious and prone to significant interobserver variability, limiting the reliability and scalability of genot...
Micronuclei (MN) are critical biomarkers for pathological conditions, yet their manual scoring is inherently laborious and prone to significant interobserver variability, limiting the reliability and scalability of genotoxicity assessments. Recent advancements in deep learning and computer vision have revolutionized automated MN detection in various assay samples, enhancing accuracy and efficiency and reducing human bias. While these artificial intelligence (AI)-powered techniques have been demonstrated in in vitro genotoxicity testing, their application to the minimally invasive buccal micronucleus cytome (BMCyt) assay for human biomonitoring remains largely unexplored. The BMCyt assay, invaluable for assessing genotoxic damage in environmentally exposed populations, presents unique challenges, including sample variability, confounding factors, and the complexity of scoring multiple cytogenetic endpoints. This review covers the evolution of AI-based MN detection, analysing key methodologies and advancements. It highlights the untapped potential of integrating AI into the BMCyt assay to overcome current analytical limitations, improve reproducibility, increase throughput, and eliminate observer bias. By facilitating more robust and scalable genomic damage monitoring, AI integration will significantly enhance the utility of the BMCyt assay in large-scale epidemiological studies and human biomonitoring.
The use of DNA repair inhibitors and the comet assay-an overview.
Saenz-Martinez E, López de Cerain A, Azqueta A
Mutagenesis · 2025 Dec · PMID 41172144 · Full text
The standard comet assay detects DNA strand breaks and alkali-labile sites, but these lesions are nonspecific. They may result directly from genotoxic agents or arise as intermediates during the repair of other DNA damag...
The standard comet assay detects DNA strand breaks and alkali-labile sites, but these lesions are nonspecific. They may result directly from genotoxic agents or arise as intermediates during the repair of other DNA damage, such as oxidized bases or bulky DNA adducts. Different approaches have been developed to generate or trap these repair intermediates, making them detectable with the comet assay. Recently, the combination of the comet assay with DNA repair inhibitors like hydroxyurea and cytosine arabinoside has been proposed to detect bulky DNA adducts. These lesions are mainly repaired through nucleotide excision repair, a process that transiently produces strand breaks when damaged oligonucleotides are excised. Normally, these intermediates are rapidly repaired by DNA resynthesis and ligation. However, by inhibiting this repair step, strand breaks persist and can be detected by the comet assay. This strategy has been applied in various fields, including genotoxicity testing, environmental toxicology, human biomonitoring, and studies on DNA repair kinetics. This review focuses specifically on the use of hydroxyurea, cytosine arabinoside, and aphidicolin in in vitro experiments to evaluate the utility and specificity of this method for detecting different types of DNA lesions. Notably, in ~70% of studies reviewed, the inclusion of DNA repair inhibitors led to a significant increase in DNA damage, highlighting the added value of this approach. However, although the method enhances sensitivity to bulky adducts, it also responds to other types of damage, such as those induced by alkylating or oxidative agents.
Innovating the buccal micronucleus cytome assay to improve its utility as a biomarker of in vivo genotoxicity.
Fenech M, Bolognesi C, Nersesyan A … +2 more , Knasmueller S, Bonassi S
Mutagenesis · 2026 Mar · PMID 41105122 · Publisher ↗
The Buccal Micronucleus Cytome (B-MNcyt) assay is used worldwide to study chromosomal abnormalities and environmental genotoxicity and cytotoxicity in humans. The aim of this article is to discuss the strengths and limit...
The Buccal Micronucleus Cytome (B-MNcyt) assay is used worldwide to study chromosomal abnormalities and environmental genotoxicity and cytotoxicity in humans. The aim of this article is to discuss the strengths and limitations of the B-MNcyt assay and to identify emerging opportunities to further improve and validate its use. This can be achieved by innovating and evolving the B-MNcyt assay by identifying and solving important knowledge and technological gaps that hinder its utility. The cells examined in the B-MNcyt assay are squamous epithelial cells that can be easily collected from the inside of the mouth. These cells are postmitotic cells generated from the proliferative basal layer and may contain micronuclei (MN). MN can be generated during mitosis of the basal cells prior to their differentiation into squamous cells. The B-MNcyt assay is increasingly being used to measure DNA damage induced in vivo by environmental genotoxins. Results with this assay have been shown to correlate positively with MN frequency measured using the well-validated lymphocyte cytokinesis-block micronucleus cytome (L-CBMNcyt) assay. However, the B-MNcyt assay has some important limitations that need to be addressed to achieve a similar level of validation and applicability to that of the L-CBMNcyt assay. These include the lack of (i) evidence that the buccal MN frequency predicts disease risk in prospective studies; (ii) an automated scoring system to score MN in buccal cells, which is essential to achieve statistically robust results and to improve the feasibility of the assay in population studies; (iii) sufficient research on the kinetics of MN expression in buccal cells to define optimal time frames to score MN after acute exposure or during chronic genotoxin exposure; and (iv) studies to test the suitability of using the B-MNcyt assay for radiation exposure biodosimetry. This article discusses these issues and provides some suggestions on how to address them.
Aneuploidy in exfoliated buccal cells: mechanisms, methods, and future perspectives.
Kirsch-Volders M, Mišík M, Fenech M
Mutagenesis · 2026 Mar · PMID 41099562 · Full text
Aneuploidy and polyploidy have a major impact in congenital and acquired diseases, in particular in cancer development. This mini-review highlights the use of exfoliated buccal cells as a non-invasive tool for monitoring...
Aneuploidy and polyploidy have a major impact in congenital and acquired diseases, in particular in cancer development. This mini-review highlights the use of exfoliated buccal cells as a non-invasive tool for monitoring aneuploidy. It offers a mechanistic overview and illustrative diagrams addressing five key areas: (i) the causes of aneuploidy; (ii) cell kinetics and aneuploidy induction in epithelial buccal cells; (iii) the methods for the detection of aneuploidy; (iv) the scientific and medical domains applying aneuploidy detection in exfoliated buccal cells; (v) the knowledge gaps and future research perspectives. Although well validated protocols, automated systems and specific probes allowing discrimination between chromosome aberration, aneuploidy and polyploidy in exfoliated buccal cells are available, large-scale cohort human studies remain lacking. These studies are crucial for evaluating aneuploidy in populations exposed to genotoxic agents or at risk for buccal dysplasia. Future validation and predictivity studies should compare fluorescence in situ hybridization and total DNA content methods such as densitometry or flow cytometry, in exposed individuals and control groups with careful control of confounding factors and adherence to standardized reporting guidelines. In addition, assessment of aneuploidy frequencies in parallel in lymphocytes and exfoliated buccal cells in the same populations would allow to compare their predictive value in both tissues. Moreover, mechanistic studies are also needed to better understand the sources of variability in aneuploidy and how buccal cell biology compares to other cell types. In conclusion, due to their ease of collection and non-invasive nature, exfoliated buccal cells represent a promising tool for aneuploidy testing for risk assessment of environmental or occupational exposures and disease prediction and monitoring.
Correction to: Re: Rather et al. Carcinogenic parasites: Insights into the epidemiology and possible mechanisms of cancer.
Mutagenesis · 2025 Dec · PMID 41048089 · Publisher ↗
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Tungsten carbide-cobalt can function as a particle positive control for genotoxicity in vitro in specific cell lines.
Burgum MJ, Evans SJ, Zanoni I … +3 more , Blosi M, Jenkins GJ, Doak SH
Mutagenesis · 2025 Dec · PMID 41042229 · Full text
Nanoparticle genotoxicity can be induced through several mechanisms, but there are currently no nanoparticle positive controls available for the evaluation of in vitro genotoxicity. Tungsten carbide-cobalt (WC/Co) has be...
Nanoparticle genotoxicity can be induced through several mechanisms, but there are currently no nanoparticle positive controls available for the evaluation of in vitro genotoxicity. Tungsten carbide-cobalt (WC/Co) has been proposed as one possible candidate. The aim of this study was therefore to investigate the genotoxic profile of WC/Co (Co 8% wt.) utilizing the cytokinesis-blocked micronucleus (CBMN) assay, the mammalian cell gene mutation test, and comet assay following a 24-hour exposure. This was conducted in human lymphoblast (TK6) and Chinese hamster lung fibroblast (V79-4) cells. No cytotoxicity was observed in the TK6 CBMN assay even when significant induction of micronuclei was observed at 100 μg/ml (2-fold over control). In contrast, V79-4 cells demonstrated no significant genotoxicity or cytotoxicity in the CBMN assay. In the gene mutation assay significant mutagenicity was observed in V79-4 cells at 100 μg/ml (2-fold over control). Cellular uptake of the WC/Co nanoparticles was not qualitatively detected in either cell type when investigated with transmission electron microscopy. No genotoxicity was observed in either cell type with the comet assay. The data generated indicates that WC/Co nanoparticles may be used as a positive particulate control in the CBMN assay when using TK6 cells only; whilst in the gene mutation assay it can be used as a positive control for V79-4 cells. However, its use as a particle positive control is only possible when applying the highest test concentration of 100 μg/ml.
Water quality assessment and genotoxicity in fishes of Karamana River, Kerala, India: an insight of microplastic pollution.
Ulakesan A, Sunil SL, Ramarajan R … +2 more , Mallikarjunaiah S, Gurushankara HP
Mutagenesis · 2025 Dec · PMID 41017440 · Publisher ↗
Microplastics are emerging pollutants of global concern, and their widespread presence poses a serious threat to aquatic and terrestrial ecosystems. The current study investigated the water quality and the presence of mi...
Microplastics are emerging pollutants of global concern, and their widespread presence poses a serious threat to aquatic and terrestrial ecosystems. The current study investigated the water quality and the presence of microplastics in water and native fish samples of the Karamana River, Kerala, India. The water quality was analyzed using various physicochemical parameters, including the dissolved oxygen, biochemical oxygen demand, and chemical oxygen demand. Microplastics isolated from water and native fish samples were characterized using Fourier transform infrared (FTIR) spectroscopy. DNA damage in fish liver and gill cells was assessed using the comet assay (single-cell gel electrophoresis). The water quality assessment revealed metals in the water within the acceptable limits, reduced dissolved oxygen, and increased biochemical oxygen demand and chemical oxygen demand, which indicate a river water ecosystem in hypoxic conditions, and the higher level of the most probable number index confirmed the presence of coliforms in this river. The microplastics isolated from the water and native fish samples were in fibers, fragments, film, pellets, and foams in nature. The abundance of microplastics in the river confirmed the load of microplastic pollution, which varied among the sites. FTIR spectroscopy analysis confirmed the presence of microplastic polymers such as polyethylene, polypropylene, polystyrene, polyamide, polyoxymethylene, and polyester in the water and native fish samples of the Karamana River. The increased percentage of tail DNA in the liver and gill cells of the fish inhabitants of the Karamana River, compared with the control fish, indicated DNA damage; this could be due to the microplastics in that aquatic ecosystem.
Influence of pH and lysis duration on DNA damage detection: a comparison of neutral and alkaline comet assays.
Pribakovic R, Bornhorst J, Stopper H … +1 more , Bankoglu EE
Mutagenesis · 2025 Oct · PMID 40844041 · Full text
The comet assay is a widely used method for measuring DNA damage and DNA repair. When DNA strand breaks happen, the supercoiling of DNA is relaxed, and after alkaline or neutral electrophoresis, depending on the type of...
The comet assay is a widely used method for measuring DNA damage and DNA repair. When DNA strand breaks happen, the supercoiling of DNA is relaxed, and after alkaline or neutral electrophoresis, depending on the type of performed comet assay, DNA moves toward the anode, forming a comet tail. Thus, with increasing frequency of DNA strand breaks, an increase in the percentage of DNA in the tail is observed. The aim of this study was to compare systematically various steps like lysis, duration of electrophoresis, and pH of the electrophoresis solution and their effect on the comet tail with regard to sensitivity for detection and quantification of DNA damage. We treated human lymphoblastoid TK6 cells with known genotoxic substances with a different mode of action and then performed both standard and modified alkaline and neutral comet assays. The modifications included Fpg- and MspI-modified comet assays. Several aspects of this comparison are investigated for the first time here. The results obtained from these experiments showed a higher %DNA in tail in the alkaline comet assay compared to the neutral comet assay. Additionally, the lysis step was not critical in the alkaline comet assay, whereas it was essential for the neutral comet assay. Results from alkaline Fpg-modified comet assay showed higher sensitivity in detecting single strand breaks and the neutral MspI-modified comet assay was better in detecting DNA double-strand breaks. Overall, our findings provided valuable insight into the differences between alkaline and neutral electrophoresis conditions in the comet assay and indicated that the alkaline comet assay is more sensitive for measuring total DNA damage.
Retraction to: Divergent molecular profile of PIK3CA gene in arsenic-associated bladder carcinoma.
Mutagenesis · 2025 Oct · PMID 40840915 · Publisher ↗
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The micronucleus assay in exfoliated buccal cells for occupational exposure studies: an overview.
Wultsch G, Nersesyan A, Mišík M … +5 more , Ferk F, Schelch K, Scharnagl M, Grusch M, Knasmüller S
Mutagenesis · 2026 Mar · PMID 40820920 · Full text
This review describes the use of the micronucleus (MN) assay with exfoliated cells from the oral mucosa in occupational studies. The molecular mechanisms leading to formation of MN (chromosomal breakage and aneuploidy) a...
This review describes the use of the micronucleus (MN) assay with exfoliated cells from the oral mucosa in occupational studies. The molecular mechanisms leading to formation of MN (chromosomal breakage and aneuploidy) are well known. In total, 222 articles have been published since the method was developed in 1982. The majority of investigations were conducted with agricultural workers, followed by petrol station attendants, painters, pathology/anatomy lab workers, and miners. Positive results were reported in the majority of studies (86%); Brazil, Italy, Mexico, and Turkey being the most productive countries. The use of this technique increased substantially in recent years, and a recent correlation analysis with data from MN studies with lymphocytes indicates that the method is useful for predicting the cancer risks of chemically and radiation-exposed workers. The methodological quality of the studies increased in recent years since standardized and validated guidelines have been published. However, major shortcomings are still the lack of adequate matching (in particular in regard to nutrition and intake of dietary supplements), the lack of chemical exposure measurements, and the use of inadequate (DNA-nonspecific) stains. The most pronounced effects were seen in metal production workers, miners, petrol station attendants, agricultural workers, and pathologists. The sampling of cells from the oral cavity is noninvasive and requires no cultivation under sterile conditions is required. The currently available data indicate that this fast and easy-to-perform procedure provides valuable information about combined effects of chemical exposures and about the efficiency of safety measurements. Therefore, it should be used in the future for the routine surveillance of workers.
Harnessing the power of an advanced in vitro 3D liver model and error-corrected duplex sequencing for the detection of mutational signatures.
Conway GE, Chavanel B, Virard F … +8 more , Shah UK, Burgum MJ, Evans SJ, Korenjak M, Thomas LE, Jenkins GJ, Zavadil J, Doak SH
Mutagenesis · 2025 Aug · PMID 40794844 · Publisher ↗
Genotoxicity testing plays a crucial role in evaluating the hazards posed by various chemicals. Traditional methods, such as the Ames test, mammalian cell mutation assays and the transgenic rodent assay have certain limi...
Genotoxicity testing plays a crucial role in evaluating the hazards posed by various chemicals. Traditional methods, such as the Ames test, mammalian cell mutation assays and the transgenic rodent assay have certain limitations including laborious procedures and/or reliance on animal models. The aim of this study was to determine the potential of using error-corrected next-generation sequencing (ecNGS), specifically duplex sequencing (DS), as an alternative method for the detection of point mutations in conjunction with advanced in vitro models. This study establishes an easy to use, adaptable in vitro 3D HepG2 model, that shows good viability, and liver functionality over 14 days. 3D HepG2 spheroids were exposed to aristolochic acid in a repeated dose regime over 4 days. This was shown to significantly induce micronucleus formation, indicative of fixed DNA damage, in a dose dependent fashion. DS coupled with mutational signature analyses revealed a predominant treatment-specific T:A > A:T-enriched mutational signature explained by COSMIC signature SBS22 derived from human cancers associated with aristolochic acid exposure. De novo extraction provided a stable signature, of which more than 40% were unambiguously explained by SBS22 These results demonstrate that the presented 3D HepG2 spheroid model is appropriate for assessing chemically induced fixed DNA damage. Additionally, we provide evidence that DS applied to the studied in vitro 3D model has the capacity to reveal specific mutational signatures of mutagenic exposures. The modern integrative approach will improve the understanding of mechanisms of carcinogenesis related to chemical exposures by providing a cost-effective and efficient means to assess genotoxicity and mutagenicity. With the inclusion of mutational signature analyses, this approach would see a reduction in reliance on animal models and enhancement of hazard assessment accuracy.
Computational prediction of mutagenicity through comprehensive cell painting analysis.
Cerisier N, Truong E, Watanabe T … +4 more , Oshiro T, Takahashi T, Ito S, Taboureau O
Mutagenesis · 2025 Oct · PMID 40757573 · Full text
The mutagenicity of chemical compounds is a key consideration in toxicology, drug development, and environmental safety. Traditional methods such as the Ames test, while reliable, are time-intensive and costly. With adva...
The mutagenicity of chemical compounds is a key consideration in toxicology, drug development, and environmental safety. Traditional methods such as the Ames test, while reliable, are time-intensive and costly. With advances in imaging and machine learning (ML), high-content assays like cell painting offer new opportunities for predictive toxicology. Cell painting captures extensive morphological features of cells, which can correlate with chemical bioactivity. In this study, we leveraged cell painting data to develop ML models for predicting mutagenicity and compared their performance with structure-based models. We used two datasets: a Broad Institute dataset containing profiles of over 30 000 molecules and a U.S.-Environmental Protection Agency dataset with images of 1200 chemicals tested at multiple concentrations. By integrating these datasets, we aimed to improve the robustness of our models. Among three algorithms tested-Random Forest, Support Vector Machine, and Extreme Gradient Boosting-the third showed the best performance for both datasets. Notably, selecting the most relevant concentration per compound, the phenotypic altering concentration, significantly improved prediction accuracy. Our models outperformed traditional quantitative structure activity relationship (QSAR) tools such as the Virtual models for property Evaluation of chemicals within a Global Architecture (VEGA) and the CompTox Dashboard for the majority of compounds, demonstrating the utility of cell painting features. The cell painting-based models revealed morphological changes related to DNA and RNA perturbation, especially in mitochondria, endoplasmic reticulum and nuclei, aligning with mutagenicity mechanisms. Despite this, certain compounds remained challenging to predict due to inherent dataset limitations and inter-laboratory variability in cell painting technology. The findings highlight the potential of cell painting in mutagenicity prediction, offering a complementary perspective to chemical structure-based models. Future work could involve harmonizing cell painting methodologies across datasets and exploring deep learning techniques to enhance predictive accuracy. Ultimately, integrating cell painting data with QSAR descriptors in hybrid models may unlock novel insights into chemical mutagenicity.
Re: Rather et al. Carcinogenic parasites: insights into the epidemiology and possible mechanisms of cancer.
Nersesyan A
Mutagenesis · 2025 Oct · PMID 40757525 · Publisher ↗
Abstract loading — click title to view on PubMed.
Understanding the cellular uptake and genotoxic potential of industrial relevant nanomaterials utilizing electron microscopy and the ToxTracker assay in vitro.
Evans SJ, Moelijker N, Brandsma I … +4 more , Burgum MJ, Elespuru R, Hendriks G, Doak SH
Mutagenesis · 2025 Oct · PMID 40671358 · Full text
Evaluating the genotoxic potential of nanomaterials (NMs) presents unique challenges not associated with traditional toxicological assessment. A key question in any NM focused toxicity study is whether the material has r...
Evaluating the genotoxic potential of nanomaterials (NMs) presents unique challenges not associated with traditional toxicological assessment. A key question in any NM focused toxicity study is whether the material has reached the target cell and what its subsequent subcellular localization is. This current study aimed to assess the potential of a panel of industrially relevant NMs; TiO2-NM102, TiO2-NM105, TiO2-E171, silica, polyethylene, polystyrene, carbon black, gold nanorods, tungsten carbide/cobalt, and tungsten carbide, to undergo cellular uptake in mouse embryonic stem cells, which are applied in the ToxTracker genotoxicity assay. Ultrastructural cellular analysis by transmission electron microscopy was undertaken following 100 μg/ml treatment with the test NMs for 24 h; any observed uptake was confirmed by energy-dispersive X-ray spectroscopy. Induction of DNA damage, cytotoxicity, p53 activation, protein stress, and oxidative stress was evaluated by the ToxTracker assay following 24-h treatment with the test NMs (0-100 μg/ml) in the absence of S9. TiO2-NM105, silica, polystyrene, carbon black, and tungsten carbide were all shown to undergo cellular uptake, localized in membrane-bound vesicles within the cytoplasm. None of the internalized NMs promoted a genotoxic response in ToxTracker, and similarly, no DNA damage was observed by the materials not internalized. Interestingly, of the internalized NMs, only polystyrene caused a slight cytotoxic response at 100 μg/ml treatment (10% loss in cell viability). Of the NMs not internalized, cytotoxicity was observed in mES cells treated with 100 μg/ml TiO2-NM102 (15%), polyethylene (15%), gold nanorods (35%), and tungsten carbide/cobalt (45%). In summary, this study demonstrated that TiO2-NM105, silica, polystyrene, carbon black, and tungsten carbide are non-genotoxic in vitro despite undergoing cell uptake in the ToxTracker cells. A continued focus is needed to supplement NM genotoxicity studies with cellular uptake analysis.
N-nitrosamines: in silico modelling of DNA reactivity and identification of metabolic precursors.
Ivanova H, Petkov PI, Kulkarni S … +6 more , Barton-Maclaren T, Kaloyanova E, Kotov S, Kirilov K, Schultz TW, Mekenyan OG
Mutagenesis · 2025 Aug · PMID 40626895 · Publisher ↗
The discovery of N-nitrosamines (NNAs) as impurities in several pharmaceuticals has renewed activities in assessing their mutagenic and carcinogenic potential. In the current investigation, the binary mutagenic potential...
The discovery of N-nitrosamines (NNAs) as impurities in several pharmaceuticals has renewed activities in assessing their mutagenic and carcinogenic potential. In the current investigation, the binary mutagenic potential of NNAs is re-investigated using the mechanism-based structure-activity approach of the TIMES models. Emphasis is placed on meeting the OECD (Q)SAR principles for model validation and the organization's (Q)SAR prediction principles. A curated data set of 41 small and complex NNA-containing substances tested in a standard battery of Salmonella typhimurium strains with and without rat microsomal activation was assessed for these tasks. Structural boundaries are initially derived from activating mechanisms for interactions of parent NNAs with DNA described in the literature. These activating mechanisms include direct-acting mutagenicity (denitrosation of parent molecules) or DNA interactions after S9 metabolic activation (alpha-hydroxylation). After analysis of the 41 NNAs, structural features that mitigate or 'mask' the covalent binding of NNAs to DNA expanded the original alert definition. The structural fragments' predictive capabilities (performance) for the activating and negating mechanisms of these 41 chemicals are excellent. Three false positives and no false negatives are reported. Moreover, the role of metabolism in the N-nitrosation of secondary amines and tertiary amines after conversion to secondary amines under in vivo conditions is explained with descriptions of new metabolic transformations. These transformation boundaries are applied to different inventories to search for parent structures that are potential in vivo metabolic precursors of NNAs.
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