Chromosome aberrations: past, present and future

Exploring cytokinesis block micronucleus assay in Croatia: A journey through the past, present, and future in biomonitoring of the general population

In this study, we used the cytokinesis-block micronucleus (CBMN) assay to evaluate the background frequency of cytogenetic damage in peripheral blood lymphocytes of the general population concerning different anthropometric data and lifestyle factors. The background frequency of CBMN assay parameters was analysed in 850 healthy, occupationally non-exposed male and female subjects (average age, 38±11 years) gathered from the general Croatian population from 2000 to 2023. The mean background values for micronuclei (MNi) in the whole population were 5.3±4.3 per 1000 binucleated cells, while the mean frequency of nucleoplasmic bridges (NPBs) was 0.7±1.3 and of nuclear buds (NBUDs) 3.1±3.2. The cut-off value, which corresponds to the 95th percentile of the distribution of 850 individual values, was 14 MNi, 3 NPBs, and 9 NBUDs. Results from our database also showed an association of the tested genomic instability parameters with age and sex but also with other lifestyle factors. These findings underscore the importance of considering several anthropometric and lifestyle factors when conducting biomonitoring studies. Overall, the normal and cut-off values attained here present normal values for the general population that can later serve as baseline values for further human biomonitoring studies either in Croatia or worldwide.

Toxicity Assessment of a No-Pain Pharmacopuncture Extract Using a Standard Battery of In Vitro Chromosome Aberration Tests

Objectives

Genotoxicity is evaluated through a chromosomal aberration test using cultured mammalian cells to determine the toxicity of no-pain pharmacopuncture (NPP), which has recently been used to treat musculoskeletal pain disorders in Korean medical clinical practice.

Methods

An initial test was performed to determine the dosage range of the NPP, followed by the main test. In this study, NPP doses of 10.0, 5.0, and 2.5%, and negative and positive controls were tested. An in vitro chromosome aberration test was performed using Chinese hamster lung cells under short-term treatment with or without metabolic activation and under continuous treatment without metabolic activation.

Results

Compared with the saline negative control group, NPP did not significantly increase the frequency of chromosomal abnormalities in Chinese hamster lung cells, regardless of the presence or absence of metabolic activation. Additionally, the number of cells with structural chromosomal abnormalities was significantly higher in the positive control group than that in the negative control group that received saline.

Conclusion

Based on the above results, the chromosomal abnormality-producing effect of NPP was determined to be negative under these test conditions.

An automatic progressive chromosome segmentation approach using deep learning with traditional image processing

The fully automatic chromosome analysis system plays an important role in the detection of genetic diseases, which in turn can reduce the diagnosis burden for cytogenetic experts. Chromosome segmentation is a critical step for such a system. However, due to the non-rigid structure of chromosomes, chromosomes may curve in any direction, and two or more chromosomes may touch or overlap to form unpredictable chromosome clusters in metaphase chromosome images, leading to automatic chromosome segmentation as a challenge. In this paper, we propose an automatic progressive segmentation approach to perform the entire metaphase chromosome image segmentation using deep learning with traditional image processing. It follows three stages. In the first stage, thresholding-based and geometric-based methods are employed to divide all chromosomes as single ones and chromosome clusters. To tackle the segmentation for unpredictable chromosome clusters, we first present a new chromosome cluster identification network named CCI-Net to classify all chromosome clusters into different types in the second stage, and then in the third stage, we combine traditional image processing with deep CNNs to accomplish chromosome instance segmentation from different types of clusters. Evaluation results on a clinical dataset of 1148 metaphase chromosome images show that the proposed automatic progressive segmentation method achieves 94.60% chromosome cluster identification accuracy and 99.15% instance segmentation accuracy. The experimental results exhibit that our proposed approach can effectively identify chromosome clusters and successfully perform fully automatic chromosome segmentation.

A gene-nutrient interaction between vitamin B6 and serine hydroxymethyltransferase (SHMT) affects genome integrity in Drosophila

Pyridoxal 5'-phosphate (PLP), the catalytically active form of vitamin B6, participates as a cofactor to one carbon (1C) pathway that produces precursors for DNA metabolism. The concerted action of PLP-dependent serine hydroxymethyltransferase (SHMT) and thymidylate synthase (TS) leads to the biosynthesis of thymidylate (dTMP), which plays an essential function in DNA synthesis and repair. PLP deficiency causes chromosome aberrations (CABs) in Drosophila and human cells, rising the hypothesis that an altered 1C metabolism may be involved. To test this hypothesis, we used Drosophila as a model system and found, firstly, that in PLP deficient larvae SHMT activity is reduced by 40%. Second, we found that RNAi-induced SHMT depletion causes chromosome damage rescued by PLP supplementation and strongly exacerbated by PLP depletion. RNAi-induced TS depletion causes severe chromosome damage, but this is only slightly enhanced by PLP depletion. dTMP supplementation rescues CABs in both PLP-deficient and PLP-proficient SHMT^RNAi . Altogether these data suggest that a reduction of SHMT activity caused by PLP deficiency contributes to chromosome damage by reducing dTMP biosynthesis. In addition, our work brings to light a gene-nutrient interaction between SHMT decreased activity and PLP deficiency impacting on genome stability that may be translated to humans.

Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture

The detection of structural chromosomal abnormalities (SCA) is crucial for diagnosis, prognosis and management of many genetic diseases and cancers. This detection, done by highly qualified medical experts, is tedious and time-consuming. We propose a highly performing and intelligent method to assist cytogeneticists to screen for SCA. Each chromosome is present in two copies that make up a pair of chromosomes. Usually, SCA are present in only one copy of the pair. Convolutional neural networks (CNN) with Siamese architecture are particularly relevant for evaluating similarities between two images, which is why we used this method to detect abnormalities between both chromosomes of a given pair. As a proof-of-concept, we first focused on a deletion occurring on chromosome 5 (del(5q)) observed in hematological malignancies. Using our dataset, we conducted several experiments without and with data augmentation on seven popular CNN models. Overall, performances obtained were very relevant for detecting deletions, particularly with Xception and InceptionResNetV2 models achieving 97.50% and 97.01% of F₁-score, respectively. We additionally demonstrated that these models successfully recognized another SCA, inversion inv(3), which is one of the most difficult SCA to detect. The performance improved when the training was applied on inversion inv(3) dataset, achieving 94.82% of F₁-score. The technique that we propose in this paper is the first highly performing method based on Siamese architecture that allows the detection of SCA. Our code is publicly available at: https://github.com/MEABECHAR/ChromosomeSiameseAD.

Unraveling the DNA Methylation in the rDNA Foci in Mutagen-Induced Brachypodium distachyon Micronuclei

Many years have passed since micronuclei were first observed then accepted as an indicator of the effect of mutagens. However, the possible mechanisms of their formation and elimination from the cell are still not fully understood. Various stresses, including mutagens, can alter gene expression through changes in DNA methylation in plants. In this study we demonstrate for the first time DNA methylation in the foci of 5S and 35S rDNA sequences in individual Brachypodium distachyon micronuclei that are induced by mutagenic treatment with maleic acid hydrazide (MH). The impact of MH on global epigenetic modifications in nuclei and micronuclei has been studied in plants before; however, no in situ analyses of DNA methylation in specific DNA sequence sites are known. To address this problem, we used sequential immunodetection of 5-methylcytosine and fluorescence in situ hybridization (FISH) with 5S and 25S rDNA probes on the non-dividing cells of B. distachyon. Such investigations into the presence or absence of DNA methylation within specific DNA sequences are extremely important in plant mutagenesis in the light of altering gene expression.

SRAS-net: Low-resolution chromosome image classification based on deep learning

Prenatal karyotype diagnosis is important to determine if the foetus has genetic diseases and some congenital diseases. Chromosome classification is an important part of karyotype analysis, and the task is tedious and lengthy. Chromosome classification methods based on deep learning have achieved good results, but if the quality of the chromosome image is not high, these methods cannot learn image features well, resulting in unsatisfactory classification results. Moreover, the existing methods generally have a poor effect on sex chromosome classification. Therefore, in this work, the authors propose to use a super‐resolution network, Self‐Attention Negative Feedback Network, and combine it with traditional neural networks to obtain an efficient chromosome classification method called SRAS‐net. The method first inputs the low‐resolution chromosome images into the super‐resolution network to generate high‐resolution chromosome images and then uses the traditional deep learning model to classify the chromosomes. To solve the problem of inaccurate sex chromosome classification, the authors also propose to use the SMOTE algorithm to generate a small number of sex chromosome samples to ensure a balanced number of samples while allowing the model to learn more sex chromosome features. Experimental results show that our method achieves 97.55% accuracy and is better than state‐of‐the‐art methods.

Can exposure to panoramic radiographs induce genotoxic effects on the oral epithelium? A systematic review with meta-analysis

OBJECTIVE

To evaluate, through a systematic review (SR) with meta-analysis, the occurrence of genotoxic effects in the oral epithelium after the exposure of patients to panoramic radiographs.

METHODS

An SR was performed with the PICOS (Population, Intervention, Comparison, Outcome, and Study design) strategy, aiming to answer the following question: "Can panoramic radiographs induce genotoxic effects on the oral epithelium?" The study was registered in the PROSPERO (International prospective register of systematic reviews) platform. A systematic search was performed in the following electronic databases: PubMed (including MedLine), Scopus, Embase, LILACS, Medline EbscoHost, and Google Scholar. Treatment effects were defined as standardized mean difference (SMD), and 95% confidence intervals (CI) were established. The Joanna Briggs Institute questionnaire for observational studies was applied to assess the risk of bias. The GRADE tool was used to assess the quality of evidence of the SR.

RESULTS

A total of 251 potentially relevant studies were selected through the search strategy. After screening titles and abstracts, 11 full-text manuscripts were assessed for eligibility and nine observational studies were included in the meta-analysis. The present study showed an increase in micronuclei after the exposure (SMD = 0.21, 95% CI, 0.03 to 0.28, p = 0.02), with a Tau²index = 0.00, Chi² = 2.35, and p-value = 0.97. Therefore, the articles selected were considered homogeneous and the I² of 0% indicated low heterogeneity.

CONCLUSION

According to the studies analysed, although the quality of evidence was considered low, panoramic radiographs can cause genotoxic damage in the oral epithelium but with a small effect size.

Evaluation of the in vitro and in vivo genotoxicity of a Dioscorea Rhizome water extract

Dioscorea Rhizome is commonly used in traditional herbal medicines for the treatment of diabetes, hyperthyroidism, liver damage, neuropathy, and asthma. Here, we investigated the genotoxicity potential of D. Rhizome water extract (DRWE) using three standard battery systems in accordance with the test guidelines of the Organisation for Economic Cooperation and Development and Ministry of Food and Drug Safety as well as the principles of Good Laboratory Practice. A bacterial reverse mutation test (Ames test) was performed using the direct plate incorporation method in the presence or absence of a metabolic activation system (S9 mixture). The tester strains used included four histidine auxotrophic strains of Salmonella typhimurium, TA100, TA1535, TA98, and TA1537, along with a tryptophan auxotrophic strain of Escherichia coli, WP2 uvrA. An in vitro chromosome aberration test was performed using CHL/IU cells originally derived from the lung of a female Chinese hamster in the presence or absence of the S9 mixture. An in vivo mouse bone marrow micronucleus test was performed using male ICR mice. The micronucleus was confirmed after observation of the micro-nucleated polychromatic. The Ames test showed that DRWE did not induce gene mutations at any dose level in any of the tested strains. Additionally, DRWE did not result in any chromosomal aberrations specified in the in vitro chromosomal aberration and in vivo micronucleus tests. These results showed that DRWE exhibited neither mutagenic nor clastogenic potential in either the in vitro or in vivo test systems.

Categorizing the characteristics of human carcinogens: a need for specificity

The International Agency for Research on Cancer (IARC) has recently proposed employing "ten key characteristics of human carcinogens" (TKCs) to determine the potential of agents for harmful effects. The TKCs seem likely to confuse the unsatisfactory correlation from testing regimes that have ignored the differences evident when cellular changes are compared in short and long-lived species, with their very different stem cell and somatic cell phylogenies. The proposed characteristics are so broad that their use will lead to an increase in the current unacceptably high rate of false positives. It could be an informative experiment to take well-established approved therapeutics with well-known human safety profiles and test them against this new TKC paradigm. Cancers are initiated and driven by heritable and transient changes in gene expression, expand clonally, and progress via additional associated acquired mutations and epigenetic alterations that provide cells with an evolutionary advantage. The genotoxicity testing protocols currently employed and required by regulation, emphasize testing for the mutational potential of the test agent. Two-year, chronic rodent cancer bioassays are intended to test for the entire spectrum of carcinogenic transformation. The use of cytotoxic doses causing increased, sustained cell proliferation that facilitates accumulated genetic damage leads to a high false-positive rate of tumor induction. Current cancer hazard assessment protocols and weight-of-the-evidence analysis of agent-specific cancer risk align poorly with the pathogenesis of human carcinoma and so need modernization and improvement in ways suggested here.

Effect of Nutritional Intervention Programs on Nutritional Status and Readmission Rate in Malnourished Older Adults with Pneumonia: A Randomized Control Trial

Pneumonia leads to changes in body composition and weakness due to the malnourished condition. In addition, patient family caregivers always have a lack of nutritional information, and they do not know how to manage patients’ nutritional intake during hospitalization and after discharge. Most intervention studies aim to provide nutritional support for older patients. However, whether long-term nutritional intervention by dietitians and caregivers from patients’ families exert clinical effects—particularly in malnourished pneumonia—on nutritional status and readmission rate at each interventional phase, from hospitalization to postdischarge, remains unclear. To investigate the effects of an individualized nutritional intervention program (iNIP) on nutritional status and readmission rate in older adults with pneumonia during hospitalization and three and six months after discharge. Eighty-two malnourished older adults with a primary diagnosis of pneumonia participated. Patients were randomly allocated to either a nutrition intervention (NI) group or a standard care (SC) group. Participants in the NI group received an iNIP according to energy and protein intake requirements in addition to dietary advice based on face-to-face interviews with their family caregivers during hospitalization. After discharge, phone calls were adopted for prescribing iNIPs. Anthropometry (i.e., body mass index, limb circumference, and subcutaneous fat thickness), blood parameters (i.e., albumin and total lymphocyte count), hospital stay, Mini-Nutritional Assessment-Short Form (MNA-SF) score, target daily calorie intake, total calorie intake adherence rate, and three-major-nutrient intakes were assessed during hospitalization and three and six months after discharge. Both groups received regular follow-up through phone calls. Furthermore, the rate of readmission resulting from pneumonia was recorded after discharge. During hospital stay, the NI group showed significant increases in daily calorie intake, total calorie intake adherence rate, and protein intake compared with the SC group (p < 0.05); however, no significant difference was found in anthropometry, blood biochemical values, MNA-SF scores, and hospital stay. At three and six months after discharge, the NI group showed significantly higher daily calorie intake and MNA-SF scores (8.2 vs. 6.5 scores at three months; 9.3 vs. 7.6 scores at six months) than did the SC group (p < 0.05). After adjusting for sex, the readmission rate for pneumonia significantly decreased by 77% in the NI group compared with that in the SC group (p = 0.03, OR: 0.228, 95% CI: 0.06–0.87). A six-month iNIP under dietitian and patient family nutritional support for malnourished older adults with pneumonia can significantly improve their nutritional status and reduce the readmission rate.

Varifocal-Net: A Chromosome Classification Approach Using Deep Convolutional Networks

Chromosome classification is critical for karyotyping in abnormality diagnosis. To expedite the diagnosis, we present a novel method named Varifocal-Net for simultaneous classification of chromosome's type and polarity using deep convolutional networks. The approach consists of one global-scale network (G-Net) and one local-scale network (L-Net). It follows three stages. The first stage is to learn both global and local features. We extract global features and detect finer local regions via the G-Net. By proposing a varifocal mechanism, we zoom into local parts and extract local features via the L-Net. Residual learning and multi-task learning strategies are utilized to promote high-level feature extraction. The detection of discriminative local parts is fulfilled by a localization subnet of the G-Net, whose training process involves both supervised and weakly supervised learning. The second stage is to build two multi-layer perceptron classifiers that exploit features of both two scales to boost classification performance. The third stage is to introduce a dispatch strategy of assigning each chromosome to a type within each patient case, by utilizing the domain knowledge of karyotyping. The evaluation results from 1909 karyotyping cases showed that the proposed Varifocal-Net achieved the highest accuracy per patient case (%) of 99.2 for both type and polarity tasks. It outperformed state-of-the-art methods, demonstrating the effectiveness of our varifocal mechanism, multi-scale feature ensemble, and dispatch strategy. The proposed method has been applied to assist practical karyotype diagnosis.

Interphase Cytogenetic Analysis of Micronucleated and Multinucleated Cells Supports the Premature Chromosome Condensation Hypothesis as the Mechanistic Origin of Chromothripsis

The discovery of chromothripsis in cancer genomes challenges the long-standing concept of carcinogenesis as the result of progressive genetic events. Despite recent advances in describing chromothripsis, its mechanistic origin remains elusive. The prevailing conception is that it arises from a massive accumulation of fragmented DNA inside micronuclei (MN), whose defective nuclear envelope ruptures or leads to aberrant DNA replication, before main nuclei enter mitosis. An alternative hypothesis is that the premature chromosome condensation (PCC) dynamics in asynchronous micronucleated cells underlie chromosome shattering in a single catastrophic event, a hallmark of chromothripsis. Specifically, when main nuclei enter mitosis, premature chromatin condensation provokes the shattering of chromosomes entrapped inside MN, if they are still undergoing DNA replication. To test this hypothesis, the agent RO-3306, a selective ATP-competitive inhibitor of CDK1 that promotes cell cycle arrest at the G2/M boundary, was used in this study to control the degree of cell cycle asynchrony between main nuclei and MN. By delaying the entrance of main nuclei into mitosis, additional time was allowed for the completion of DNA replication and duplication of chromosomes inside MN. We performed interphase cytogenetic analysis using asynchronous micronucleated cells generated by exposure of human lymphocytes to γ-rays, and heterophasic multinucleated Chinese hamster ovary (CHO) cells generated by cell fusion procedures. Our results demonstrate that the PCC dynamics during asynchronous mitosis in micronucleated or multinucleated cells are an important determinant of chromosome shattering and may underlie the mechanistic origin of chromothripsis.

Detecting Brachypodium distachyon Chromosomes Bd4 and Bd5 in MH- and X-Ray-Induced Micronuclei Using mcFISH

Micronuclei are biomarkers of genotoxic effects and chromosomal instability. They are formed when chromosome fragments or whole chromosomes fail to disjoin into daughter nuclei. We present qualitative and quantitative analyses of the involvement of specific chromosome regions of chromosomes Bd4 and Bd5 in the formation of micronuclei of Brachypodium distachyon root tip cells following maleic hydrazide (MH) treatment and X-radiation. This is visualised by cytomolecular approaches using bacterial artificial chromosome (BAC)-based multicolour fluorescence in situ hybridisation (mcFISH) in combination with 5S and 25S rDNA probes. The results showed that the long arm of submetacentric chromosome Bd4 forms micronuclei at twice the frequency of its short arm, suggesting that the former is more prone to double-strand breaks (DSBs). In contrast, no difference was observed in the frequency of micronuclei derived from the long and short arms of submetacentric chromosome Bd5. Interestingly, the proximal region of the short arm of Bd5 is more prone to DSBs than its distal part. This demonstrates that 5S rDNA and 35S rDNA loci are not "hot spots" for DNA breaks after the application of these mutagens.

Vitamin D Resists Cyclophosphamide-Induced Genomic and DNA Damage in CHL Cells In Vitro and in Mice In Vivo

Vitamin D as an adjuvant therapy for cancer patients is hoped to have a beneficial outcome based on its physiological activity, but clinical trials so far by addition of vitamin D show unremarkable curative improvement, mechanism for explain this phenomena is not well-understood. The aim of this study was to determine whether vitamin D resists cyclophosphamide (CP)-induced genomic and DNA damage. In CHL cells in vitro, 1α,25-(OH)₂D₃ at 10, 50, and 100 nM was found to alleviate the frequency of chromosomal aberration with an alleviation range of 40.7-44.0%. There was a dose-dependent decrease for a proportion of γ-H2AX foci positive cells in response to an increase in 1α,25-(OH)₂D₃ concentration. Two vitamin D₃ injections of 1,000, 5,000, or 10,000 IU suppressed CP-induced micronucleus formation in mice BMCs with an alleviation range of 36.7-44.5%, mitigated lymphocytes DNA damage reflected by lower tail DNA, tail length and olive tail moment parameter in comet assay. Vitamin D showed an antagonistic effect on CP-induced genomic and DNA damage. Our data suggest that vitamin D as an adjuvant combine antineoplastic drug with genotoxicity administer to tumor patients is contraindicant.

THE INVESTIGATION OF MICRONUCLEI FREQUENCY DISTRIBUTION FOR EXPOSED AND UNEXPOSED PERSONNEL TO IONIZING RADIATION

To establish at which extent the micronuclei (MN) frequency is influenced by occupational exposure to ionizing radiation, peripheral blood samples collected from 2151 subjects of both genders, smokers and non-smokers were analyzed. Among them, 378 (17.6%) were unexposed while the other 1773 (82.4%) were exposed to ionizing radiation for periods between 1 year and more than 30 years, at levels never overpassing legally regulated limits. The final results showed that for all investigated categories, MN frequency monotonously increases with the age by 1.75 ± 0.17 times in the case of exposed subjects, but independent on gender and smoking habit.

Effects of sewage sludge application on unfertile tropical soils evaluated by multiple approaches: A field experiment in a commercial Eucalyptus plantation

Sewage sludge (SS) reuse in forest plantation as soil fertilizer/amendment has tremendously increased in recent years. However, SS may have high concentrations of potentially toxic elements (PTE), representing a potential risk for soil and the whole ecosystem. This paper was aimed to assess the toxicity of PTE in unfertile tropical soils amended with SS in a commercial Eucalyptus plantation, with an integrated multiple approaches combining: i) the use of a battery of bioassays (Daphnia magna, Pseudokcrichirella subcapitata, Lactuca sativa, and Allium cepa); and ii) the evaluation of some PTE (Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) and their availability into the pedoenvironment. Differences in total and available PTE between SS doses and time of treatments were evaluated using ANOVA; correlations between PTE and bioassays by a sparse partial robust M-regression (SPRM), while multiple correlations among parameters were performed by principal factor analysis (PFA). Results show that PTE contents in soils tended to increase with SS application doses. However this cannot be assumed as a general rule since in all the investigated treatments the PTE concentrations were consistently below both soil natural background concentrations and quality reference values. Bioassays showed a generalized low eco- and genotoxicity of SS with an increase in toxicity at increasing SS doses but with a clear decreasing trend as time went by. A. cepa was the most sensitive bioassay followed by P. subcapitata > D. magna > L. sativa. Overall, the results indicate that in realistic open field conditions SS risk may be lower than expected due to dynamic decrease in PTE toxicity with time after application. This study has an important implication that open-field trials should be strongly encouraged for evaluating environmental risk of SS application in forestry.

The mutagenic effect of psychostimulant modafinil in Wistar rats in vivo

The demands imposed by today's world require a fast and efficient society, then, significant section of the population looks for support from psychotropic medicine. Modafinil is a psychostimulant that promotes wakefulness, it being recommended for treatment of narcolepsy, obstructive sleep apnea, and shift-work sleep disorder, besides being a cognitive function potentiator. However, chemical components of drugs can alter genetic material. Thus, the present study evaluated the cytotoxic and clastogenic/mutagenic potential of 0.25, 0.50, and 0.75 mg of Modafinil/mL of corn oil/100g body weight in acute treatments and subacute treatments, 15 days, to Rattus norvegicus, treated via gavage in a single daily dose. The drug was not cytotoxic at any of the evaluated doses in either of the treatments. However, the medicine showed clastogenic/mutagenic activity in the acute treatment group at the standard dose and at double dose. Data from the present study indicates that there should be greater caution as to the use of this psychostimulant by human beings.

History and evolution of cytogenetic techniques: Current and future applications in basic and clinical research

Chromosomes are the vehicles of genes, which are the functional units of a cell's nucleus. In humans, there are more than 20,000 genes that are distributed among 46 chromosomes in somatic cells. The study of chromosome structure and function is known as cytogenetics which is historically a field of hybrid science encompassing cytology and genetics. The field of cytogenetics has undergone rapid developments over the last several decades from classical Giemsa staining of chromosomes to 3-dimensional spatial organization of chromosomes with a high resolution mapping of gene structure at the nucleotide level. Improved molecular cytogenetic techniques have opened up exciting possibilities for understanding the chromosomal/molecular basis of various human diseases including cancer and tissue degeneration. This review summaries the history and evolution of various cytogenetic techniques and their current and future applications in diverse areas of basic research and medical diagnostics.

Assessment of ecotoxicological effects of ciprofloxacin in Daphnia magna: life-history traits, biochemical and genotoxic effects

Antibiotics (e.g. ciprofloxacin) have been detected in surface water and groundwater for several decades. In order to understand the potential impact of the continuous exposure of aquatic organisms to ciprofloxacin, a chronic assay was carried out with Daphnia magna. This approach allowed evaluation of the effects of ciprofloxacin on life-history and sub-individual parameters (antioxidant status and metabolic response: activities of catalase and glutathione S-transferases - GSTs; peroxidative damage; thiobarbituric acid reactive substances and genotoxic effects (genetic damage index, measured by the comet assay). Life-history parameters of D. magna showed no significant effects after ciprofloxacin exposure. Concerning oxidative stress and metabolism parameters, no significant alterations were reported for catalase and GSTs activities. However, a dual response was observed, with a significant decrease in lipid peroxidation levels at low ciprofloxacin concentrations (<0.013 mg/L), while a significant increase was verified at high ciprofloxacin concentrations (0.078 mg/L). The genotoxicity assay detected a significant increase in genetic damage index up to 0.013 mg/L of ciprofloxacin. The here-tested ciprofloxacin concentrations, which are ecologically relevant, did not cause significant impacts concerning the life-history parameters of D. magna; however, at the same levels of ciprofloxacin an oxidative stress and genotoxic damage scenarios were recorded.

Cancer etiology: Variation in cancer risk among tissues is poorly explained by the number of gene mutations

Recent evidence indicates that the risk of being diagnosed with cancer in a tissue is strongly correlated (0.80) with the number of stem cell divisions accumulated by the tissue. Since cell division can generate random mutations during DNA replication, this correlation has been used to propose that cancer is largely caused by the accumulation of unavoidable mutations in driver genes. However, no correlation between the number of gene mutations and cancer risk across tissues has been reported. Because many somatic mutations in cancers originate prior to tumor initiation and the number of cell divisions occurring during tumor growth is similar among tissues, I use whole genome sequencing information from 22 086 cancer samples and incidence data from the largest cancer registry in each continent to study the relationship between the number of gene mutations and the risk of cancer across 33 tissue types. Results show a weak positive correlation (mean = 0.14) between these 2 parameters in each of the 5 cancer registries. The correlation became stronger (mean = 0.50) when gender-related cancers were excluded. Results also show that 1003 samples from 29 cancer types have zero mutations in genes. These data suggest that cancer etiology can be better explained by the accumulation of stem cell divisions than by the accumulation of gene mutations. Possible mechanisms by which the accumulation of cell divisions in stem cells increases the risk of cancer are discussed.

In silico genotoxicity of coumarins: application of the Phenol-Explorer food database to functional food science

Coumarins are a group of phytochemicals that may be beneficial or harmful to health depending on their type and dosage and the matrix that contains them. Some of these compounds have been proven to display pro-oxidant and clastogenic activities. Therefore, in the current work, we have studied the coumarins that are present in food sources extracted from the Phenol-Explorer database in order to predict their clastogenic activity and identify the structure-activity relationships and genotoxic structural alerts using alternative methods in the field of computational toxicology. It was necessary to compile information on the type and amount of coumarins in different food sources through the analysis of databases of food composition available online. A virtual screening using a clastogenic model and different software, such as MODESLAB, ChemDraw and STATISTIC, was performed. As a result, a table of food composition was prepared and qualitative information from this data was extracted. The virtual screening showed that the esterified substituents inactivate molecules, while the methoxyl and hydroxyl substituents contribute to their activity and constitute, together with the basic structures of the studied subclasses, clastogenic structural alerts. Chemical subclasses of simple coumarins and furocoumarins were classified as active (xanthotoxin, isopimpinellin, esculin, scopoletin, scopolin and bergapten). In silico genotoxicity was mainly predicted for coumarins found in beer, sherry, dried parsley, fresh parsley and raw celery stalks. The results obtained can be interesting for the future design of functional foods and dietary supplements. These studies constitute a reference for the genotoxic chemoinformatic analysis of bioactive compounds present in databases of food composition.

Utilização de biomarcadores de genotoxicidade e expressão gênica na avaliação de trabalhadores de postos de combustíveis expostos a vapores de gasolina

Resumo Introdução: a avaliação de uma exposição mensura sua intensidade, frequência e duração, podendo detectar danos precoces que, se ignorados, podem evoluir para um quadro nocivo. Nos campos da saúde ambiental e ocupacional, os biomarcadores de genotoxicidade tem sido largamente utilizados para essa avaliação. Objetivo: identificar, descrever e discutir os principais bioindicadores de genotoxicidade e seu uso conjunto com técnicas de avaliação de expressão gênica em estudos de exposição ocupacional ao benzeno em postos de revenda de combustíveis (PRC). Métodos: revisão bibliográfica de trabalhos publicados entre 1995 e 2015. Resultados: as técnicas identificadas foram: ensaio cometa, estresse oxidativo, micronúcleos, aberrações cromossômicas, polimorfismos, adutos de DNA e proteínas, fatores epigenéticos e expressão gênica. Foi observado que testes de danos genéticos e epigenéticos são utilizados em frentistas de PRC que participam de programas de saúde do trabalhador ou de pesquisas, embora um baixo número de publicações sobre o tema tenha sido identificado. Esse fato talvez possa ser explicado pelos poucos países onde a profissão persiste e pelas limitações para o desenvolvimento de pesquisas nesses países. Conclusão: os bioindicadores de genotoxicidade e as técnicas de expressão gênica são úteis na detecção de dano precoce desta exposição ocupacional e devem ser avaliados em conjunto.

Stability of radiation-damaged DNA after multiple strand breaks

Radiation induced double-strand breaks in DNA are more stable against thermal and mechanical stress than usually thought.

Biodosimetry for High-Dose Exposures Based on Dicentric Analysis in Lymphocytes Released from the G2-Block by Caffeine

High-dose assessments using the conventional dicentric assay are essentially restricted to doses up to 5 Gy and only to lymphocytes that succeed to proceed to first post-exposure mitosis. Since G2-checkpoint activation facilitates DNA damage recognition and arrest of damaged cells, caffeine is used to release G2-blocked lymphocytes overcoming the mitotic index and dicentric yield saturation problems, enabling thus dicentric analysis even at high-dose exposures. Using the fluorescence in situ hybridization technique with telomere and centromere peptide nucleic acid probes, the released lymphocytes, identified as metaphases with decondensed chromosomes following 1.5 h caffeine treatment, show increased yield of dicentrics compared to that obtained in lymphocytes that reach metaphase without G2-checkpoint abrogation by caffeine. Here, a 3-h caffeine/colcemid co-treatment before harvesting at 55 h post-exposure is used so that the dicentric analysis using Giemsa staining is based predominantly on lymphocytes released from the G2-block, increasing thus dicentric yield and enabling construction of a dose-response calibration curve with improved precision of high-dose estimates.

Cytotoxicity of Spent Pot Liner on Allium cepa root tip cells: A comparative analysis in meristematic cell type on toxicity bioassays

Spent Pot Liner (SPL) is a waste generated during the production of aluminum. It is comprised of a mixture of substances most of which, like cyanide, aluminum and fluoride, are toxic. Previous studies indicate the highly toxic nature of SPL. However studies using cells of the differentiation/elongation zone of the root meristem (referred as M2 cells in this study) after a proper recovery period in water were never considered. Using these cells could be useful to further understanding the toxicity mechanisms of SPL. A comparative approach between the effects on M2 cells and meristematic cells of the proximal meristem zone (referred as M1 cells in this study) could lead to understanding how DNA damage caused by SPL behaves on successive generations of cells. Allium cepa cells were exposed to 4 different concentrations of SPL (2.5, 5, 7.5 and 10gL(-1)) mixed with soil and diluted in a CaCl2 0.01M to simulate the ionic forces naturally encountered on the environment. A solution containing only soil diluted on CaCl2 0.01M was used as control. M1 and M2 cells were evaluated separately, taking into account four different parameters: (1) mitotic alterations (MA); (2) presence of condensed nuclei (CN); (3) mitotic index (MI); (4) presence of micronucleus (MCN). Significant differences were observed between M1 and M2 roots tip cells for these four parameters accessed. M1 cells was more prompt to reveal citogenotoxicity through the higher frequency of MA observed. Meanwhile, for M2 cells higher frequencies of MCN and CN was noticed, followed by a reduction of MI. Also, it was possible to detect significant differences between the tested treatments and the control on every case. These results indicate SPL toxic effects carries on to future cells generations. This emphasizes the need to properly manage this waste. Joint evaluation of cells from both M1 and M2 regions was proven valuable for the evaluation of a series of parameters on all toxicity tests.

High-Throughput and High-Content Micronucleus Assay in CHO-K1 Cells

Visualization of micronuclei induction by chemicals and drugs enables measurement of possible compound genotoxicity. A loss of entire chromosome or a fragment of chromosome can lead to formation of micronuclei (MNi). The in vitro micronucleus assay can be conducted using nuclear dyes with high-content imaging platforms. This chapter describes the cytochalasin block method of measuring micronuclei in CHO-K1 cell lines.

Analysis of the Possible Persistent Genotoxic Damage in Workers Linked to the Ardystil Syndrome

BACKGROUND

A combination of several factors including a change in the paint application system; a lack of proper hygiene; and inadequate safety measures caused a severe health impact in the workers of some textile painting factories. This outbreak, mainly characterized by respiratory disorders, caused the death of six people and it has been classified as Ardystil syndrome.

MATERIALS AND METHODS

Fifty-two workers involved in the outbreak and 48 healthy subjects not known to have exposed to the potentially mutagenic agents participated in the study. The program evaluated possible genotoxic damage through the sister chromatid exchange (SCE) cytogenetic biomarker assay. We determined the frequency of SCE, high-frequency cells (HFCs), and a ratio, which can be considered as a new parameter, allowing for the study of the SCE distribution pattern among the chromosomes.

RESULTS

There was no statistically significant difference in the SCE frequency and in the mean number of HFCs between the control and the Ardystil-affected groups. However, smoking increased the incidence of all parameters studied in both the case and control groups.

CONCLUSIONS

This study shows that workers involved in the Ardystil syndrome did not suffer genotoxic damage as measured by SCE and HFCs when compared with the control group.

Analysis of Genetic Damage in Lymphocytes of Former Uranium Processing Workers

The frequency of cells containing micronuclei (MN) and the presence of centromeres in these MN were analyzed in lymphocytes of 98 men from Southern Bohemia. Forty-six of them had worked at the uranium processing plant ‘MAPE Mydlovary' which was closed in 1991, and 52 men were controls from the same area. FISH using human pan-centromeric chromosome paint was employed to detect centromere-positive (CEN+) and -negative (CEN-) MN. A total of 1,000 binucleated cells (BNC) per participant were analyzed after cytochalasin B treatment. All BNC with MN (CEN+ or CEN-) were recorded. No differences were found between formerly exposed workers and the control group, neither in the total frequency of cells with MN per 1,000 BNC (mean levels ± SD, 9.1 ± 3.1 and 9.8 ± 2.5, respectively) nor in the percentage of CEN- MN, which were equal (50 ± 18 and 49 ± 17, respectively). Also, there was no difference between individuals living in the 3 villages closest to the uranium processing plant and those living further away. Considering the fact that effective doses of the workers at MAPE Mydlovary were overall similar to those of former uranium miners in whom higher frequencies of CEN- MN have been found more than 10 years after they had finished working underground, these results are somewhat surprising. A more detailed analysis of the exposures indicates that uranium miners received a greater percentage of their effective dose from the inhalation of radon and its daughters, whereas uranium processing workers received it from the incorporation of long-lived radioactive nuclides such as uranium. If, as has been suggested before, the higher level of DNA damage in miners is due to induced genomic instability, then this phenomenon may be related to radon exposure rather than exposure to uranium.

Stress induced by premature chromatin condensation triggers chromosome shattering and chromothripsis at DNA sites still replicating in micronuclei or multinucleate cells when primary nuclei enter mitosis

Combination of next-generation DNA sequencing, single nucleotide polymorphism array analyses and bioinformatics has revealed the striking phenomenon of chromothripsis, described as complex genomic rearrangements acquired in a single catastrophic event affecting one or a few chromosomes. Via an unproven mechanism, it is postulated that mechanical stress causes chromosome shattering into small lengths of DNA, which are then randomly reassembled by DNA repair machinery. Chromothripsis is currently examined as an alternative mechanism of oncogenesis, in contrast to the present paradigm that considers a stepwise development of cancer. While evidence for the mechanism(s) underlying chromosome shattering during cancer development remains elusive, a number of hypotheses have been proposed to explain chromothripsis, including ionizing radiation, DNA replication stress, breakage-fusion-bridge cycles, micronuclei formation and premature chromosome compaction. In the present work, we provide experimental evidence on the mechanistic basis of chromothripsis and on how chromosomes can get locally shattered in a single catastrophic event. Considering the dynamic nature of chromatin nucleoprotein complex, capable of rapid unfolding, disassembling, assembling and refolding, we first show that chromatin condensation at repairing or replicating DNA sites induces the mechanical stress needed for chromosome shattering to ensue. Premature chromosome condensation is then used to visualize the dynamic nature of interphase chromatin and demonstrate that such mechanical stress and chromosome shattering can also occur in chromosomes within micronuclei or asynchronous multinucleate cells when primary nuclei enter mitosis. Following an aberrant mitosis, chromosomes could find themselves in the wrong place at the wrong time so that they may undergo massive DNA breakage and rearrangement in a single catastrophic event. Specifically, our results support the hypothesis that premature chromosome condensation induces mechanical stress and triggers shattering and chromothripsis in chromosomes or chromosome arms still undergoing DNA replication or repair in micronuclei or asynchronous multinucleate cells, when primary nuclei enter mitosis.

Mutagenicity of two herbicides widely used on soybean crops by the Allium cepa test

This study evaluated the mutagenic effects of two herbicides: Clorimurom Nortox(®) and Imazaquim Ultra Nortox(®) widely used on soybean crops in Brazil. As a test system, Allium cepa assay was used, which analyzes the frequency of micronuclei (MN), chromosomal aberrations (CA) and the mitotic index (MI). Four concentrations of each herbicide (50, 75, 100 and 125 %) were tested in triplicate using distilled water (negative control) and methyl methanesulfonate (positive control) as controls. Three experimental repetitions were realized. Clorimurom Nortox(®) showed a significantly lower MI than the negative control for the concentrations of 75, 100 and 125 %, but the CA was significantly increased at all concentrations. There was no recovery for CA or MI. The 125 % concentration of Imazaquim Ultra Nortox(®) was cytotoxic and also exerted an effect on the other parameters. The concentration of 100 % showed a statistically increased MN and there was no recovery, while the 75 % concentration significantly affected CA, with recovery observed. The two herbicides showed mutagenic damage in Allium cepa cells, which implies a careful handling of these products, to minimize the risk of human and environmental contamination.

Evaluation of DNA damage in Type 2 diabetes mellitus patients with and without peripheral neuropathy: A study in South Indian population

Background:

The increasing incidence of Type 2 diabetes mellitus globally has collaterally increased the incidence of diabetes-associated complications such as neuropathy. Oxidative stress induced DNA damage is one of the mechanisms implicated in the pathogenesis of diabetic complications. Here we aimed to evaluate the extent of DNA damage in diabetes patients with and without clinical neuropathy using the Cytokinesis Block Micronucleus Cytome assay, in a group of South Indian population.

Materials and Methods:

The Cytokinesis Block Micronucleus Cytome assay was performed in lymphocyte cultures of 42 type 2 diabetes patients (22 with neuropathy and 20 without neuropathy) and 42 age and sex matched controls. Nuclear aberrations like Nuclear Buds, Nucleoplasmic Bridges and Micronuclei were analyzed.

Results:

The frequency of nuclear aberrations in diabetes patients with neuropathy was higher than compared to diabetes patients without neuropathy. The mean frequencies of nuclear aberrations per cell in diabetes patients with neuropathy and without neuropathy were 0.02 ± 0.02 and 0.01 ± 0.01, respectively. This was significantly higher than in the controls (0.002 ± 0.002) (P < 0.0001). An increasing trend of nuclear aberrations in correlation with the duration of diabetes was observed.

Conclusion:

This study highlights the use of the Cytokinesis Block Micronucleus Cytome assay as a potent tool for the identification of DNA damage, which may prove to be useful biomarker to assess the severity diabetes-associated complications such as neuropathy. Implementation of this technique at the clinical level would potentially enhance the quality of management of patients with diabetes and its complications like neuropathy.

Protein energy-malnutrition: does the in vitro zinc sulfate supplementation improve chromosomal damage repair?

Protein-energy malnutrition (PEM) is originated by a cellular imbalance between nutrient/energy supply and body's demand. Induction of genetic damage by PEM was reported. The purpose of this study was to determine the genetic effect of the in vitro zinc sulfate (ZnSO4) supplementation of cultured peripheral blood lymphocytes from children with PEM. Twenty-four samples from 12 children were analyzed. Anthropometric and biochemical diagnosis was made. For the anthropometric assessment, height-for-age index, weight-for-age index, and weight-for-height index were calculated (WHO, 2005). Micronutrient status was evaluated. A survey for assessed previous exposure to potentially genotoxic agents was applied. Results were statistically evaluated using paired sample t test and χ (2) test. Each sample was fractionated and cultured in two separate flasks to performed two treatments. One was added with 180 μg/dl of ZnSO4 (PEMs/ZnSO4) and the other remains non-supplemented (PEMs). Cytotoxic effects and chromosomal damage were assessed using the cytokinesis-block micronucleus assay (CBMN). All participants have at least one type of malnutrition and none have anemia, nor iron, folate, vitamin A, and zinc deficiency. All PEMs/ZnSO4 samples have a significant reduction in the micronucleus (MNi) frequency compared with PEMs (t = 6.25685; p < 0.001). Nuclear division index (NDI) increase in PEMs/ZnSO4 (t = -17.4226; p < 0.001). Nucleoplasmic bridge (NPBs) frequency was four times smaller in PEMs/ZnSO4 (χ (2) = 40.82; p < 0.001). No nuclear buds (NBuds) were observed. Cytotoxic effects and chromosomal damage observed in children suffering from PEM can be repaired in vitro with zinc sulfate supplementation.

Evaluation of the in vitro cytogenotoxicity profile of antipsychotic drug haloperidol using human peripheral blood lymphocytes

Haloperidol (HLP) is a potent antipsychotic drug that is commonly used for the treatments of schizophrenia and bipolar disorders but has a tendency to cause adverse effects. In the present study, the cyto/genotoxic potential of clinically relevant concentrations of HLP was evaluated in human peripheral blood lymphocytes (HPBLs) as sensitive biomarkers of exposure. HLP was administered as HLP hydrochloride in the final concentrations of 5, 10 and 20 ng/ml for 4 and 24 h period. Cytotoxicity was determined using differential staining of HPBLs with acridine orange and ethidium bromide while chromosomal aberrations, micronucleus and comet assays were applied to estimate the chromosomal and DNA damage after the treatment. The results of the present study indicate that HLP is capable of inducing cyto/genotoxicity in tested cells. Present study has also confirmed the need for further cytogenetic research and regular patient monitoring to minimize the risk of any possible adverse events.

Induction of sister chromatid exchanges and cell division delays by clomiphene citrate in human lymphocytes

Objective:

Clomiphene citrate (CC) is a selective estrogen receptor modulator and is used for the treatment of in vitro fertilization, intracytoplasmic sperm injection, intrauterine insemination, and so on. In this study, sister chromatid exchanges (SCEs) and cell cycle delays were analyzed to investigate genotoxicity and cytotoxicity of CC in peripheral blood lymphocytes of healthy women.

Methods:

Human peripheral blood lymphocytes obtained from two donors were used to detect genotoxicity and cytotoxicity of CC. Lymphocytes were treated with various concentrations (0.40, 0.80, 1.60, and 3.20 µg/ml) of CC. A negative (distilled water) and a positive control (mitomycin-C = 0.20 µg/ml) were also used simultaneously with test substance-treated cultures. SCEs and cell division delays were measured from 25 cells and 100 cells perdonor, respectively.

Results:

CC significantly increased the mean SCE value at all concentrations compared with the negative control. This increase was found to be dose dependent ( r = 0.83) and at the highest concentration, nearly two times higher increase was observed than the negative control. However, replication index was not affected by the CC treatment.

Conclusion:

The present study shows that CC is genotoxic for human lymphocytes in vitro. Further investigations, especially in vivo are now needed in different test organisms to clarify the genotoxic activity of CC, which should also help to better understand genotoxic mechanism of this ovulation-stimulating drug.

Evaluation of cytotoxicity and mutagenicity of the benzodiazepine flunitrazepam in vitro and in vivo

Flunitrazepam (FNZ) is a sedative benzodiazepine prescribed for the short-term treatment of insomnia. However, there are concerns regarding possible carcinogenic or genotoxic effects of this medicine. Thus, the aim of this study was to evaluate the cytotoxic, clastogenic and aneugenic effects of FNZ in hepatoma cells from Rattus norvegicus (HTC) in vitro and in bone marrow cells of Wistar rats in vivo. These effects were examined in vitro following treatment with 0.2, 1.0, 5.0 or 10 μg/mL FNZ using a micronucleus test with a cytokinesis block or in vivo using a chromosomal aberration test following treatment with 7, 15 or 30 μg/mL/kg body weight. The results showed that the benzodiazepine concentrations tested were not cytotoxic, aneugenic or clastogenic. However, considering the adverse effects of using this benzodiazepine, more studies are required.

Cytotoxic and phytotoxic effects of the main chemical components of spent pot-liner: a comparative approach

Spent pot-liner (SPL) is a hazardous solid waste produced by the aluminum industry. Although its composition may vary, fluoride and cyanide salts as well as aluminum are predominant components. A seed-germination and root-elongation test was performed with Lactuca sativa seeds as a test system. SPL induced decrease of seed germination rate and root elongation. The concentration of 26.5g/L SPL was established from a regression curve as the IC50 (inhibition concentration 50%). Through chemical analyses, the concentrations of fluoride, cyanide and aluminum in SPL solutions of 26.5g/L (IC50), 39.75g/L (1.5IC50) and 13.25g/L (0.5IC50) were determined. Further, a cell-cycle test was conducted with root tips of L. sativa exposed to these same SPL solutions. All test chemicals presented toxic effects on meristematic cells of L. sativa. Aluminum was identified as the SPL component mainly responsible for reduction of the mitotic index. Chromosomal alterations resulted from the interactions among the three main chemical components of SPL, without a clear predominantly responsible agent. Induction of condensed nuclei was mainly due to effects of aluminum and fluoride, and may serve as an indicator of induced cell death.

Mutagenicity and genotoxicity of dicapthon insecticide

Mutagenic and genotoxic effects of dicapthon were investigated by using the bacterial reverse mutation assay in Salmonella typhimurium TA97, TA98, TA100 and TA102 strains with or without metabolic activation system (S9 mix), and chromosome aberrations (CAs), sister chromatid exchanges (SCEs), and micronucleus (MN) tests in human peripheral blood lymphocytes in vitro. Dicapthon was dissolved in dimethyl sulfoxide for all test systems. 0.1, 1, 10 and 100 μg/plate doses of dicapthon were found to be weakly mutagenic on S. typhimurium TA 98 without S9 mix. The human peripheral lymphocytes were treated with four experimental concentrations of dicapthon (25, 50, 100, and 200 μg/mL) for 24 and 48 h. Dicapthon increased the frequency of SCE only at the 100 μg/mL concentration for the 24 and 48 h applications. Dicapthon also induced abnormal cell frequency, CA/cell ratio and frequency of MN dose dependently for 24 and 48 h. Dicapthon showed a statistically significant cytotoxic effect by decreasing the mitotic index in all concentrations and a cytostatic effect by decreasing nuclear division index in 100 and 200 μg/mL concentrations for both treatment periods when compared with both untreated and solvent controls. These values decreased also in a dose dependent manner.