Selective entrapment of extrachromosomally amplified DNA by nuclear budding and micronucleation during S phase

Metal accumulation in female green sea turtles (Chelonia mydas) from Eastern Atlantic affects their egg quality with potential implications for embryonic development

Sea turtles, with their global distribution and complex life cycle, often accumulate pollutants such as metals and metalloids due to their extended lifespan and feeding habits. However, there are limited studies exploring the impact of metal pollution on the reproductive health of female sea turtles, specifically focusing on the quality of their eggs, which has significant implications for the future generations of these charismatic animals. São Tomé Island, a crucial nesting and feeding habitat for green sea turtles, underscores the urgent need for comprehensive research in this ecologically significant area. This study aimed to investigate whether metals and metalloids in the blood of nesting female green sea turtles induce genotoxic effects in their erythrocytes and affect their egg morphometric characteristics and the composition of related compartments. Additionally, this study aimed to evaluate whether the quality of energetic reserves for embryo development (fatty acids in yolk's polar and neutral lipids) is influenced by the contamination status of their predecessors. Results revealed correlations between Cu and Hg levels and increased "lobed" erythrocytes, while As and Cu negatively influenced shell thickness. In terms of energy reserves, both polar and neutral lipid fractions contained primarily saturated and monounsaturated fatty acids, with prevalent 18:1n-9, 18:0, 16:0, 14:0, and 12:0 fatty acids in yolk samples. The yolk polar fraction was more susceptible to contaminant levels in female sea turtles, showing consistent negative correlations between pollution load index and essential n3 fatty acids, including linolenic, eicosatrienoic, eicosapentaenoic, and docosapentaenoic acids, crucial for embryonic development. These metals accumulation, coupled with the reduced availability of these key fatty acids, may disrupt the eicosanoid and other important pathways, affecting reproductive development. This study reveals a negative correlation between metal contamination in female sea turtles' blood and egg lipid reserves, raising concerns about embryonic development and the species' future generations.

Hematological and genotoxic biomarkers in a natural population of freshwater turtles Trachemys dorbigni (Duméril & Bibron, 1835) (Testudines: Emydidae) living in an urban area in Southern Brazil

The present study aimed to report the morphometric and hematological indices and genotoxicity of a free-life population of D'Orbigny's slider turtles (Trachemys dorbigni) living in an urban area in Southern Brazil. For that, 16 specimens were randomly captured in an urban canal that receives irregular releases of wastewater. Biometrics and external visual changes were analyzed, such as turtle shell deformities, and the presence of parasites. Blood samples were collected to evaluate the hematological profile and the presence of micronuclei and other erythrocyte nuclear abnormalities as potential mutagenic and genotoxic effects. Water physicochemical parameters were also measured. Organisms with ectoparasites (31.25%) and small carapace deformations (56.25%) were observed, but maximum carapace length and weight were considered normal for the species according to the literature. The blood profile indicated low hemoglobin and hematocrit and a high number of total leukocytes, particularly eosinophils which characterize parasitic infections. A frequency of 0.12% for the micronucleus was considered basal, but the frequency of other erythrocyte abnormalities was evident, mainly of blebbed nuclei (63.79%), indicating chromosomal damage in the early stage. The results of this study suggest that natural populations of chelonian inhabiting urbanized areas are impacted by anthropogenic activities in the surrounding environment. Furthermore, it provides comprehensive data which can serve as a comparative model for environmental monitoring studies involving turtles.

Influence of ozonation and UV/H2O2 on the genotoxicity of secondary wastewater effluents

The implementation of novel wastewater treatment technologies, including Advanced Oxidation Processes (AOPs) such as ozonation and ultraviolet radiation (UV) combined with hydrogen peroxide (H2O2), can be a promising strategy for enhancing the quality of these effluents. However, during effluent oxidation AOPs may produce toxic compounds that can compromise the water reuse and the receiving water body. Given this possibility, the aim of this study was to evaluate the genotoxic potential of secondary effluents from two different Wastewater Treatment Plants (WWTP) that were subjected to ozonation or UV/H2O2 for periods of 20 (T1) and 40 (T2) minutes. The genotoxic potential was carried out with the Comet assay (for clastogenic damage) and the Micronucleus assay (for clastogenic and aneugenic damage) in HepG2/C3A cell culture (metabolizing cell line). The results of the comet assay revealed a significant increase in tail intensity in the Municipal WWTP (dry period) effluents treated with UV/H2O2 (T1 and T2). MN occurrence was noted across all treatments in both Pilot and Municipal WWTP (dry period) effluents, whereas nuclear buds (NBs) were noted for all Pilot WWTP treatments and UV/H2O2 treatments of Municipal WWTP (dry period). Moreover, the UV/H2O2 (T1) treatment of Municipal WWTP (dry period) exhibited a noteworthy incidence of multiple alterations per cell (MN + NBs). These findings imply that UV/H2O2 treatment demonstrates higher genotoxic potential compared to ozonation. Furthermore, seasonal variations can have an impact on the genotoxicity of the samples. Results of the study emphasize the importance of conducting genotoxicological tests using human cell cultures, such as HepG2/C3A, to assess the final effluent quality from WWTP before its discharge or reuse. This precaution is essential to safeguard the integrity of the receiving water body and, by extension, the biotic components it contains.

Claudin-4 modulates autophagy via SLC1A5/LAT1 as a tolerance mechanism for genomic instability in ovarian cancer

Genome instability is key for tumor heterogeneity and derives from defects in cell division and DNA damage repair. Tumors show tolerance for this characteristic, but its accumulation is regulated somehow to avoid catastrophic chromosomal alterations and cell death. Claudin-4 is upregulated and closely associated with genome instability and worse patient outcome in ovarian cancer. This protein is commonly described as a junctional protein participating in processes such as cell proliferation and DNA repair. However, its biological association with genomic instability is still poorly-understood. Here, we used CRISPRi and a claudin mimic peptide (CMP) to modulate the cladudin-4 expression and its function, respectively in in-vitro (high-grade serous carcinoma cells) and in-vivo (patient-derived xenograft in a humanized-mice model) systems. We found that claudin-4 promotes a protective cellular-mechanism that links cell-cell junctions to genome integrity. Disruption of this axis leads to irregular cellular connections and cell cycle that results in chromosomal alterations, a phenomenon associated with a novel functional link between claudin-4 and SLC1A5/LAT1 in regulating autophagy. Consequently, claudin-4's disruption increased autophagy and associated with engulfment of cytoplasm-localized DNA. Furthermore, the claudin-4/SLC1A5/LAT1 biological axis correlates with decrease ovarian cancer patient survival and targeting claudin-4 in-vivo with CMP resulted in increased niraparib (PARPi) efficacy, correlating with increased tumoral infiltration of T CD8+ lymphocytes. Our results show that the upregulation of claudin-4 enables a mechanism that promotes tolerance to genomic instability and immune evasion in ovarian cancer; thus, suggesting the potential of claudin-4 as a translational target for enhancing ovarian cancer treatment.

Novel insights into the ecDNA formation mechanism involving MSH3 in methotrexate‑resistant human colorectal cancer cells

Extrachromosomal DNAs (ecDNAs), also known as double minutes (DMs), can induce a fast increase in gene copy numbers and promote the development of cancer, including drug resistance. MutS homolog 3 (MSH3), a key protein in mismatch repair, has been indicated to participate in the regulation of DNA double‑strand break (DSB) repair, which has been reported to be associated with the formation of ecDNAs. However, it remains unclear whether MSH3 can influence drug resistance via ecDNAs in cancer. In the present study, high MSH3 expression was observed in methotrexate (MTX)‑resistant HT29 cells [DM‑ and homogeneously staining region (HSR)‑containing cells] compared with parental HT29 cells. Additionally, decreased amounts of ecDNAs, HSRs and amplified genes locating on ecDNAs and HSRs were detected following depletion of MSH3 and this could be reversed by overexpressing MSH3 in DM‑containing cells. No corresponding changes were found in HSR‑containing cells. The present study further verified the involvement of MSH3‑regulated DNA DSB repair pathways in the formation of ecDNAs by detecting the expression of core proteins and pathway activity. Furthermore, expulsion of ecDNAs/HSRs was detected and increased frequencies of micronuclei/nuclear buds with dihydrofolate reductase (DHFR) signals were observed in MSH3‑depleted DM‑containing cells. Finally, changes in MSH3 expression could affect DHFR amplification‑derived DHFR expression and cell sensitivity to MTX, suggesting that MSH3 may influence cancer drug resistance by altering the amount of ecDNAs. In conclusion, the present study revealed a novel mechanism involving MSH3 in the regulation of ecDNAs by DSB repair, which will have clinical value in the treatment of ecDNA‑based drug resistance in cancer.

Mutagenicity, hepatotoxicity, and neurotoxicity of glyphosate and fipronil commercial formulations in Amazon turtles neonates (Podocnemis expansa)

Pesticides are considered one of the main causes of the population decline of reptiles worldwide, with freshwater turtles being particularly susceptible to aquatic contamination. In this context, we investigated the potential mutagenic, hepatotoxic, and neurotoxic effects in neonates of Podocnemis expansa exposed to substrate contaminated with different concentrations of glyphosate and/or fipronil during embryonic development. Eggs collected from the natural environment were artificially incubated in sand moistened with pure water, water added with glyphosate Atar 48® at concentrations of 65 and 6500 μg/L (groups G1 and G2, respectively), water added with fipronil Regent® 800WG at 4 and 400 μg/L (groups F1 and F2, respectively) and, water added with the combination of 65 μg/L glyphosate and 4 μg/L fipronil or with 6500 μg/L glyphosate and 400 μg/L fipronil (groups GF1 and GF2, respectively). For mutagenicity analysis, we evaluated the frequency of micronuclei (MN) and other erythrocyte nuclear abnormalities (ENAs), while for evaluation of hepatotoxicity and neurotoxicity, livers and encephalon were analyzed for histopathological alterations. Exposure to pesticides, alone or in combination, increased the frequency of erythrocyte nuclear abnormalities, particularly blebbed nuclei, moved nuclei, and notched nuclei. Individuals exposed to fipronil exhibited congestion and inflammatory infiltrate in their liver tissue, while, in the encephalon, congestion, and necrosis were present. Our study confirms that the incubation of eggs in substrate polluted with glyphosate and fipronil causes histopathological damage and mutagenic alteration in P. expansa, highlighting the importance of using different biomarkers to evaluate the ecotoxicological effects of these pesticides, especially in oviparous animals.

A dedicated cytoplasmic container collects extrachromosomal DNA away from the mammalian nucleus

Expression from transfected plasmid DNA is generally transient, but it is unclear what process terminates it. We show that DNA entering mammalian cells is rapidly surrounded by a double membrane in the cytoplasm, in some cases after leaving the nucleus. This cytoplasmic container, termed exclusome, frequently also contains extrachromosomal telomeric DNA, and is maintained by the cell over several division cycles. The exclusome envelope contains endoplasmic reticulum proteins and the inner-nuclear membrane proteins Lap2β and Emerin, but differs from the nuclear envelope by its fenestrations and the absence of the Lamin B Receptor and nuclear pore complexes. Reduction of exclusome frequency upon overexpressing Emerin's LEM-domain suggests a role for Emerin in plasmid DNA compartmentalization. Thus, cells distinguish extrachromosomal DNA and chromosomes and wrap them into similar yet distinct envelopes keeping the former in the exclusome but the latter in the nucleus, where transcription occurs.

Nuclear and morpho-histopathological alterations in Astyanax altiparanae exposed to effluent from the process of anodizing aluminum

Aluminum is a metal widely used from household utensils to civil construction. Anodizing aluminum is a procedure to form a thick layer of aluminum oxide on the surface in order to confer greater resistance to the material. This process generates an effluent with acidic pH and a high concentration of sulfate. Alternatives for the treatment of this effluent involve the use of the chemical precipitation technique, which can be used with salts of barium chloride (BaCl2), calcium chloride (CaCl2), and aluminum hydroxide with commercial limestone (Cc/Al (OH)3). The objective of this study was to evaluate the toxicity of effluents on Astyanax altiparanae (Lambari), by means of somatic, genetic, morphological, and histological markers after 24 and 96 h of exposure. After measuring the biometric data of the animals and the weight of the liver, we found that the condition factor (K) of individuals exposed to the effluent CaCl2 showed a slight reduction in growth after 96 h while the hepatosomatic index (HSI) remained unchanged for all effluents in both sampling times. The micronucleus test with erythrocytes indicated that the raw effluent (E2) induced nuclear changes after 24 h; however, this effect did not persist after 96 h of exposure. Branchial arches were collected and according to Bernet's index for histopathology, all effluents except Cc/Al (OH)3, induced significant changes in the gills. In accordance with the index of Poleksic and Mitrovic-Tutundzic, CaCl2 was the only effluent to compromise branchial operation. The branchial morphology investigated by SEM showed that the raw effluent (E1) induced injuries and compromised gill functions. This study reinforces the importance of biological tests for the assessment and validation of physical chemicals used and effluent treatment techniques as well as the development and application of biological parameters before the wastewater release, whether in a raw state or a treated one.

Gene amplifications and extrachromosomal circular DNAs: function and biogenesis

Gene amplification is an increase in the copy number of restricted chromosomal segments that contain gene(s) and frequently results in the over-expression of the corresponding gene(s). Amplification may be found in the form of extrachromosomal circular DNAs (eccDNAs) or as linear repetitive amplicon regions that are integrated into chromosomes, which may form cytogenetically observable homogeneously staining regions or may be scattered throughout the genome. eccDNAs are structurally circular and in terms of their function and content, they can be classified into various subtypes. They play pivotal roles in many physiological and pathological phenomena such as tumor pathogenesis, aging, maintenance of telomere length and ribosomal DNAs (rDNAs), and gain of resistance against chemotherapeutic agents. Amplification of oncogenes is consistently seen in various types of cancers and can be associated with prognostic factors. eccDNAs are known to be originated from chromosomes as a consequence of various cellular events such as repair processes of damaged DNA or DNA replication errors. In this review, we highlighted the role of gene amplification in cancer, the functional aspects of eccDNAs subtypes, the proposed biogenesis mechanisms, and their role in gene or segmental-DNA amplification.

Paraoxon and glyphosate induce DNA double-strand breaks but are not type II topoisomerase poisons

We tested the hypothesis that the pesticides paraoxon and glyphosate cause DNA double-strand breaks (DSB) by poisoning the enzyme Type II topoisomerase (topo II). Peripheral lymphocytes in G0 phase, treated with the pesticides, plus or minus ICRF-187, an inhibitor of Topo II, were stimulated to proliferate; induced cytogenetic damage was measured. Micronuclei, chromatin buds, nucleoplasmic bridges, and extranuclear fragments were induced by treatments with the pesticides, irrespective of the pre-treatment with ICRF-187. These results indicate that the pesticides do not act as topo II poisons. The induction of DSB may occur by other mechanisms, such as effects on other proteins involved in recombination repair.

Towards prevention of aneuploidy-associated cellular senescence and aging: more questions than answers?

The aim of this review is to discuss how aneuploidy contributes to the aging process, and to identify plausible strategies for its prevention. After an overview of mechanisms leading to aneuploidy and the major features of cellular senescence, we discuss the link between (i) aneuploidy and cellular senescence; (ii) aneuploidy and aging; and (iii) cellular senescence and aging. We also consider (i) interactions between aneuploidy, micronuclei, cellular senescence and aging, (ii) the potential of nutritional treatments to prevent aneuploidy-associated senescence and aging, and (iii) knowledge and technological gaps. Evidence for a causal link between aneuploidy, senescence and aging is emerging. In vitro, aneuploidy accompanies the entry into cellular senescence and can itself induce senescence. How aneuploidy contributes in vivo to cellular senescence is less clear. Several routes depending on aneuploidy and/or senescence converge towards chronic inflammation, the major driver of unhealthy aging. Aneuploidy can induce the pro-inflammatory Senescence Associated Secretory Phenotype (SASP), either directly or as a result of micronucleus (MN) induction leading to leakage of DNA into the cytoplasm and triggering of the cGAS-STING pathway of innate immune response. A major difficulty in understanding the impact of aneuploidy on senescence and aging in vivo, results from the heterogeneity of cellular senescence in different tissues at the cytological and molecular level. Due to this complexity, there is at the present time no biomarker or biomarker combination characteristic for all types of senescent cells. In conclusion, a deeper understanding of the critical role aneuploidy plays in cellular senescence and aging is essential to devise practical strategies to protect human populations from aneuploidy-associated pathologies. We discuss emerging evidence, based on in vitro and in vivo studies, that adequate amounts of specific micronutrients are essential for prevention of aneuploidy in humans and that precise nutritional intervention may be essential to help avoid the scourge of aneuploidy-driven diseases.

Extrachromosomal circular DNA in colorectal cancer: biogenesis, function and potential as therapeutic target

Extrachromosomal circular DNA (ecDNA) has gained renewed interest since its discovery more than half a century ago, emerging as critical driver of tumor evolution. ecDNA is highly prevalent in many types of cancers, including colorectal cancer (CRC), which is one of the most deadly cancers worldwide. ecDNAs play an essential role in regulating oncogene expression, intratumor heterogeneity, and resistance to therapy independently of canonical chromosomal alterations in CRC. Furthermore, the existence of ecDNAs is attributed to the patient's prognosis, since ecDNA-based oncogene amplification adversely affects clinical outcomes. Recent understanding of ecDNA put an extra layer of complexity in the pathogenesis of CRC. In this review, we will discuss the current understanding on mechanisms of biogenesis, and distinctive features of ecDNA in CRC. In addition, we will examine how ecDNAs mediate oncogene overexpression, gene regulation, and topological interactions with active chromatin, which facilitates genetic heterogeneity, accelerates CRC malignancy, and enhances rapid adaptation to therapy resistance. Finally, we will discuss the potential diagnostic and therapeutic implications of ecDNAs in CRC.

Description and quantification of micronucleus and nuclear abnormalities in erythrocytes of the sentinel green turtle (Chelonia mydas) with fluorescence microscopy

Contamination in marine ecosystems is of the most critical threats to marine turtles. The identification of useful biomarkers to detect and monitor the physiological and clinical effects of pollutants on these populations will allow early detection of alterations (e.g., mutagenic damages) that could risk their viability or favor the development of diseases, thus threatening the biodiversity of these ecosystems and human population. This study is aimed at describing and quantifying nuclear anomalies in peripheral blood erythrocytes of green turtles (Chelonia mydas) from three distinct foraging areas in Mexico (Akumal, Xcalak, and Punta Herrero). We developed a novel morphological index that could be used as a biomarker to identify abnormal nuclei in peripheral blood erythrocytes. Here we describe for the first time in C. mydas, with a species-specific staining protocol, distinct nuclear abnormalities such as blebbed, lobed, notched, eight shape nuclei, and binucleated cells. These nuclear abnormalities were present in > 90 % of the subjects (n = 30). Moreover, 50 % of the organisms presented erythrocytes with micronuclei. The number of nuclear abnormalities did not correlate with size of the green turtles or differ between sites, or health status. We found a higher frequency of green turtles with nuclear abnormalities in the southern region (Punta Herrero and Xcalak) with the highest frequency of micronucleus and buds. The former could be associated to the constant exposure to chemical pollutants of oceanographic origin in the southern coast of Quintana Roo. Furthermore, the increasing anthropogenic pollution in Akumal could also explain the highest variability in the number of nuclear abnormalities presented in resident individuals. We propose that a long-term monitoring programs of green turtle populations in the Mexican Caribbean that include a micronucleus test could be a useful to determine possible mutagenic damage in these animals.

Urbanity as a source of genotoxicity in the synanthropic Kelp Gull (Larus dominicanus)

Increases in human population lead to an increase in urban wastes, which could affect wildlife in several ways. Urban pollutants can affect erythrocytes of birds generating morphological membrane and nuclear anomalies. The Kelp Gull (Larus dominicanus) is an opportunistic species, which take advantage of urban environments, thus being highly exposed to environmental pollution. In northeastern Patagonia, the dynamic of the waste management was transformed in the last decade and consequently, gulls changed their movements in response to changes in waste management systems. The food available to the seagulls went from being a mixture of urban/fishing discards until 2015, when this landfill closures, to being domestic urban offerings. In order of evaluating genotoxicity and changes in pollutants exposition due to these changes, we analyzed the frequencies of erythrocytes nuclear abnormalities and micronuclei (ENAs and MN respectively) in 58 blood smears from adults extracted during the non-breeding season in two periods in landfills with different waste compositions: a mixed landfill (ML) in 2013 before closure (n = 24) versus an urban landfill (UL) (n = 34) in 2021. We found that the Kelp Gull showed high values of abnormalities with an average of 151.5 /10,000 RBC in comparison with other seabird species. The bud and notched types of ENAs were the most prevalent abnormalities in both sites. We did not find significate differences in the overall abnormality frequency between sites, however we found significant higher frequencies in displaced and tailed types of ENAs in ML. We also found poikilocytosis, as seen previously in other animals exposed experimentally to pollutants such as metals and crude oil. Cellular abnormalities found in the Kelp Gull suggest an exposition of individuals to pollutants in foraging areas. The hemispheric distribution and the synanthropic characteristics of the species denote its importance as a suitable global monitor of genotoxicity.

Extrachromosomal DNA amplifications in cancer

Extrachromosomal DNA (ecDNA) amplification is an important driver alteration in cancer. It has been observed in most cancer types and is associated with worse patient outcome. The functional impact of ecDNA has been linked to its unique properties, such as its circular structure that is associated with altered chromatinization and epigenetic regulatory landscape, as well as its ability to randomly segregate during cell division, which fuels intercellular copy number heterogeneity. Recent investigations suggest that ecDNA is structurally more complex than previously anticipated and that it localizes to specialized nuclear bodies (hubs) and can act in trans as an enhancer for genes on other ecDNAs or chromosomes. In this Review, we synthesize what is currently known about how ecDNA is generated and how its genetic and epigenetic architecture affects proto-oncogene deregulation in cancer. We discuss how recently identified ecDNA functions may impact oncogenesis but also serve as new therapeutic vulnerabilities in cancer.

Extrachromosomal circular DNA: biogenesis, structure, functions and diseases

Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to genomic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. In addition, the origin of eccDNA is considered to be associated with essential chromatin-related events, including the formation of super-enhancers and DNA repair machineries. Moreover, our understanding of the properties and functions of eccDNA has continuously and greatly expanded. Emerging investigations demonstrate that eccDNAs serve as multifunctional molecules in various organisms during diversified biological processes, such as epigenetic remodeling, telomere trimming, and the regulation of canonical signaling pathways. Importantly, its special distribution potentiates eccDNA as a measurable biomarker in many diseases, especially cancers. The loss of eccDNA homeostasis facilitates tumor initiation, malignant progression, and heterogeneous evolution in many cancers. An in-depth understanding of eccDNA provides novel insights for precision cancer treatment. In this review, we summarized the discovery history of eccDNA, discussed the biogenesis, characteristics, and functions of eccDNA. Moreover, we emphasized the role of eccDNA during tumor pathogenesis and malignant evolution. Therapeutically, we summarized potential clinical applications that target aberrant eccDNA in multiple diseases.

Demystifying Extrachromosomal DNA Circles: Categories, Biogenesis, and Cancer Therapeutics

Since the advent of sequencing technologies in the 1990s, researchers have focused on the association between aberrations in chromosomal DNA and disease. However, not all forms of the DNA are linear and chromosomal. Extrachromosomal circular DNAs (eccDNAs) are double-stranded, closed-circled DNA constructs free from the chromosome that reside in the nuclei. Although widely overlooked, the eccDNAs have recently gained attention for their potential roles in physiological response, intratumoral heterogeneity and cancer therapeutics. In this review, we summarize the history, classifications, biogenesis, and highlight recent progresses on the emerging topic of eccDNAs and comment on their potential application as biomarkers in clinical settings.

Extrachromosomal DNA in Cancer

In cancer, complex genome rearrangements and other structural alterations, including the amplification of oncogenes on circular extrachromosomal DNA (ecDNA) elements, drive the formation and progression of tumors. ecDNA is a particularly challenging structural alteration. By untethering oncogenes from chromosomal constraints, it elevates oncogene copy number, drives intratumoral genetic heterogeneity, promotes rapid tumor evolution, and results in treatment resistance. The profound changes in DNA shape and nuclear architecture generated by ecDNA alter the transcriptional landscape of tumors by catalyzing new types of regulatory interactions that do not occur on chromosomes. The current suite of tools for interrogating cancer genomes is well suited for deciphering sequence but has limited ability to resolve the complex changes in DNA structure and dynamics that ecDNA generates. Here, we review the challenges of resolving ecDNA form and function and discuss the emerging tool kit for deciphering ecDNA architecture and spatial organization, including what has been learned to date about how this dramatic change in shape alters tumor development, progression, and drug resistance.

A unifying model for extrachromosomal circular DNA load in eukaryotic cells

Extrachromosomal circular DNA (eccDNA) with exons and whole genes are common features of eukaryotic cells. Work from especially tumours and the yeast Saccharomyces cerevisiae has revealed that eccDNA can provide large selective advantages and disadvantages. Besides the phenotypic effect due to expression of an eccDNA fragment, eccDNA is different from other mutations in that it is released from 1:1 segregation during cell division. This means that eccDNA can quickly change copy number, pickup secondary mutations and reintegrate into a chromosome to establish substantial genetic variation that could not have evolved via canonical mechanisms. We propose a unifying 5-factor model for conceptualizing the eccDNA load of a eukaryotic cell, emphasizing formation, replication, segregation, selection and elimination. We suggest that the magnitude of these sequential events and their interactions determine the copy number of eccDNA in mitotically dividing cells. We believe that our model will provide a coherent framework for eccDNA research, to understand its biology and the factors that can be manipulated to modulate eccDNA load in eukaryotic cells.

Bisphenols induce human genomic damage and modulate HERVs/env expression

Bisphenol A (BPA), a recognized endocrine-disrupting chemical, is used in the production of epoxy and polycarbonate resins. Since human exposure to BPA has been associated with increased cancer susceptibility, the market has shifted to products often labeled as "BPA free" containing BPA analogs such as bisphenol F (BPF) and bisphenol S (BPS). However, the European legislation on BPF and BPS is still unclear. This study analyzed the effects of BPA, BPF, and BPS exposure on human peripheral blood mononuclear cells by using in vitro micronucleus assay. Furthermore, it investigated the impact of bisphenols exposure on human endogenous retroviruses (HERVs) expression, which is implicated with the pathogenesis of several human diseases. The micronucleus assay revealed a significant genotoxic effect in peripheral blood cells after exposure to BPA and BPF at concentrations of 0.1, 0.05, and 0.025 μg/ml, and to BPS at 0.1 and 0.05 μg/ml. In addition, BPA exposure seems to upregulate the expression of HERVs, while a downregulation was observed after BPF and BPS treatments. Overall, our data showed the toxic effect of BPA and its analogs on circulating cells in the blood and demonstrated that they could modulate the HERVs expression.

Toxicogenetic assessment of a pre-workout supplement: In vitro mutagenicity, cytotoxicity, genotoxicity and glutathione determination in liver cell lines and in silico ADMET approaches

The benefits of practicing physical activity, such as weight loss and control, are commonly associated with caloric restriction diets and may be improved by the ingestion of thermogenic and ergogenic supplements. However, there is a lack of safety data on commonly marketed nutritional supplements. Therefore, this investigation aims to evaluate a pre-workout supplement for mutagenicity using the Ames test, hepatocytoxicity in HepG2 and F C3H cells after 24 h, 48 h and 72 h, genotoxicity using the CBMN assay, determination of gluthatione activity and computational prediction of the three major isolated compounds present in the supplement. The mutagenicity test showed a mutagenic response in TA98 His⁺ revertants of 5 mg/plate in the presence of metabolic activation, cytotoxicity in TA98 of 5 mg/plate in the absence of metabolic conditions, and in TA102 of 0.5 mg/plate both in the presence and absence of metabolic activation. In our in vitro eukaryotic cell viability, WST-1, LDH and alkaline phosphatase assays, the supplement showed hepatocytotoxicity both dose-dependently and time-dependently. In the cytokinesis blocking micronuclei assay, the supplement induced micronuclei, nuclear buds, nucleoplasmatic, bridge formation, and a decreased in nuclear division. In addition, the supplement decreased intra and extracellular GSH. Computational analysis showed that the three isolated compounds most present in the supplement have the potential to cause hepatotoxicity. In the present investigation, the pre-workout supplement induced mutagenic, genotoxic, and cytotoxic responses and GSH decrease. Thus, considering food safety and public health sanitary vigilance, the consumption of this pre-workout supplement may harm the health of its consumers.

Toxicity evaluation of the combination of emerging pollutants with polyethylene microplastics in zebrafish: Perspective study of genotoxicity, mutagenicity, and redox unbalance

Despite the toxicity of microplastics (MPs) in freshwater fish has been demonstrated in previous studies, their effects when mixed with other pollutants (organic and inorganic) are poorly understood. Thus, we aimed to test the hypothesis that the association of polyethylene MPs (PE-MPs) to a mix of emerging pollutants induces more adverse genotoxic, mutagenic, and redox unbalance effects in adult zebrafish (Danio rerio), after 15 days of exposure. Although the accumulation of MPs in animals was greater in animals exposed to PE-MPs alone, erythrocyte DNA damage (comet assay) and the frequency of erythrocytic nuclear abnormalities (ENAs) evidenced in zebrafish exposed to PE-MPs alone were as pronounced as those observed in animals exposed to the mix of pollutant (alone or in combination with MPs), which constitutes the big picture of the current study. Moreover, we noticed that such effects were associated with an imbalance between pro-and antioxidant metabolism in animals, whose activity of superoxide dismutase (SOD) and catalase (CAT) was assessed in different organs which were not sufficient to counterbalance the production of reactive oxygen species [hydrogen peroxide (H₂O₂)] and nitrogen [nitric oxide (NO)] evaluated. The principal component analysis (PCA) also revealed that while the antioxidant activity was more pronounced in the brain and liver of animals, the highest production of H₂O₂ was perceived in the gills and muscles, suggesting that the biochemical response of the animals was organ-dependent. Thus, the present study did not demonstrate antagonistic, synergistic, or additive effects on animals exposed to the combination between PE-MPs and a mix of pollutants in the zebrafish, which reinforces the theory that interactions between pollutants in aquatic ecosystems may be as complex as their effects on freshwater ichthyofauna.

Revisiting characteristics of oncogenic extrachromosomal DNA as mobile enhancers on neuroblastoma and glioma cancers

Cancer can be induced by a variety of possible causes, including tumor suppressor gene failure and proto-oncogene hyperactivation. Tumor-associated extrachromosomal circular DNA has been proposed to endanger human health and speed up the progression of cancer. The amplification of ecDNA has raised the oncogene copy number in numerous malignancies according to whole-genome sequencing on distinct cancer types. The unusual structure and function of ecDNA, and its potential role in understanding current cancer genome maps, make it a hotspot to study tumor pathogenesis and evolution. The discovery of the basic mechanisms of ecDNA in the emergence and growth of malignancies could lead researchers to develop new cancer therapies. Despite recent progress, different aspects of ecDNA require more investigation. We focused on the features, and analyzed the bio-genesis, and origin of ecDNA in this review, as well as its functions in neuroblastoma and glioma cancers.

Genotoxic, biochemical and histological biomarkers of subacute concentrations of paraquat and glyphosate in Nile Tilapia

The use of herbicides for increased food production may pose risk to non-target organisms. This study evaluated the acute toxicity, genotoxic, biochemical, and histological biomarkers of subacute concentrations of paraquat and glyphosate in Oreochromis niloticus (Nile Tilapia) for 28 days following standard methods. Glyphosate (96 hLC50 value-1.23 mg/L) was 9x more toxic than paraquat (96 hLC50 value-11.20 mg/L) against O. niloticus. Average micronucleated cells were significantly higher in the erythrocytes of O. niloticus exposed to the higher (1.12 mg/L) concentration of paraquat at day 14, both subacute concentrations of paraquat at day 28, and lower concentration (0.01 mg/L) of glyphosate at days 14 and 28 compared to the other treatments and controls. Biochemical biomarkers (MDA and GST) activities were significantly higher at both subacute concentrations of the herbicides in the exposed fish compared to the controls at day 28 only. GSH activity was significantly higher in the 0.11 mg/L paraquat concentration while SOD activity was significantly lower at both subacute concentrations of glyphosate in exposed fish compared to controls at day 28. Histological alterations observed were mild to severe shortening of the gill primary lamellar and hepatic portal inflammation of exposed fish compared to the controls. This study demonstrates the risk to non-target organisms due to herbicides’ run-off from agricultural farmlands into aquatic ecosystems at environmentally relevant or subacute concentrations. Sensitization on the responsible use of pesticides is recommended to promote responsible consumption and production and sustain life below water (United Nations Sustainable Development Goals 12 and 14 respectively).

Can Lemna minor mitigate the effects of cadmium and nickel exposure in a Neotropical fish?

We aimed to evaluate if Lemna minor can mitigate the observed effects of cadmium (Cd) and nickel (Ni) exposure in Prochilodus lineatus. Fish were exposed for 96 h to 20 µg L^-1 of Cd, 1.5 mg L^-1 of Ni, or to a mixture of these two metals. In all tests, one group was exposed to the metals with duckweed on the water surface, and other group was exposed only to the metals, without plants. After each exposure, samples of P. lineatus tissues were collected to evaluate multiple biomarkers. Duckweed prevented bioaccumulation in some fish tissues and attenuated changes in acetylcholinesterase activity, increases in erythrocytic nuclear abnormality frequency, and hyperglycemia. However, the changes in plasma ion concentrations, reduction in activity of ion transport enzymes, and histological damage were not mitigated. Therefore, we concluded that L. minor partially attenuates the effects caused by Cd and Ni exposure.

Life of double minutes: generation, maintenance, and elimination

Advances in genome sequencing have revealed a type of extrachromosomal DNA, historically named double minutes (also referred to as ecDNA), to be common in a wide range of cancer types, but not in healthy tissues. These cancer-associated circular DNA molecules contain one or a few genes that are amplified when double minutes accumulate. Double minutes harbor oncogenes or drug resistance genes that contribute to tumor aggressiveness through copy number amplification in combination with favorable epigenetic properties. Unequal distribution of double minutes over daughter cells contributes to intratumoral heterogeneity, thereby increasing tumor adaptability. In this review, we discuss various models delineating the mechanism of generation of double minutes. Furthermore, we highlight how double minutes are maintained, how they evolve, and discuss possible mechanisms driving their elimination.

Impact of Nuclear Envelope Stress on Physiological and Pathological Processes in Central Nervous System

The nuclear envelope (NE) separates genomic DNA from the cytoplasm and provides the molecular platforms for nucleocytoplasmic transport, higher-order chromatin organization, and physical links between the nucleus and cytoskeleton. Recent studies have shown that the NE is often damaged by various stresses termed "NE stress", leading to critical cellular dysfunction. Accumulating evidence has revealed the crucial roles of NE stress in the pathology of a broad spectrum of diseases. In the central nervous system (CNS), NE dysfunction impairs neural development and is associated with several neurological disorders, such as Alzheimer's disease and autosomal dominant leukodystrophy. In this review, the structure and functions of the NE are summarized, and the concepts of NE stress and NE stress responses are introduced. Additionally, the significant roles of the NE in the development of CNS and the mechanistic connections between NE stress and neurological disorders are described.

Mitochondrial dysfunction in mandibular hypoplasia, deafness and progeroid features with concomitant lipodystrophy (MDPL) patients

Mandibular hypoplasia, Deafness and Progeroid features with concomitant Lipodystrophy is a rare, genetic, premature aging disease named MDPL Syndrome, due to almost always a de novo variant in POLD1 gene, encoding the DNA polymerase δ. In previous in vitro studies, we have already described several hallmarks of aging, including genetic damage, telomere shortening, cell senescence and proliferation defects. Since a clear connection has been reported between telomere shortening and mitochondria malfunction to initiate the aging process, we explored the role that mitochondrial metabolism and activity play in pathogenesis of MDPL Syndrome, an aspect that has not been addressed yet. We thus evaluated mtDNA copy number, assessing a significant decrease in mutated cells.

The expression level of genes related to mitochondrial biogenesis and activity also revealed a significant reduction, highlighting a mitochondrial dysfunction in MDPL cells. Even the expression levels of mitochondrial marker SOD2, as assessed by immunofluorescence, were reduced. The decrease in this antioxidant enzyme correlated with increased production of mitochondrial ROS in MDPL cells, compared to WT. Consistent with these data, Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) analysis revealed in MDPL cells fewer mitochondria, which also displayed morphological abnormalities. Accordingly, we detected autophagic vacuoles containing partially digested mitochondria.

Overall, our results demonstrate a dramatic impairment of mitochondrial biogenesis and activity in MDPL Syndrome. Administration of Metformin, though unable to restore mitochondrial impairment, proved efficient in rescuing nuclear abnormalities, suggesting its use to specifically ameliorate the premature aging phenotype.

The genomic and spatial mobility of extrachromosomal DNA and its implications for cancer therapy

Extrachromosomal DNA (ecDNA) amplification has been observed in at least 30 different cancer types and is associated with worse patient outcomes. This has been linked to increased oncogene dosage because both oncogenes and associated enhancers can occupy ecDNA. New data challenge the view that only oncogene dosage is affected by ecDNA, and raises the possibility that ecDNA could disrupt genome-wide gene expression. Recent investigations suggest that ecDNA localizes to specialized nuclear bodies (hubs) in which they can act in trans as ectopic enhancers for genes on other ecDNA or chromosomes. Moreover, ecDNA can reintegrate into the genome, possibly further disrupting the gene regulatory landscape in tumor cells. In this Perspective, we discuss the emerging properties of ecDNA and highlight promising avenues to exploit this new knowledge for the development of ecDNA-directed therapies for cancer.

Giant Toads (Rhinella marina) From the Industrial Zones of Low Basin of the Coatzacoalcos River (Veracruz, MX) Presents Genotoxicity in Erythrocytes

The lower basin of Coatzacoalcos River is one of the most polluted regions of the southern Gulf of Mexico. Organochlorine compounds, polybrominated diphenyl ethers, polycyclic aromatic hydrocarbons, and heavy metals have been registered in this region. In the present study, genotoxicity was evaluated in the blood of giant toads (Rhinella marina) from Coatzacoalcos' rural and industrial zones, and compared with laboratory toads. Determination of the frequency of micronucleus and erythrocyte nuclear abnormalities by the light microscope and cell cycle and apoptosis by flow cytometry were used as biomarkers of genotoxicity. We found more variability in micronucleus and more nuclear buds in toads from industrial zones. Also, cell cycle alterations and an increase of apoptosis in erythrocytes were found in toads from rural and industrial zones. Multivariate statistics show that the toads from the industrial zone were more affected than toads from laboratory and rural zones.

A link between mitotic defects and mitotic catastrophe: detection and cell fate

Although the phenomenon of mitotic catastrophe was first described more than 80 years ago, only recently has this term been used to explain a mechanism of cell death linked to delayed mitosis. Several mechanisms have been suggested for mitotic catastrophe development and cell fate. Depending on molecular perturbations, mitotic catastrophe can end in three types of cell death, namely apoptosis, necrosis, or autophagy. Moreover, mitotic catastrophe can be associated with different types of cell aging, the development of which negatively affects tumor elimination and, consequently, reduces the therapeutic effect. The effective triggering of mitotic catastrophe in clinical practice requires induction of DNA damage as well as inhibition of the molecular pathways that regulate cell cycle arrest and DNA repair. Here we discuss various methods to detect mitotic catastrophe, the mechanisms of its development, and the attempts to use this phenomenon in cancer treatment.

Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA hubs in cancer

Oncogenic extrachromosomal DNA elements (ecDNAs) play an important role in tumor evolution, but our understanding of ecDNA biology is limited. We determined the distribution of single-cell ecDNA copy number across patient tissues and cell line models and observed how cell-to-cell ecDNA frequency greatly varies. The exceptional intratumoral heterogeneity of ecDNA suggested ecDNA-specific replication and propagation mechanisms. To evaluate the transfer of ecDNA genetic material from parental to offspring cells during mitosis, we established the CRISPR-based ecTag method. EcTag leverages ecDNA-specific breakpoint sequences to tag ecDNA with fluorescent markers in living cells. Applying ecTag during mitosis revealed disjointed ecDNA inheritance patterns, enabling rapid ecDNA accumulation in individual cells. Post-mitosis, ecDNAs clustered into ecDNA hubs, and ecDNA hubs colocalized with RNA polymerase II, promoting transcription of cargo oncogenes. Our observations provide direct evidence for uneven segregation of ecDNA and shed new light on mechanisms through which ecDNAs contribute to oncogenesis.

Effect of Angiotensin-I Converting Enzyme Gene Insertion/Deletion Polymorphism on genome instability in children living in Russian Arctic

Main risks of arterial hypertension manifest in childhood. Children living in the Far North are especially susceptible to this. There is a need for an inexpensive, non-invasive and simple diagnosis of the risk of childhood pathologies. It was previously found that the genotype DD of the in/del polymorphic marker of the ACE gene is found in people at risk of developing cardiovascular pathologies. Buccal micronucleus cytome assay and genetic analysis were used in the work. In total, 77 schoolchildren from the city of Apatity, aged 15-17 years old, were examined. We have shown that carriers of the D allele have a tendency to an increase in the frequency of cells with micronuclei. In the case of homozygous I/I variant, the frequency of occurrence of cells with karyopycnosis is significantly higher than in carriers of allele D. Polymorphic marker in/del of the ACE gene is associated with apoptotic changes in the cells of the studied children. The in/del polymorphic marker of the ACE gene can be used as a prognostic marker of the processes of genome destabilization at the early stages of development of the human body.

Gene Amplification and the Extrachromosomal Circular DNA

Oncogene amplification is closely linked to the pathogenesis of a broad spectrum of human malignant tumors. The amplified genes localize either to the extrachromosomal circular DNA, which has been referred to as cytogenetically visible double minutes (DMs), or submicroscopic episome, or to the chromosomal homogeneously staining region (HSR). The extrachromosomal circle from a chromosome arm can initiate gene amplification, resulting in the formation of DMs or HSR, if it had a sequence element required for replication initiation (the replication initiation region/matrix attachment region; the IR/MAR), under a genetic background that permits gene amplification. In this article, the nature, intracellular behavior, generation, and contribution to cancer genome plasticity of such extrachromosomal circles are summarized and discussed by reviewing recent articles on these topics. Such studies are critical in the understanding and treating human cancer, and also for the production of recombinant proteins such as biopharmaceuticals by increasing the recombinant genes in the cells.

Extra chromosomal DNA in different cancers: Individual genome with important biological functions

Cancer can be caused by various factors, including the malfunction of tumor suppressor genes and the hyper-activation of proto-oncogenes. Tumor-associated extrachromosomal circular DNA (eccDNA) has been shown to adversely affect human health and accelerate malignant actions. Whole-genome sequencing (WGS) on different cancer types suggested that the amplification of ecDNA has increased the oncogene copy number in various cancers. The unique structure and function of ecDNA, its profound significance in cancer, and its help in the comprehension of current cancer genome maps, renders it as a hotspot to explore the tumor pathogenesis and evolution. Illumination of the basic mechanisms of ecDNA may provide more insights into cancer therapeutics. Despite the recent advances, different features of ecDNA require further elucidation. In the present review, we primarily discussed the characteristics, biogenesis, genesis, and origin of ecDNA and later highlighted its functions in both tumorigenesis and therapeutic resistance of different cancers.

Cancer evolution: Darwin and beyond

Clinical and laboratory studies over recent decades have established branched evolution as a feature of cancer. However, while grounded in somatic selection, several lines of evidence suggest a Darwinian model alone is insufficient to fully explain cancer evolution. First, the role of macroevolutionary events in tumour initiation and progression contradicts Darwin's central thesis of gradualism. Whole-genome doubling, chromosomal chromoplexy and chromothripsis represent examples of single catastrophic events which can drive tumour evolution. Second, neutral evolution can play a role in some tumours, indicating that selection is not always driving evolution. Third, increasing appreciation of the role of the ageing soma has led to recent generalised theories of age-dependent carcinogenesis. Here, we review these concepts and others, which collectively argue for a model of cancer evolution which extends beyond Darwin. We also highlight clinical opportunities which can be grasped through targeting cancer vulnerabilities arising from non-Darwinian patterns of evolution.

Multiple toxicity endpoints induced by carbon nanofibers in Amazon turtle juveniles: Outspreading warns about toxicological risks to reptiles

The toxicity of carbon-based nanomaterials (CNs) has been observed in different organisms; however, little is known about the impact of water polluted with carbon nanofibers (CNFs) on reptiles. Thus, the aim of the current study was to assess the chronic effects (7.5 months) of 1 and 10 mg/L of CNF on Podocnemis expansa (Amazon turtle) juveniles (4 months old) based on different biomarkers. Increased total organic carbon (TOC) concentrations observed in the liver and brain (which suggests CNF uptake) were closely correlated to changes in REDOX systems of turtles exposed to CNFs, mainly to higher nitrite, hydrogen peroxide and lipid peroxidation levels. Increased levels of antioxidants such as total glutathione, catalase and superoxide dismutase in the exposed animals were also observed. The uptake of CNFs and the observed biochemical changes were associated with higher frequency of erythrocyte nuclear abnormalities (assessed through micronucleus assays), as well as with both damage in erythrocyte DNA (assessed through comet assays) and higher apoptosis and necrosis rates in erythrocytes of exposed turtles. Cerebral and hepatic acetylcholinesterase (AChE) increased in turtles exposed to CNFs, and this finding suggested the neurotoxic effect of these nanomaterials. Data in the current study reinforced the toxic potential of CNFs and evidenced the biochemical, mutagenic, genotoxic, cytotoxic, and neurotoxic effects of CNFs on P. expansa.

Genotoxic and cytotoxic effects of polyethylene microplastics on human peripheral blood lymphocytes

Currently, we need emerging initial data regarding how plastic exposures affect cellular and molecular components and how such interactions will be crucial for human health. We aimed to determine the genotoxic and cytotoxic effects of microplastic (MPs,10-45 μm, polyethylene) on human peripheral lymphocytes by using the cytokinesis-block micronucleus cytome (CBMN) assay, which is a comprehensive method to reveal a range of mechanisms, not only diseases but also response to environmental exposures. We measured micronucleation (MN), nucleoplasmic bridge formation (NPB), and nuclear bud formation (NBUD) in human peripheral blood lymphocytes. We also measured the cytokinesis-block proliferation index (CBPI) to calculate cytostasis, which indicates cytotoxicity in lymphocytes treated with five different MPs concentrations for 48 h. Even lower concentrations of MPs increased the level of genomic instability. We found that the in vitro MP exposure significantly increased MN, NPB, and NBUD frequencies. Since we investigated the effect of larger particles relative to the lymphocytes, mechanic interaction of MPs with cells, the release of monomer and additives from MPs could be suggested as possible mechanisms accounting for increasing genomic instabilities. We did not observe a decrease in the cell proliferation index, indicating a lack of MPs' cytotoxic potential. To the best of our knowledge, our study is the first to identify MPs' genotoxic potential in human peripheral blood lymphocytes. We suggested further studies to investigate the genotoxic and cytotoxic potential of smaller plastics and the chronic effect of MP on the human population.

Small ring has big potential: insights into extrachromosomal DNA in cancer

Recent technical advances have led to the discovery of novel functions of extrachromosomal DNA (ecDNA) in multiple cancer types. Studies have revealed that cancer-associated ecDNA shows a unique circular shape and contains oncogenes that are more frequently amplified than that in linear chromatin DNA. Importantly, the ecDNA-mediated amplification of oncogenes was frequently found in most cancers but rare in normal tissues. Multiple reports have shown that ecDNA has a profound impact on oncogene activation, genomic instability, drug sensitivity, tumor heterogeneity and tumor immunology, therefore may offer the potential for cancer diagnosis and therapeutics. Nevertheless, the underlying mechanisms and future applications of ecDNA remain to be determined. In this review, we summarize the basic concepts, biological functions and molecular mechanisms of ecDNA. We also provide novel insights into the fundamental role of ecDNA in cancer.

Causes and consequences of micronuclei

Micronuclei are small membrane-bounded compartments with a DNA content encapsulated by a nuclear envelope and spatially separated from the primary nucleus. Micronuclei have long been linked to chromosome instability, genome rearrangements, and mutagenesis. They are frequently found in cancers, during senescence, and after genotoxic stress. Compromised integrity of the micronuclear envelope delays or disrupts DNA replication, inhibits DNA repair, and exposes micronuclear DNA directly to cytoplasm. Micronuclei play a central role in tumorigenesis, with micronuclear DNA being a source of complex genome rearrangements (including chromothripsis) and promoting a cyclic GMP-AMP synthase (cGAS)-mediated cellular immune response that may contribute to cancer metastasis. Here, we discuss recent findings on how micronuclei are generated, what the consequences are, and what cellular mechanisms can be applied to protect against micronucleation.

Trophic transfer of carbon nanofibers among eisenia fetida, danio rerio and oreochromis niloticus and their toxicity at upper trophic level

Although the toxicity of carbon-based nanomaterials has already been demonstrated in several studies, their transfer in the food chain and impact on the upper trophic level remain unexplored. Thus, based on the experimental food chain "Eisenia fetida → Danio rerio → Oreochromis niloticus", the current study tested the hypothesis that carbon nanofibers (CNFs) accumulated in animals are transferred to the upper trophic level and cause mutagenic and cytotoxic changes. E. fetida individuals were exposed to CNFs and offered to D. rerio, which were later used to feed O. niloticus. The quantification of total organic carbon provided evidence of CNFs accumulation at all evaluated trophic levels. Such accumulation was associated with higher frequency of erythrocyte nuclear abnormalities such as constricted erythrocyte nuclei, vacuole, blebbed, kidney-shaped and micronucleated erythrocytes in Nile tilapia exposed to CNFs via food chain. The cytotoxic effect was inferred based on the smaller size of the erythrocyte nuclei and on the lower "nuclear/cytoplasmic" area ratio in tilapia exposed to CNFs via food chain. Our study provided pioneering evidence about CNFs accumulation at trophic levels of the experimental chain, as well as about the mutagenic and cytotoxic effect of these materials on O. niloticus.

Toxicity and trophic transfer of polyethylene microplastics from Poecilia reticulata to Danio rerio

The potential transfer of microplastics (MPs) between vertebrates belonging to the same taxonomic group, and the impact of such a transfer on higher trophic levels remains little explored. An experimental food chain with two fish species was installed to test the hypothesis that polyethylene MPs (PE MPs) can accumulate in animals and cause behavioral, mutagenic and cytotoxic changes at upper trophic levels. Poecilia reticulata fry were exposed to MPs for 48 h and, subsequently, offered (as food) to Danio rerio adults for 10 days to simulate an upper level food chain. PE MPs quantification in fry and in different Danio rerio tissues evidenced their accumulation at the two assessed trophic levels. This finding suggested their absorption, adherence and translocation from one organism to another. The accumulation seen in D. rerio directly exposed to MPs was associated with behavioral disorders at upper trophic level. These animals presented behavior suggestive of anti-predatory response deficit when they were confronted with a potential aquatic predator (Geophagus brasiliensis). This finding was inferred through lower school cohesion, shallower school depth and shorter distance from the potential predator. In addition, animals exposed to MPs recorded higher nuclear abnormality rates and changes in the size and shape of erythrocytes and in their nuclei; this outcome has suggested mutagenic and cytotoxic effects, respectively. Based on the current results, MPs are transferred through a food chain that only involves two vertebrates. MPs enter the vertebrates' organs, change their behavior and induce mutagenic and cytotoxic processes in animals, which can cause significant ecological consequences in freshwater ecosystems.

Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms

Through various pathways of cell death, degradation, and regulated extrusion, partial or complete genomes of various origins (e.g., host cells, fetal cells, and infiltrating viruses and microbes) are continuously shed into human body fluids in the form of segmented cell-free DNA (cfDNA) molecules. While the genetic complexity of total cfDNA is vast, the development of progressively efficient extraction, high-throughput sequencing, characterization via bioinformatics procedures, and detection have resulted in increasingly accurate partitioning and profiling of cfDNA subtypes. Not surprisingly, cfDNA analysis is emerging as a powerful clinical tool in many branches of medicine. In addition, the low invasiveness of longitudinal cfDNA sampling provides unprecedented access to study temporal genomic changes in a variety of contexts. However, the genetic diversity of cfDNA is also a great source of ambiguity and poses significant experimental and analytical challenges. For example, the cfDNA population in the bloodstream is heterogeneous and also fluctuates dynamically, differs between individuals, and exhibits numerous overlapping features despite often originating from different sources and processes. Therefore, a deeper understanding of the determining variables that impact the properties of cfDNA is crucial, however, thus far, is largely lacking. In this work we review recent and historical research on active vs. passive release mechanisms and estimate the significance and extent of their contribution to the composition of cfDNA.

Novel insights into extrachromosomal DNA: redefining the onco-drivers of tumor progression

Extrachromosomal DNA (ecDNA), gene-encoding extrachromosomal particles of DNA, is often present in tumor cells. Recent studies have revealed that oncogene amplification via ecDNA is widespread across a diverse range of cancers. ecDNA is involved in increasing tumor heterogeneity, reverting tumor phenotypes, and enhancing gene expression and tumor resistance to chemotherapy, indicating that it plays a significant role in tumorigenesis. In this review, we summarize the characteristics and genesis of ecDNA, connect these characteristics with their concomitant influences on tumorigenesis, enumerate the oncogenes encoded by ecDNA in multiple cancers, elaborate the roles of ecDNA in tumor pathogenesis and progression, and propose the considerable research and therapeutic prospects of ecDNA in cancer.

Mutagenic, genotoxic and morphotoxic potential of different pesticides in the erythrocytes of Podocnemis expansa neonates

Despite the damaging effects of pesticides glyphosate (Gly), atrazine (Atra) and fipronil (Fip) on different organisms, the mutagenic, genotoxic and morphotoxic potential of testudine erythrocytes in freshwater remains unknown. Thus, the aim of the present study is to assess the toxicological potential of these compounds in Podocnemis expansa (Amazonian turtles) neonates from eggs artificially incubated in substrate at different concentrations of herbicides Gly and Atra and insecticide Fip. Micronucleus test and other nuclear abnormalities, as well as comet assay and morphometric measurements taken of models' circulating erythrocytes were used as toxicity biomarkers. Pups exposed to Gly (groups Gly-65 ppb and Gly-6500 ppb) were the ones recording the largest amount of nuclear abnormalities; erythrocytes with multilobulated, notched and displaced nucleus were mostly frequent in groups Atra-2 ppb and Gly -65 ppb. All treatments (Gly-6500 ppb, Atra-2 ppb, Atra-200 ppb, Fip-4 ppb and Fip-400 ppb), except for group Gly-65 ppb, led to decreased erythrocyte area, increased "nuclear area: erythrocyte area" ratio, as well as to decreased erythrocyte and erythrocyte nuclei circularity, which highlights the clear effect on the size and shape of these cells. On the other hand, the comet assay did not evidence any genotoxic effect caused by the assessed pesticides. This is a pioneer study on the mutagenic and morphotoxic potential of pesticides in P. expansa eclodides exposed in ovo to Gly, Atra and Fip; therefore, it is an insight on how these compounds can affect the health of these animals.

Current understanding of extrachromosomal circular DNA in cancer pathogenesis and therapeutic resistance

Extrachromosomal circular DNA was recently found to be particularly abundant in multiple human cancer cells, although its frequency varies among different tumor types. Elevated levels of extrachromosomal circular DNA have been considered an effective biomarker of cancer pathogenesis. Multiple reports have demonstrated that the amplification of oncogenes and therapeutic resistance genes located on extrachromosomal DNA is a frequent event that drives intratumoral genetic heterogeneity and provides a potential evolutionary advantage. This review highlights the current understanding of the extrachromosomal circular DNA present in the tissues and circulation of patients with advanced cancers and provides a detailed discussion of their substantial roles in tumor regulation. Confirming the presence of cancer-related extrachromosomal circular DNA would provide a putative testing strategy for the precision diagnosis and treatment of human malignancies in clinical practice.

Classification of extrachromosomal circular DNA with a focus on the role of extrachromosomal DNA (ecDNA) in tumor heterogeneity and progression

Although the eukaryotic genome is mainly comprised of linear chromosomal DNA, genes can also be found outside of chromosomes. The unconventional presence of extrachromosomal genes is usually found to be circular, and these structures are named extrachromosomal circular DNA (eccDNA), which are often observed in cancer cells. Various types of eccDNA including small polydispersed DNA (spcDNA), telomeric cirlces, microDNA, etc. have been discovered. Among these eccDNA, extrachromosomal DNA (ecDNA), which encompasses the full spectrum of large, gene-containing extrachromosomal particles, has regained great research interest due to recent technological advances such as next-generation sequencing and super-resolution microscopy. In this review, we summarize the different types of eccDNA and discuss the role of eccDNA, especially ecDNA in tumor heterogeneity and progression. Additionally, we discuss some possible future investigative directions related to ecDNA biogenesis and its clinical application.

Cytokinesis-Block Micronucleus Assay Using Human Lymphocytes as a Sensitive Tool for Cytotoxicity/Genotoxicity Evaluation of AgNPs

Silver nanoparticles (AgNPs) are the most used nanomaterials worldwide due to their excellent antibacterial, antiviral, and antitumor activities, among others. However, there is scarce information regarding their genotoxic potential measured using human peripheral blood lymphocytes. In this work, we present the cytotoxic and genotoxic behavior of two commercially available poly(vinylpyrrolidone)-coated silver nanoparticle (PVP-AgNPs) formulations that can be identified as noncytotoxic and nongenotoxic by just evaluating micronuclei (MNi) induction and the mitotic index, but present enormous differences when other parameters such as cytostasis, apoptosis, necrosis, and nuclear damage (nuclear buds (NBUDs) and nucleoplasmic bridges (NPBs)) are analyzed. The results show that Argovit (35 nm PVP-AgNPs) and nanoComposix (50 nm PVP-AgNPs), at concentrations from 0.012 to 12 μg/mL, produce no changes in the nuclear division index (NDI) or micronuclei (MNi) frequency compared with the values found on control cultures of human blood peripheral lymphocytes from a healthy donor. Still, 50 nm PVP-AgNPs significantly decrease the replication index and significantly increase cytostasis, apoptosis, necrosis, and the frequencies of nuclear buds (NBUDs) and nucleoplasmic bridges (NPBs). These results provide evidence that the cytokinesis-block micronucleus (CBMN) assay using human lymphocytes and evaluating the eight parameters provided by the technique is a sensitive, fast, accurate, and inexpensive detection tool to support or discard AgNPs or other nanomaterials, which is worthwhile for continued testing of their effectiveness and toxicity for biomedical applications. In addition, it provides very important information about the role played by the [coating agent]/[metal] ratio in the design of nanomaterials that could reduce adverse effects as much as possible while retaining their therapeutic capabilities.

Experimental simulation of somatic and germ cell genotoxicity in male Mus musculus fed extracts of lead contaminated Pleurotus ostreatus (white rot fungi)

Exposure to lead (Pb) is a major risk factor in reproductive toxicity, somatic, and germ cell genotoxicity. Exposure via deteriorating Pb paints and contaminated air, soil, and water had been the primary routes. However, with increasing reports of Pb accumulation in mushrooms and other food items may increase the etiology of Pb poisoning. The study herein investigated somatic genotoxicity and reproductive abnormalities in mice fed extracts of Pb-contaminated Pleurotus ostreatus. Male mice were fed aqueous extracts of P. ostreatus cultivated in 0, 10, 20, 100, 200, 500, and 1000 mg/L of Pb-contaminated rice straw for 35 days. Testes were analyzed for Pb accumulation, histopathology and relative weight gain, caudal epididymis for abnormal sperm morphology, and bone marrow for micronucleus test. Concentration-related significant increase in Pb accumulation was observed in P. ostreatus and testes of exposed mice. Decrease testicular weight, congestion of blood vessels, necrosis, and disorganization of the seminiferous tubules were observed in treated mice. In addition, fold increase of 2.78, 3.39, 6.67, 7.21, 9.63, and 9.70 in abnormal sperm morphology in accordance with the Pb concentrations respectively, confirmed reproductive toxicity. Significant increase in micronucleated polychromatic (PCE) and normochromatic (NCE) erythrocytes and concentration-related decrease PCE-NCE ratio in the bone marrow of treated mice suggest genome instability. Pb-contaminated P. ostreatus increased somatic and germ cell genotoxicity in mice. This may predispose the mice to genetic related syndromes and reproductive syndromes. It further suggests caution in the consumption of metal laden wild mushrooms and crop plants.