Sister chromatid exchanges are mediated by homologous recombination in vertebrate cells

Homologous recombination contributes to the repair of acetaldehyde-induced DNA damage

Acetaldehyde, a chemical that can cause DNA damage and contribute to cancer, is prevalently present in our environment, e.g. in alcohol, tobacco, and food. Although aldehyde potentially promotes crosslinking reactions among biological substances including DNA, RNA, and protein, it remains unclear what types of DNA damage are caused by acetaldehyde and how they are repaired. In this study, we explored mechanisms involved in the repair of acetaldehyde-induced DNA damage by examining the cellular sensitivity to acetaldehyde in the collection of human TK6 mutant deficient in each genome maintenance system. Among the mutants, mismatch repair mutants did not show hypersensitivity to acetaldehyde, while mutants deficient in base and nucleotide excision repair pathways or homologous recombination (HR) exhibited higher sensitivity to acetaldehyde than did wild-type cells. We found that acetaldehyde-induced RAD51 foci representing HR intermediates were prolonged in HR-deficient cells. These results indicate a pivotal role of HR in the repair of acetaldehyde-induced DNA damage. These results suggest that acetaldehyde causes complex DNA damages that require various types of repair pathways. Mutants deficient in the removal of protein adducts from DNA ends such as TDP1-/- and TDP2-/- cells exhibited hypersensitivity to acetaldehyde. Strikingly, the double mutant deficient in both TDP1 and RAD54 showed similar sensitivity to each single mutant. This epistatic relationship between TDP1-/- and RAD54-/- suggests that the protein-DNA adducts generated by acetaldehyde need to be removed for efficient repair by HR. Our study would help understand the molecular mechanism of the genotoxic and mutagenic effects of acetaldehyde.

The proofreading exonuclease of leading-strand DNA polymerase epsilon prevents replication fork collapse at broken template strands

Leading-strand DNA replication by polymerase epsilon (Polϵ) across single-strand breaks (SSBs) causes single-ended double-strand breaks (seDSBs), which are repaired via homology-directed repair (HDR) and suppressed by fork reversal (FR). Although previous studies identified many molecules required for hydroxyurea-induced FR, FR at seDSBs is poorly understood. Here, we identified molecules that specifically mediate FR at seDSBs. Because FR at seDSBs requires poly(ADP ribose)polymerase 1 (PARP1), we hypothesized that seDSB/FR-associated molecules would increase tolerance to camptothecin (CPT) but not the PARP inhibitor olaparib, even though both anti-cancer agents generate seDSBs. Indeed, we uncovered that Polϵ exonuclease and CTF18, a Polϵ cofactor, increased tolerance to CPT but not olaparib. To explore potential functional interactions between Polϵ exonuclease, CTF18, and PARP1, we created exonuclease-deficient POLE1exo-/-, CTF18-/-, PARP1-/-, CTF18-/-/POLE1exo-/-, PARP1-/-/POLE1exo-/-, and CTF18-/-/PARP1-/- cells. Epistasis analysis indicated that Polϵ exonuclease and CTF18 were interdependent and required PARP1 for CPT tolerance. Remarkably, POLE1exo-/- and HDR-deficient BRCA1-/- cells exhibited similar CPT sensitivity. Moreover, combining POLE1exo-/- with BRCA1-/- mutations synergistically increased CPT sensitivity. In conclusion, the newly identified PARP1-CTF18-Polϵ exonuclease axis and HDR act independently to prevent fork collapse at seDSBs. Olaparib inhibits this axis, explaining the pronounced cytotoxic effects of olaparib on HDR-deficient cells.

Identification of Genomic Instability in Cows Infected with BVD Virus

An important factor for dairy cattle farmers is the profitability of cattle rearing, which is influenced by the animals' health and reproductive parameters, as well as their genomic stability and integrity. Bovine viral diarrhea (BVD) negatively affects the health of dairy cattle and causes reproductive problems. The aim of the study was to identify genomic instability in cows with reproductive disorders following infection with the BVD virus. The material for analysis was peripheral blood from Holstein-Friesian cows with reproductive problems, which had tested positive for BVD, and from healthy cows with no reproductive problems, which had tested negative for BVD. Three cytogenetic tests were used: the sister chromatid exchange assay, fragile sites assay, and comet assay. Statistically significant differences were noted between the groups and between the individual cows in the average frequency of damage. The assays were good biomarkers of genomic stability and enabled the identification of individuals with an increased frequency of damage to genetic material that posed a negative impact on their health. The assays can be used to prevent disease during its course and evaluate the genetic resistance of animals. This is especially important for the breeder, both for economic and breeding reasons. Of the three assays, the comet assay proved to be the most sensitive for identifying DNA damage in the animals.

Prolonged particulate hexavalent chromium exposure induces RAD51 foci inhibition and cytoplasmic accumulation in immortalized and primary human lung bronchial epithelial cells

Hexavalent chromium [Cr(VI)] is a human lung carcinogen with widespread exposure risks. Cr(VI) causes DNA double strand breaks that if unrepaired, progress into chromosomal instability (CIN), a key driving outcome in Cr(VI)-induced tumors. The ability of Cr(VI) to cause DNA breaks and inhibit repair is poorly understood in human lung epithelial cells, which are extremely relevant since pathology data show Cr(VI)-induced tumors originate from bronchial epithelial cells. In the present study, we considered immortalized and primary human bronchial epithelial cells. Cells were treated with zinc chromate at concentrations ranging 0.05 to 0.4μg/cm2 for acute (24 h) and prolonged (120 h) exposures. DNA double strand breaks (DSBs) were measured by neutral comet assay and the status of homologous recombination repair, the main pathway to fix Cr(VI)-induced DSBs, was measured by RAD51 foci formation with immunofluorescence, RAD51 localization with confocal microscopy and sister chromatid exchanges. We found acute and prolonged Cr(VI) exposure induced DSBs. Acute exposure induced homologous recombination repair, but prolonged exposure inhibited it resulting in chromosome instability in immortalized and primary human bronchial epithelial cells.

Fanconi anemia and Aldehyde Degradation Deficiency Syndrome: Metabolism and DNA repair protect the genome and hematopoiesis from endogenous DNA damage

We have identified a set of Japanese children with hypoplastic anemia caused by combined defects in aldehyde degrading enzymes ADH5 and ALDH2. Their clinical characteristics overlap with a hereditary DNA repair disorder, Fanconi anemia. Our discovery of this disorder, termed Aldehyde Degradation Deficiency Syndrome (ADDS), reinforces the notion that endogenously generated aldehydes exert genotoxic effects; thus, the coupled actions of metabolism and DNA repair are required to maintain proper hematopoiesis and health.

Using Sister Chromatid Exchange Assay to Detect Homologous Recombination Deficiency in Epigenetically Deregulated Urothelial Carcinoma Cells

Sister chromatid exchange (SCE) is the process of exchanging regions between two sister chromatids during DNA replication. Exchanges between replicated chromatids and their sisters can be visualized in cells when DNA synthesis in one chromatid is labelled by 5-bromo-2'-deoxyuridine (BrdU). Homologous recombination (HR) is considered as the principal mechanism responsible for the sister chromatid exchange (SCE) upon replication fork collapse, and therefore SCE frequency upon genotoxic conditions reflects the capacity of HR repair to respond to replication stress. During tumorigenesis, inactivating mutations or altered transcriptome can affect a plethora of epigenetic factors that participate in DNA repair processes, and there are an increasing number of reports which demonstrate a link between epigenetic deregulation in cancer and homologous recombination deficiency (HRD). Therefore, the SCE assay can provide valuable information regarding the HR functionality in tumors with epigenetic deficiencies. In this chapter, we provide a method to visualize SCEs. The technique outlined below is characterized by high sensitivity and specificity and has been successfully applied to human bladder cancer cell lines. In this context, this technique could be used to characterize the dynamics of HR repair in tumors with deregulated epigenome.

TRIP13 Participates in Immediate-Early Sensing of DNA Strand Breaks and ATM Signaling Amplification through MRE11

Thyroid hormone receptor-interacting protein 13 (TRIP13) participates in various regulatory steps related to the cell cycle, such as the mitotic spindle assembly checkpoint and meiotic recombination, possibly by interacting with members of the HORMA domain protein family. Recently, it was reported that TRIP13 could regulate the choice of the DNA repair pathway, i.e., homologous recombination (HR) or nonhomologous end-joining (NHEJ). However, TRIP13 is recruited to DNA damage sites within a few seconds after damage and may therefore have another function in DNA repair other than regulation of the pathway choice. Furthermore, the depletion of TRIP13 inhibited both HR and NHEJ, suggesting that TRIP13 plays other roles besides regulation of choice between HR and NHEJ. To explore the unidentified functions of TRIP13 in the DNA damage response, we investigated its genome-wide interaction partners in the context of DNA damage using quantitative proteomics with proximity labeling. We identified MRE11 as a novel interacting partner of TRIP13. TRIP13 controlled the recruitment of MDC1 to DNA damage sites by regulating the interaction between MDC1 and the MRN complex. Consistently, TRIP13 was involved in ATM signaling amplification. Our study provides new insight into the function of TRIP13 in immediate-early DNA damage sensing and ATM signaling activation.

Alternative end-joining originates stable chromosome aberrations induced by etoposide during targeted inhibition of DNA-PKcs in ATM-deficient tumor cells

ATM and DNA-PKcs coordinate the DNA damage response at multiple levels following the exposure to chemotherapy. The Topoisomerase II poison etoposide (ETO) is an effective chemotherapeutic agent that induces DNA double-strand breaks (DSB), but it is responsible from the chromosomal rearrangements frequently found in therapy-related secondary tumors. Targeted inhibition of DNA-PKcs in ATM-defective tumors combined with radio- or chemotherapy has been proposed as relevant therapies. Here, we explored the DNA repair mechanisms and the genetic consequences of targeting the non-oncogenic addiction to DNA-PKcs of ATM-defective tumor cells after exposure to ETO. We demonstrated that chemical inhibition of DNA-PKcs followed by treatment with ETO resulted in the accumulation of chromatid breaks and decreased mitotic index in both A-T cells and ATM-knocked-down (ATM^kd) tumor cells. The HR repair process in DNA-PKcs-inhibited ATM^kd cells amplified the RAD51 foci number, with no correlated increase in sister chromatid exchanges. The analysis of post-mitotic DNA lesions presented an augmented number of persistent unresolved DSB, without alterations in the cell cycle progression. Long-term examination of chromosome aberrations revealed a strikingly high number of chromatid and chromosome exchanges. By using genetic and pharmacological abrogation of PARP-1, we demonstrated that alternative end-joining (alt-EJ) repair pathway is responsible for those chromosome abnormalities generated by limiting c-NHEJ activities during directed inhibition of DNA-PKcs in ATM-deficient cells. Targeting the non-oncogenic addiction to DNA-PKcs of ATM-defective tumors stimulates the DSB repair by alt-EJ, which is liable for the origin of cells carrying stable chromosome aberrations that may eventually restrict the therapeutic strategy.

Sister chromatid exchanges induced by perturbed replication can form independently of BRCA1, BRCA2 and RAD51

Sister chromatid exchanges (SCEs) are products of joint DNA molecule resolution, and are considered to form through homologous recombination (HR). Indeed, SCE induction upon irradiation requires the canonical HR factors BRCA1, BRCA2 and RAD51. In contrast, replication-blocking agents, including PARP inhibitors, induce SCEs independently of BRCA1, BRCA2 and RAD51. PARP inhibitor-induced SCEs are enriched at difficult-to-replicate genomic regions, including common fragile sites (CFSs). PARP inhibitor-induced replication lesions are transmitted into mitosis, suggesting that SCEs can originate from mitotic processing of under-replicated DNA. Proteomics analysis reveals mitotic recruitment of DNA polymerase theta (POLQ) to synthetic DNA ends. POLQ inactivation results in reduced SCE numbers and severe chromosome fragmentation upon PARP inhibition in HR-deficient cells. Accordingly, analysis of CFSs in cancer genomes reveals frequent allelic deletions, flanked by signatures of POLQ-mediated repair. Combined, we show PARP inhibition generates under-replicated DNA, which is processed into SCEs during mitosis, independently of canonical HR factors.

DNA Polymerase Theta Plays a Critical Role in Pancreatic Cancer Development and Metastasis

Pancreatic ductal adenocarcinoma (PDAC), due to its genomic heterogeneity and lack of effective treatment, despite decades of intensive research, will become the second leading cause of cancer-related deaths by 2030. Step-wise acquisition of mutations, due to genomic instability, is considered to drive the development of PDAC; the KRAS mutation occurs in 95 to 100% of human PDAC, and is already detectable in early premalignant lesions designated as pancreatic intraepithelial neoplasia (PanIN). This mutation is possibly the key event leading to genomic instability and PDAC development. Our study aimed to investigate the role of the error-prone DNA double-strand breaks (DSBs) repair pathway, alt-EJ, in the presence of the KRAS G12D mutation in pancreatic cancer development. Our findings show that oncogenic KRAS contributes to increasing the expression of Polθ, Lig3, and Mre11, key components of alt-EJ in both mouse and human PDAC models. We further confirm increased catalytic activity of alt-EJ in a mouse and human model of PDAC bearing the KRAS G12D mutation. Subsequently, we focused on estimating the impact of alt-EJ inactivation by polymerase theta (Polθ) deletion on pancreatic cancer development, and survival in genetically engineered mouse models (GEMMs) and cancer patients. Here, we show that even though Polθ deficiency does not fully prevent the development of pancreatic cancer, it significantly delays the onset of PanIN formation, prolongs the overall survival of experimental mice, and correlates with the overall survival of pancreatic cancer patients in the TCGA database. Our study clearly demonstrates the role of alt-EJ in the development of PDAC, and alt-EJ may be an attractive therapeutic target for pancreatic cancer patients.

Genomic instability and the link to infertility: A focus on microsatellites and genomic instability syndromes

Infertility is associated to multiple types of different genomic instabilities and is a genetic feature of genomic instability syndromes. While the mismatch repair machinery contributes to the maintenance of genome integrity, surprisingly its potential role in infertility is overlooked. Defects in mismatch repair mechanisms contribute to microsatellite instability and genomic instability syndromes, due to the inability to repair newly replicated DNA. This article reviews the literature to date to elucidate the contribution of microsatellite instability to genomic instability syndromes and infertility. The key findings presented reveal microsatellite instability is poorly researched in genomic instability syndromes and infertility.

Cell Cycle Stage and DNA Repair Pathway Influence CRISPR/Cas9 Gene Editing Efficiency in Porcine Embryos

CRISPR/Cas9 technology is a powerful tool used for genome manipulation in different cell types and species. However, as with all new technologies, it still requires improvements. Different factors can affect CRISPR/Cas efficiency in zygotes, which influence the total cost and complexity for creating large-animal models for research. This study evaluated the importance of zygote cell cycle stage between early-injection (within 6 h post activation/fertilization) versus late-injection (14–16 h post activation/fertilization) when the CRISPR/Cas9 components were injected and the inhibition of the homologous recombination (HR) pathway of DNA repair on gene editing, embryo survival and development on embryos produced by fertilization, sperm injection, somatic cell nuclear transfer, and parthenogenetic activation technologies. Injections at the late cell cycle stage decreased embryo survival (measured as the proportion of unlysed embryos) and blastocyst formation (68.2%; 19.3%) compared to early-stage injection (86.3%; 28.8%). However, gene editing was higher in blastocysts from late-(73.8%) vs. early-(63.8%) injected zygotes. Inhibition of the HR repair pathway increased gene editing efficiency by 15.6% in blastocysts from early-injected zygotes without compromising embryo development. Our finding shows that injection at the early cell cycle stage along with HR inhibition improves both zygote viability and gene editing rate in pig blastocysts.

Bloom syndrome and the underlying causes of genetic instability

Autosomal hereditary recessive diseases characterized by genetic instability are often associated with cancer predisposition. Bloom syndrome (BS), a rare genetic disorder, with <300 cases reported worldwide, combines both. Indeed, patients with Bloom's syndrome are 150 to 300 times more likely to develop cancers than normal individuals. The wide spectrum of cancers developed by BS patients suggests that early initial events occur in BS cells which may also be involved in the initiation of carcinogenesis in the general population and these may be common to several cancers. BS is caused by mutations of both copies of the BLM gene, encoding the RecQ BLM helicase. This review discusses the different aspects of BS and the different cellular functions of BLM in genome surveillance and maintenance through its major roles during DNA replication, repair, and transcription. BLM's activities are essential for the stabilization of centromeric, telomeric and ribosomal DNA sequences, and the regulation of innate immunity. One of the key objectives of this work is to establish a link between BLM functions and the main clinical phenotypes observed in BS patients, as well as to shed new light on the correlation between the genetic instability and diseases such as immunodeficiency and cancer. The different potential implications of the BLM helicase in the tumorigenic process and the use of BLM as new potential target in the field of cancer treatment are also debated.

Analysis of disease model iPSCs derived from patients with a novel Fanconi anemia-like IBMFS ADH5/ALDH2 deficiency

We have recently discovered Japanese children with a novel Fanconi anemia-like inherited bone marrow failure syndrome (IBMFS). This disorder is likely caused by the loss of a catabolic system directed toward endogenous formaldehyde due to biallelic variants in ADH5 combined with a heterozygous ALDH2*2 dominant-negative allele (rs671), which is associated with alcohol-induced Asian flushing. Phytohemagglutinin-stimulated lymphocytes from these patients displayed highly increased numbers of spontaneous sister chromatid exchanges (SCEs), reflecting homologous recombination repair of formaldehyde damage. Here, we report that, in contrast, patient-derived fibroblasts showed normal levels of SCEs, suggesting that different cell types or conditions generate various amounts of formaldehyde. To obtain insights about endogenous formaldehyde production and how defects in ADH5/ALDH2 affect human hematopoiesis, we constructed disease model cell lines, including induced pluripotent stem cells (iPSCs). We found that ADH5 is the primary defense against formaldehyde, and ALDH2 provides a backup. DNA repair capacity in the ADH5/ALDH2-deficient cell lines can be overwhelmed by exogenous low-dose formaldehyde, as indicated by higher levels of DNA damage than in FANCD2-deficient cells. Although ADH5/ALDH2-deficient cell lines were healthy and showed stable growth, disease model iPSCs displayed drastically defective cell expansion when stimulated into hematopoietic differentiation in vitro, displaying increased levels of DNA damage. The expansion defect was partially reversed by treatment with a new small molecule termed C1, which is an agonist of ALDH2, thus identifying a potential therapeutic strategy for the patients. We propose that hematopoiesis or lymphocyte blastogenesis may entail formaldehyde generation that necessitates elimination by ADH5/ALDH2 enzymes.

Genetic evidence for the involvement of mismatch repair proteins, PMS2 and MLH3, in a late step of homologous recombination

Homologous recombination (HR) repairs DNA double-strand breaks using intact homologous sequences as template DNA. Broken DNA and intact homologous sequences form joint molecules (JMs), including Holliday junctions (HJs), as HR intermediates. HJs are resolved to form crossover and noncrossover products. A mismatch repair factor, MLH3 endonuclease, produces the majority of crossovers during meiotic HR, but it remains elusive whether mismatch repair factors promote HR in nonmeiotic cells. We disrupted genes encoding the MLH3 and PMS2 endonucleases in the human B cell line, TK6, generating null MLH3^-/- and PMS2^-/- mutant cells. We also inserted point mutations into the endonuclease motif of MLH3 and PMS2 genes, generating endonuclease death MLH3^DN/DN and PMS2^EK/EK cells. MLH3^-/- and MLH3^DN/DN cells showed a very similar phenotype, a 2.5-fold decrease in the frequency of heteroallelic HR-dependent repair of restriction enzyme-induced double-strand breaks. PMS2^-/- and PMS2^EK/EK cells showed a phenotype very similar to that of the MLH3 mutants. These data indicate that MLH3 and PMS2 promote HR as an endonuclease. The MLH3^DN/DN and PMS2^EK/EK mutations had an additive effect on the heteroallelic HR. MLH3^DN/DN/PMS2^EK/EK cells showed normal kinetics of γ-irradiation-induced Rad51 foci but a significant delay in the resolution of Rad51 foci and a 3-fold decrease in the number of cisplatin-induced sister chromatid exchanges. The ectopic expression of the Gen1 HJ re-solvase partially reversed the defective heteroallelic HR of MLH3^DN/DN/PMS2^EK/EK cells. Taken together, we propose that MLH3 and PMS2 promote HR as endonucleases, most likely by processing JMs in mammalian somatic cells.

A Newly Assigned Role of CTCF in Cellular Response to Broken DNAs

Best known as a transcriptional factor, CCCTC-binding factor (CTCF) is a highly conserved multifunctional DNA-binding protein with 11 zinc fingers. It functions in diverse genomic processes, including transcriptional activation/repression, insulation, genome imprinting and three-dimensional genome organization. A big surprise has recently emerged with the identification of CTCF engaging in the repair of DNA double-strand breaks (DSBs) and in the maintenance of genome fidelity. This discovery now adds a new dimension to the multifaceted attributes of this protein. CTCF facilitates the most accurate DSB repair via homologous recombination (HR) that occurs through an elaborate pathway, which entails a chain of timely assembly/disassembly of various HR-repair complexes and chromatin modifications and coordinates multistep HR processes to faithfully restore the original DNA sequences of broken DNA sites. Understanding the functional crosstalks between CTCF and other HR factors will illuminate the molecular basis of various human diseases that range from developmental disorders to cancer and arise from impaired repair. Such knowledge will also help understand the molecular mechanisms underlying the diverse functions of CTCF in genome biology. In this review, we discuss the recent advances regarding this newly assigned versatile role of CTCF and the mechanism whereby CTCF functions in DSB repair.

Pold4, the fourth subunit of replicative polymerase δ, suppresses gene conversion in the immunoglobulin-variable gene in avian DT40 cells

The replicative polymerase δ (Polδ), consisting of four subunits, plays a pivotal role in chromosomal replication. Pold4, the smallest subunit of Polδ, is believed to contribute to the regulation of replication by facilitating repair in response to DNA damage. However, that contribution has not been fully elucidated. We here show that Pold4 contributes to the suppression of gene conversion in immunoglobulin-variable (IgV) gene diversification in the chicken DT40 lymphocyte cell line, where gene conversion diversifies the IgV gene through intragenic homologous recombination (HR) between diverged pseudo-V segments. IgV gene conversion is initiated by activation-induced cytidine deaminase-mediated uracil formation in the IgV gene, which in turn converts into an abasic site, leading to replication arrest. POLD4^-/- cells exhibited an increased rate of IgV gene conversion. Moreover, the gene-conversion tract was lengthened and the usage of pseudo-V segments was altered, showing a preference, to use the diverged sequence as a donor in POLD4^-/- cells. These data suggest that Pold4 is involved in the regulation of HR-mediated gene conversion in IgV diversification. By contrast, the rate in HR-mediated, sister-chromatid exchange and gene-targeting induced by an I-SceI endonclease-mediated DNA double-strand break exhibited by POLD4^-/- cells was indistinguishable from that by wild-type cells. These findings indicate that the functionality of general HR is preserved in POLD4^-/- cells. In conclusion, Pold4 is involved in the suppression of IgV-gene conversion without affecting the general functionality of HR.

Activation of DNA damage response signaling in mammalian cells by ionizing radiation

Cellular responses to DNA damage are fundamental to preserve genomic integrity during various endogenous and exogenous stresses. Following radiation therapy and chemotherapy, this DNA damage response (DDR) also determines development of carcinogenesis and therapeutic outcome. In humans, DNA damage activates a robust network of signal transduction cascades, driven primarily through phosphorylation events. These responses primarily involve two key non-redundant signal transducing proteins of phosphatidylinositol 3-kinase-like (PIKK) family - ATR and ATM, and their downstream kinases (hChk1 and hChk2). They further phosphorylate effectors proteins such as p53, Cdc25A and Cdc25C which function either to activate the DNA damage checkpoints and cell death mechanisms, or DNA repair pathways. Identification of molecular pathways that determine signaling after DNA damage and trigger DNA repair in response to differing types of DNA lesions allows for a far better understanding of the consequences of radiation and chemotherapy on normal and tumor cells. Here we highlight the network of DNA damage response pathways that are activated after treatment with different types of radiation. Further, we discuss regulation of cell cycle checkpoint and DNA repair processes in the context of DDR in response to radiation.

The Sister-Chromatid Exchange Assay in Human Cells

The semiconservative nature of DNA replication allows the differential labeling of sister chromatids that is the fundamental requirement to perform the sister-chromatid exchange (SCE) assay. SCE assay is a powerful technique to visually detect the physical exchange of DNA between sister chromatids. SCEs could result as a consequence of DNA damage repair by homologous recombination (HR) during DNA replication. Here, we provide the detailed protocol to perform the SCE assay in cultured human cells. Cells are exposed to the thymidine analog 5-bromo-2'-deoxyuridine (BrdU) during two cell cycles, resulting in the two sister chromatids having differential incorporation of the analog. After metaphase spreads preparation and further processing, SCEs are nicely visualized under the microscope.

Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mice and Humans

Reactive aldehydes arise as by-products of metabolism and are normally cleared by multiple families of enzymes. We find that mice lacking two aldehyde detoxifying enzymes, mitochondrial ALDH2 and cytoplasmic ADH5, have greatly shortened lifespans and develop leukemia. Hematopoiesis is disrupted profoundly, with a reduction of hematopoietic stem cells and common lymphoid progenitors causing a severely depleted acquired immune system. We show that formaldehyde is a common substrate of ALDH2 and ADH5 and establish methods to quantify elevated blood formaldehyde and formaldehyde-DNA adducts in tissues. Bone-marrow-derived progenitors actively engage DNA repair but also imprint a formaldehyde-driven mutation signature similar to aging-associated human cancer mutation signatures. Furthermore, we identify analogous genetic defects in children causing a previously uncharacterized inherited bone marrow failure and pre-leukemic syndrome. Endogenous formaldehyde clearance alone is therefore critical for hematopoiesis and in limiting mutagenesis in somatic tissues.

Fragile site instability: measuring more than breaks

Genome instability is not only a hallmark of cancer, it is necessary for its initiation and evolution, and naturally accumulates as cells age. Replication stress is a potent source of genome instability found in many tumor types [1]. Chromosomal fragile sites are genomic loci highly prone to DNA damage specifically from replication stress and are frequently mutated in cancer [2-4]2-4]. While tracking the origin of individual mutations has proved challenging, measuring DNA damage and repair at endogenous sites can offer key insights into understanding the etiology of cancer. In the past 15 years, the causal link between replication stress, oncogene activation, and tumor initiation and evolution has become increasingly clear [1, 5-9]. Replication-associated damage accumulates at early stages of tumorigenesis and may promote further transformation. Studying the causes and consequences of fragile site instability can offer a window into the earliest stages of carcinogenesis [10-13]. In particular, fragile site studies will help us understand the molecular underpinnings influencing the frequency of DNA breakage, successful repair processes suppressing genome instability, and unsuccessful repair leading to mutations and chromosome rearrangements. Of these, measuring successful repair is the most challenging as it leaves little evidence behind.

In Vitro Genotoxicity and Molecular Docking Study of Ellagic Acid

Background:

Ellagic Acid (EA) is a polyphenolic compound that is classified in the natural antioxidants group. Polyphenolic compounds that exert antioxidant activity possess particular importance for scientists, food producers and consumers due to their positive effects on human health. However, despite considerable evidence that EA shows antigenotoxic activity by binding to DNA, there is no systematic genotoxicity study of this substance, which can covalently bind to DNA. This study aims to reveal the possible genotoxic activity of EA using widely accepted assays for the assessment of DNA clastogenic activity: sister chromatid exchange, chromosome aberration, micronucleus and comet assays as well as to predict the interactions among EA and DNA through molecular docking.

Methods:

Different assays were carried out to identify the clastogenic activity of EA on human lymphocyte DNA using Sister Chromatid Exchange (SCE), Chromosome Aberration (CA), Micronucleus (MN) and single-cell gel electrophoresis (SCGE/comet) assays. For this aim, human peripheral blood lymphocytes were treated with EA (60, 80 and 100 μg/ml) for 24 and 48 hrs in the SCE, CA and MN assays and for 1 hr in the comet assay. Furthermore, molecular docking experiments were also performed to calculate the binding energy of EA on human B-DNA structure (B-DNA dodecamer) as well as to predict noncovalent interactions among these macromolecules.

Results:

At the concentrations and treatment times (24- or 48-hr) tested, EA did not induce either SCE or Chromosome Aberrations (CAs) as compared to the negative and solvent controls. Although EA slightly increased the percentage of Micronucleated Binuclear (%MNBN) cells as well as the percentage of Micronucleus (%MN) in 24 or 48-hr treatment periods at all concentrations, this increase was not statistically significant as compared to both controls. The effect of EA on DNA replication (nuclear division) was determined by the Proliferation Index (PI), the Nuclear Division Index (NDI) and the Mitotic Index (MI). No statistically significant differences were observed in the PI or NDI in 24- or 48-hr treatment periods in human lymphocyte cultures treated with EA at various concentrations. EA generally had no significant effect on the MI, as observed with the PI and NDI.

Discussion:

Although the concentrations of 60 and 80 μg/mL at a 24-hr treatment period and the concentrations of 60 μg/mL and 100 μg/mL at 48-hr treatment period generally decreased the MI, those decreases were not statistically significant when compared to negative and solvent controls. Moreover, none of the concentrations of EA tested in this study were able to increase DNA damage determined by the tail DNA length, %DNA in tail and tail moment parameters in the comet assay. Although the amount of DNA damage in the comet assay decreased with increasing concentrations of EA, this decrease was not statistically significant as compared to both controls. However, molecular docking experiments interestingly showed that the binding free energy of EA with B-DNA was -7.84 kcal/mol-1, indicating a strong interaction between the two molecules.

Conclusion :

Although the findings of our study show that EA does not have genotoxic potential in human chromosomes, molecular docking experiments revealed strong hydrogen bonding between EA and B-DNA molecules. Therefore, it has been proposed that the prevailing information suggesting that the molecules that bind to DNA cause genotoxic effects should be reconsidered from a wider perspective.

Distinct roles of BRCA2 in replication fork protection in response to hydroxyurea and DNA interstrand cross-links

DNA interstrand cross-links (ICLs) are a form of DNA damage that requires the interplay of a number of repair proteins including those of the Fanconi anemia (FA) and the homologous recombination (HR) pathways. Pathogenic variants in the essential gene BRCA2/FANCD1, when monoallelic, predispose to breast and ovarian cancer, and when biallelic, result in a severe subtype of Fanconi anemia. BRCA2 function in the FA pathway is attributed to its role as a mediator of the RAD51 recombinase in HR repair of programmed DNA double-strand breaks (DSB). BRCA2 and RAD51 functions are also required to protect stalled replication forks from nucleolytic degradation during response to hydroxyurea (HU). While RAD51 has been shown to be necessary in the early steps of ICL repair to prevent aberrant nuclease resection, the role of BRCA2 in this process has not been described. Here, based on the analysis of BRCA2 DNA-binding domain (DBD) mutants (c.8488-1G>A and c.8524C>T) discovered in FA patients presenting with atypical FA-like phenotypes, we establish that BRCA2 is necessary for the protection of DNA at ICLs. Cells carrying BRCA2 DBD mutations are sensitive to ICL-inducing agents but resistant to HU treatment consistent with relatively high HR repair in these cells. BRCA2 function at an ICL protects against DNA2-WRN nuclease-helicase complex and not the MRE11 nuclease that is implicated in the resection of HU-induced stalled replication forks. Our results also indicate that unlike the processing at HU-induced stalled forks, the function of the SNF2 translocases (SMARCAL1, ZRANB3, or HLTF), implicated in fork reversal, are not an integral component of the ICL repair, pointing to a different mechanism of fork protection at different DNA lesions.

Assessment of chromosome stability in boars

Chromosome instability adversely affects animal fertility and reproduction. Analysis of instability can be a valuable diagnostic tool. Helpful tests for assessment of instabilities include the sister chromatid exchange assay, identification of fragile sites, the bleomycin assay and the comet assay. These techniques can be used to assess and compare the chromosome stability of individual breeds of animals. The aim of the study was to assess chromosome stability in boars: Duroc, Duroc x Pietrain and Pietrain x Duroc crossbreds, Polish Large White, and the Neckar, P76 and PIC lines. The study assessed the chromosome stability of boars. The distribution of instabilities in individual breeds was varied. The average frequency of chromatid exchange was 4.8 ± 1.5, while that of fragile sites was 3.9 ± 1.4. The mean level of DNA damage (% tail DNA) was 9.4 ± 8.3, while in the bleomycin assay b/c and %AM were 0.6 ± 0.7 and 44.4 ± 4.1. A higher rate of instability was found in older individuals than in younger ones. The cytogenetic assays used to identify various forms of chromosome instability can be used to evaluate boars intended for breeding.

Bisphenol A and Phthalates Exhibit Similar Toxicogenomics and Health Effects

Bisphenol A and phthalates are most frequently detected organic pollutants found in our surroundings because of their regular use as plasticizers in daily use polymeric products. BPA is used in manufacturing baby feeding bottles, water pipes, canned food linings, and food packaging materials. Phthalates are used in polyvinyl chloride products including clothing, toys, medical devices, and food packaging. These chemicals are not bound to the matrix and leach out into the surroundings on slight change in the environment, like alteration in pH, temperature, and pressure. Humans are continuously exposed to these chemicals through skin contact, inhalation, or ingestion when the leachates enter food, drinks, air, water, or soil. The Comparative Toxicogenomics Database (CTD) revealed that Bisphenol A has 1932 interactions with genes/proteins and few frequently used phthalates (DEHP, MEHP, DBP, BBP, and MBP) showed 484 gene/protein interactions. Similar toxicogenomics and adverse effects of Bisphenol A and phthalates on human health are attributed to their 89 common interacting genes/proteins.

DNA repair inhibitors to enhance radiotherapy: Progresses and limitations

Radiotherapy is one of the most common form of treatment in oncology care. Indeed, radiotherapy proved to be very effective in treating a wide range of malignancies. Nevertheless, certain tumours are intrinsically radioresistant or may evolve to become radioresistant. Resistance to radiotherapy is often associated with dysregulated DNA damage response and repair. Recently, a number of strategies have been developed to improve radiotherapy efficacy by targeting the DNA damage response and repair pathways. Ongoing clinical trials showed the potential of some of these approaches in enhancing radiotherapy, but also highlighted the possible limitations. Here, we will describe (i) the main mechanisms involved in double-strand break repair; (ii) available strategies that target these DNA repair processes to improve radiotherapy and (iii) the clinical outcomes and challenges that have emerged so far.

Increased Non-Homologous End Joining Makes DNA-PK a Promising Target for Therapeutic Intervention in Uveal Melanoma

Uveal melanoma (UM) is the most common primary intraocular tumour in adults, with a mean survival of six months following metastasis. The survival rates have not improved in over 30 years. This study has shown that sister chromatid exchange (SCE) is low in UM which is likely due to a reduced expression of FANCD2. As FANCD2 can function to suppress non-homologous end joining (NHEJ), this study therefore investigated NHEJ in UM. The activation of the catalytic subunit of the NHEJ pathway protein DNA-dependent protein kinase (DNA-PK) was measured by analysing the foci formation and the ligation efficiency by NHEJ determined using a plasmid-based end-joining assay. Using small-interfering RNA (siRNA) knock-down, and chemical inhibitors of DNA-PK, the survival of primary UM cultures and two cell lines were determined. To assess the homologous recombination capacity in response to the inhibition of DNA-PK, a SCE analysis was performed. In addition, to support the findings, the messenger RNA (mRNA) expression of genes associated with NHEJ was analysed using the Cancer Genome Atlas (TCGA)-UM RNAseq data (n = 79). The NHEJ activity and DNA-PKcs activation was upregulated in UM and the inhibition of DNA-PK selectively induced apoptosis and sensitized to ionising radiation and inter-strand cross-linking agents. The inhibition of the NHEJ protein DNA-PK is lethal to UM, indicating a potentially effective therapeutic option, either alone or as a sensitizer for other treatments.

Assessment of genome stability in various breeds of cattle

Chromosomal instability is a type of genome instability involving changes in genetic information at the chromosomal level. The basic tests used to identify this form of instability are sister chromatid exchange (SCE) tests and identification of fragile sites (FS). SCE is the process by which sister chromatids become fragmented as a result of DNA strand breakage and reassembly, followed by exchange of these fragments. FS can be observed in the form of breaks, gaps or constrictions on chromosomes, which often result from multiple nucleotide repeats in DNA that are difficult to replicate. The research material was the peripheral blood of ten breeds of cattle raised in Poland, including four native breeds covered by a genetic resources conservation programme, i.e. Polish Red, Polish Red-and-White, White-Backed, and Polish Black-and-White, as well as Polish Holstein-Friesian, Simmental, Montbéliarde, Jersey, Limousine and Danish Red. Two tests were performed on chromosomes obtained from in vitro cultures: SCE and FS. The average frequency of SCE was 5.08 ± 1.31, while the incidence of FS was 3.45 ± 0.94. Differences in the incidence of SCE and FS were observed between breeds. The least damage was observed in the Polish Red and White-Backed breeds, and the most in Polish Holstein-Friesians. The most damage was observed in the interstitial part of the chromosomes. Age was shown to significantly affect the incidence of SCE and FS. Younger cows showed less damage than older ones (SCE: 4.84 ± 1.25; 5.34 ± 1.24; FS: 3.10 ± 0.88, 3.80 ± 0.92).

PDIP38/PolDIP2 controls the DNA damage tolerance pathways by increasing the relative usage of translesion DNA synthesis over template switching

Replicative DNA polymerases are frequently stalled at damaged template strands. Stalled replication forks are restored by the DNA damage tolerance (DDT) pathways, error-prone translesion DNA synthesis (TLS) to cope with excessive DNA damage, and error-free template switching (TS) by homologous DNA recombination. PDIP38 (Pol-delta interacting protein of 38 kDa), also called Pol δ-interacting protein 2 (PolDIP2), physically associates with TLS DNA polymerases, polymerase η (Polη), Polλ, and PrimPol, and activates them in vitro. It remains unclear whether PDIP38 promotes TLS in vivo, since no method allows for measuring individual TLS events in mammalian cells. We disrupted the PDIP38 gene, generating PDIP38^-/- cells from the chicken DT40 and human TK6 B cell lines. These PDIP38^-/- cells did not show a significant sensitivity to either UV or H₂O₂, a phenotype not seen in any TLS-polymerase-deficient DT40 or TK6 mutants. DT40 provides a unique opportunity of examining individual TLS and TS events by the nucleotide sequence analysis of the immunoglobulin variable (Ig V) gene as the cells continuously diversify Ig V by TLS (non-templated Ig V hypermutation) and TS (Ig gene conversion) during in vitro culture. PDIP38^-/- cells showed a shift in Ig V diversification from TLS to TS. We measured the relative usage of TLS and TS in TK6 cells at a chemically synthesized UV damage (CPD) integrated into genomic DNA. The loss of PDIP38 also caused an increase in the relative usage of TS. The number of UV-induced sister chromatid exchanges, TS events associated with crossover, was increased a few times in PDIP38^-/- human and chicken cells. Collectively, the loss of PDIP38 consistently causes a shift in DDT from TLS to TS without enhancing cellular sensitivity to DNA damage. We propose that PDIP38 controls the relative usage of TLS and TS increasing usage of TLS without changing the overall capability of DDT.

Biological relevance of CuFeO2 nanoparticles: Antibacterial and anti-inflammatory activity, genotoxicity, DNA and protein interactions

Heterometal oxide nanoparticles of bioessential metals are shedding new light to nanoparticle-inspired bioapplications. Pairing bioreactive elements like copper and iron can affect the redox dynamic and biological profile of the nanomaterial. Given the complexity of physicochemical properties, biological activity and toxicity concerns, extensive exploration is demanded, especially when active and less active oxidation states participate as in case of cuprous-ferric delafossite CuFeO₂ (copper(I)-iron(III)), a less widespread nanomaterial. In that vein, CuFeO₂ nanoparticles were synthesized and biological profile was evaluated in comparison with cuprous oxide (Cu₂O NPs) counterpart, an already established antimicrobial agent. Interactions with bacteria, proteins and DNA were examined. Cu₂O NPs exhibited stronger antibacterial activity (IC₅₀ < 25 μg/ml) than CuFeO₂ NPs (IC₅₀ > 100 μg/ml). In vitro exposure of nanoparticles on plasmid DNA unveiled toxicity in the form of DNA damage for Cu₂O and enhanced biocompatibility for CuFeO₂ NPs. Genotoxicity estimated by the frequency of sister chromatid exchanges, cytostaticity based on the proliferating rate indices and cytotoxicity based on the mitotic indices at human peripheral lymphocyte cultures were all significantly lower in the case of CuFeO₂ NPs. Furthermore, through in vitro albumin denaturation assay, CuFeO₂ NPs showed better performance in protein denaturation protection, correlating in superior anti-inflammatory activity than Cu₂O and similar to acetylsalicylic acid. Synergy of copper(I)-iron(III) in nanoscale is apparent and gives rise to fruitful bioapplications and perspectives.

Analysis of chromatin instability of somatic cells in sheep

Cytogenetic tests are highly reliable, sensitive indicators of the early effects of genomic instability. Their results provide information on the organism’s susceptibility to exogenous and endogenous factors and are measures of the degree of repair of DNA damage. Our study assessed spontaneously occurring damage in following four breeds of sheep: Polish Heath, Polish Lowland (Zelazna variety), Polish Blackhead, and Berrichon du Cher. Instability was identified using the following three different tests: a sister chromatid exchange (SCE) assay, identification of fragile sites, and the comet assay. The distribution of instabilities varied depending on the breed. The mean frequency of SCEs was 5.13 ± 1.58, whereas that of fragile sites was 3.30 ± 1.24. The mean level of DNA damage (% head DNA) was 96.52 ± 6.59. The most damage to genetic material was observed in the Berrichon du Cher sheep, and the least in the Polish Heath sheep. The tests used are reliable biomarkers of genome stability in animal breeds, as well as in individuals within breeds.

SUMOylation of PCNA by PIAS1 and PIAS4 promotes template switch in the chicken and human B cell lines

DNA damage tolerance (DDT) releases replication blockage caused by damaged nucleotides on template strands employing two alternative pathways, error-prone translesion DNA synthesis (TLS) and error-free template switch (TS). Lys164 of proliferating cell nuclear antigen (PCNA) is SUMOylated during the physiological cell cycle. To explore the role for SUMOylation of PCNA in DDT, we characterized chicken DT40 and human TK6 B cells deficient in the PIAS1 and PIAS4 small ubiquitin-like modifier (SUMO) E3 ligases. DT40 cells have a unique advantage in the phenotypic analysis of DDT as they continuously diversify their immunoglobulin (Ig) variable genes by TLS and TS [Ig gene conversion (GC)], both relieving replication blocks at abasic sites without accompanying by DNA breakage. Remarkably, PIAS1 ^-/- /PIAS4 ^-/- cells displayed a multifold decrease in SUMOylation of PCNA at Lys164 and over a 90% decrease in the rate of TS. Likewise, PIAS1 ^-/- /PIAS4 ^-/- TK6 cells showed a shift of DDT from TS to TLS at a chemosynthetic UV lesion inserted into the genomic DNA. The PCNA ^K164R/K164R mutation caused a ∼90% decrease in the rate of Ig GC and no additional impact on PIAS1 ^-/- /PIAS4 ^-/- cells. This epistatic relationship between the PCNA ^K164R/K164R and the PIAS1 ^-/- /PIAS4 ^-/- mutations suggests that PIAS1 and PIAS4 promote TS mainly through SUMOylation of PCNA at Lys164. This idea is further supported by the data that overexpression of a PCNA-SUMO1 chimeric protein restores defects in TS in PIAS1 ^-/- /PIAS4 ^-/- cells. In conclusion, SUMOylation of PCNA at Lys164 promoted by PIAS1 and PIAS4 ensures the error-free release of replication blockage during physiological DNA replication in metazoan cells.

Mutagenic assessment of chemotherapy and Smac mimetic drugs in cells with defective DNA damage response pathways

DNA damaging therapies can spur the formation of therapy-related cancers, due to mis-repair of lesions they create in non-cancerous cells. This risk may be amplified in patients with impaired DNA damage responses. We disabled key DNA damage response pathways using genetic and pharmacological approaches, and assessed the impact of these deficiencies on the mutagenicity of chemotherapy drugs or the "Smac mimetic" GDC-0152, which kills tumor cells by targeting XIAP, cIAP1 and 2. Doxorubicin and cisplatin provoked mutations in more surviving cells deficient in ATM, p53 or the homologous recombination effector RAD51 than in wild type cells, but suppressing non-homologous end joining (NHEJ) by disabling DNA-PKcs prevented chemotherapy-induced mutagenesis. Vincristine-induced mutagenesis required p53 and DNA-PKcs but was not affected by ATM status, consistent with it provoking ATM-independent p53-mediated activation of caspases and CAD, which creates DNA lesions in surviving cells that could be mis-repaired by NHEJ. Encouragingly, GDC-0152 failed to stimulate mutations in cells with proficient or defective DNA damage response pathways. This study highlights the elevated oncogenic risk associated with treating DNA repair-deficient patients with genotoxic anti-cancer therapies, and suggests a potential advantage for Smac mimetic drugs over traditional therapies: a reduced risk of therapy-related cancers.

Warsaw breakage syndrome DDX11 helicase acts jointly with RAD17 in the repair of bulky lesions and replication through abasic sites

Warsaw breakage syndrome, a developmental disorder caused by mutations in the conserved DDX11/ChlR1 DNA helicase, shows features of genome instability partly overlapping with those of Fanconi anemia (FA). Here, using avian cellular models of DDX11 deficiency, we find that DDX11 functions as backup to the FA pathway and facilitates, jointly with the checkpoint clamp 9-1-1, a homologous recombination pathway of DNA bulky-lesion repair that does not affect replication fork speed and stalled fork stability. DDX11 also promotes diversification of the immunoglobulin-variable gene locus by facilitating hypermutation and gene conversion at programmed abasic sites that constitute endogenous replication blocks. The results suggest commonality between postreplicative gap filling and replication through abasic sites and pinpoint DDX11 as a critical player in both these processes.

Warsaw breakage syndrome, a developmental disorder caused by mutations in the DDX11/ChlR1 helicase, shows cellular features of genome instability similar to Fanconi anemia (FA). Here we report that DDX11-deficient avian DT40 cells exhibit interstrand crosslink (ICL)-induced chromatid breakage, with DDX11 functioning as backup for the FA pathway in regard to ICL repair. Importantly, we establish that DDX11 acts jointly with the 9-1-1 checkpoint clamp and its loader, RAD17, primarily in a postreplicative fashion, to promote homologous recombination repair of bulky lesions, but is not required for intra-S checkpoint activation or efficient fork progression. Notably, we find that DDX11 also promotes diversification of the chicken Ig-variable gene, a process triggered by programmed abasic sites, by facilitating both hypermutation and homeologous recombination-mediated gene conversion. Altogether, our results uncover that DDX11 orchestrates jointly with 9-1-1 and its loader, RAD17, DNA damage tolerance at sites of bulky lesions, and endogenous abasic sites. These functions may explain the essential roles of DDX11 and its similarity with 9-1-1 during development.

SPARTAN promotes genetic diversification of the immunoglobulin-variable gene locus in avian DT40 cells

Prolonged replication arrest on damaged templates is a cause of fork collapse, potentially resulting in genome instability. Arrested replication is rescued by translesion DNA synthesis (TLS) and homologous recombination (HR)-mediated template switching. SPARTAN, a ubiquitin-PCNA-interacting regulator, regulates TLS via mechanisms incompletely understood. Here we show that SPARTAN promotes diversification of the chicken DT40 immunoglobulin-variable λ gene by facilitating TLS-mediated hypermutation and template switch-mediated gene-conversion, both induced by replication blocks at abasic sites. SPARTAN^-/- and SPARTAN^-/-/Polη^-/-/Polζ^-/- cells showed defective and similar decrease in hypermutation rates, as well as alterations in the mutation spectra, with decreased dG-to-dC transversions and increased dG-to-dA transitions. Strikingly, SPARTAN^-/- cells also showed reduced template switch-mediated gene-conversion at the immunoglobulin locus, while being proficient in HR-mediated double strand break repair, and sister chromatid recombination. Notably, SPARTAN's ubiquitin-binding zinc-finger 4 domain, but not the PCNA interacting peptide domain or its DNA-binding domain, was specifically required for the promotion of immunoglobulin gene-conversion, while all these three domains were shown to contribute similarly to TLS. In all, our results suggest that SPARTAN mediates TLS in concert with the Polη-Polζ pathway and that it facilitates HR-mediated template switching at a subset of stalled replication forks, potentially by interacting with unknown ubiquitinated proteins.

Genotoxic and mutagenic studies of teratogens in developing rat and mouse

In this review, genotoxic and mutagenic effects of teratogenic chemical agents in both rat and mouse have been reviewed. Of these chemicals, 97 are drugs and 33 are pesticides or belong to other groups. Large literature searches were conducted to determine the effects of chemicals on chromosome abnormalities, sister chromatid exchanges, and micronucleus formation in experimental animals such as rats and mice. In addition, studies that include unscheduled DNA synthesis, DNA adduct formations, and gene mutations, which help to determine the genotoxicity or mutagenicity of chemicals, have been reviewed. It has been estimated that 46.87% of teratogenic drugs and 48.48% of teratogenic pesticides are positive in all tests. So, all of the teratogens involved in this group have genotoxic and mutagenic effects. On the other hand, 36.45% of the drugs and 21.21% of the pesticides have been found to give negative results in at least one test, with the majority of the tests giving positive results. However, only 4.16% of the drugs and 18.18% of the pesticides were determined to give negative results in the majority of the tests. Among tests with major negative results, 12.50% of the teratogenic drugs and 12.12% of the teratogenic pesticides were negative in all conducted tests.

Shielding effect of anethole against arsenic induced genotoxicity in cultured human peripheral blood lymphocytes and effect of GSTO1 polymorphism

Chronic exposure of inorganic arsenic compounds is responsible for the manifestation of various tumours as well as other diseases. The principal mechanism behind arsenic toxicity is the induction of a strong oxidative stress with production of free radicals in cells. The present study was aimed to explore the shielding effect of anethole against oxidative damage induced by arsenic in cultured human peripheral blood lymphocytes and the effect of GSTO1 polymorphism. Sister chromatid exchange (SCE) frequency, comet tail moment and lipid peroxidation levels were used as biomarkers to assess the oxidative damage. Heparinised venous blood was collected from healthy individuals and treated with sodium arsenite (50 µM) in the presence of anethole (25 and 50 µM) for the analysis of shielding effect of anethole. For the genotyping of GSTO1, PCR RFLP method was adopted. A significant dose-dependent increase in the frequency of SCEs, tail moment and lipid peroxidation levels, was observed when lymphocytes were treated with sodium arsenite. Anethole in combination with sodium arsenite has shown a dose-dependent significant decrease in the frequency of SCEs, tail moment and lipid peroxidation levels. Genetic polymorphism of GSTO1 was found to effect individual susceptibility towards arsenic-mediated genotoxicity and was found insignificant when antigenotoxic effect of anethole was considered. GSTO1 mutant genotypes were found to have significant higher genotoxicity of sodium arsenite as compared to wild-type genotype. The results of the present study suggest ameliorative effects of anethole against arsenic-mediated genotoxic damage in cultured human peripheral blood lymphocytes. A significant effect of GSTO1 polymorphism was observed on genotoxicity of sodium arsenite.

ATR/CHK1 inhibitors and cancer therapy

The cell cycle checkpoint proteins ataxia-telangiectasia-mutated-and-Rad3-related kinase (ATR) and its major downstream effector checkpoint kinase 1 (CHK1) prevent the entry of cells with damaged or incompletely replicated DNA into mitosis when the cells are challenged by DNA damaging agents, such as radiation therapy (RT) or chemotherapeutic drugs, that are the major modalities to treat cancer. This regulation is particularly evident in cells with a defective G1 checkpoint, a common feature of cancer cells, due to p53 mutations. In addition, ATR and/or CHK1 suppress replication stress (RS) by inhibiting excess origin firing, particularly in cells with activated oncogenes. Those functions of ATR/CHK1 make them ideal therapeutic targets. ATR/CHK1 inhibitors have been developed and are currently used either as single agents or paired with radiotherapy or a variety of genotoxic chemotherapies in preclinical and clinical studies. Here, we review the status of the development of ATR and CHK1 inhibitors. We also discuss the potential mechanisms by which ATR and CHK1 inhibition induces cell killing in the presence or absence of exogenous DNA damaging agents, such as RT and chemotherapeutic agents. Lastly, we discuss synthetic lethality interactions between the inhibition of ATR/CHK1 and defects in other DNA damage response (DDR) pathways/genes.

Zebularine induces replication-dependent double-strand breaks which are preferentially repaired by homologous recombination

Zebularine is a second-generation, highly stable hydrophilic inhibitor of DNA methylation with oral bioavailability that preferentially target cancer cells. It acts primarily as a trap for DNA methyl transferases (DNMTs) protein by forming covalent complexes between DNMT protein and zebularine-substrate DNA. It's well documented that replication-blocking DNA lesions can cause replication fork collapse and thereby to the formation of DNA double-strand breaks (DSB). DSB are dangerous lesions that can lead to potentially oncogenic genomic rearrangements or cell death. The two major pathways for repair of DSB are non-homologous end joining (NHEJ) and homologous recombination (HR). Recently, multiple functions for the HR machinery have been identified at arrested forks. Here we investigate in more detail the importance of the lesions induced by zebularine in terms of DNA damage and cytotoxicity as well as the role of HR in the repair of these lesions. When we examined the contribution of NHEJ and HR in the repair of DSB induced by zebularine we found that these breaks were preferentially repaired by HR. Also we show that the production of DSB is dependent on active replication. To test this, we determined chromosome damage by zebularine while transiently inhibiting DNA synthesis. Here we report that cells deficient in single-strand break (SSB) repair are hypersensitive to zebularine. We have observed more DSB induced by zebularine in XRCC1 deficient cells, likely to be the result of conversion of SSB into toxic DSB when encountered by a replication fork. Furthermore we demonstrate that HR is required for the repair of these breaks. Overall, our data suggest that zebularine induces replication-dependent DSB which are preferentially repaired by HR.

Distinct cellular phenotype linked to defective DNA interstrand crosslink repair and homologous recombination

Repair of DNA interstrand crosslinks (ICLs) predominantly involves the Fanconi anemia (FA) pathway and homologous recombination (HR). The HR repair system eliminates DNA double strand breaks (DSBs) that emerge during ICLs removal. The current study presents a novel cell line, CL-V8B, representing a new complementation group of Chinese hamster cell mutants hypersensitive to DNA crosslinking factors. CL-V8B exhibits increased sensitivity to various DNA-damaging agents, including compounds leading to DSBs formation (bleomycin and 6-thioguanine), and is extremely sensitive to poly (ADP-ribose) polymerase inhibitor (>400-fold), which is typical for HR-defective cells. In addition, this cell line exhibits a reduced number of spontaneous and induced sister chromatid exchanges, which suggests likely impairment of HR in CL-V8B cells. However, in contrast to other known HR mutants, CL-V8B cells do not show defects in Rad51 foci induction, but only slight alterations in the focus formation kinetics. CL-V8B is additionally characterized by a considerable chromosomal instability, as indicated by a high number of spontaneous and MMC-induced chromosomal aberrations, and a twice as large proportion of cells with abnormal centrosomes than that in the wild type cell line. The molecular defect present in CL-V8B does not affect the efficiency and stabilization of replication forks. However, stalling of the forks in response to replication stress is observed relatively rarely, which suggests an impairment of a signaling mechanism. Exposure of CL-V8B to crosslinking agents results in S-phase arrest (as in the wild type cells), but also in larger proportion of G₂/M-phase cells and apoptotic cells. CL-V8B exhibits similarities to HR- and/or FA-defective Chinese hamster mutants sensitive to DNA crosslinking agents. However, the unique phenotype of this new mutant implies that it carries a defect of a yet unidentified gene involved in the repair of ICLs.

Coordination of DNA single strand break repair

The genetic material of all organisms is susceptible to modification. In some instances, these changes are programmed, such as the formation of DNA double strand breaks during meiotic recombination to generate gamete variety or class switch recombination to create antibody diversity. However, in most cases, genomic damage is potentially harmful to the health of the organism, contributing to disease and aging by promoting deleterious cellular outcomes. A proportion of DNA modifications are caused by exogenous agents, both physical (namely ultraviolet sunlight and ionizing radiation) and chemical (such as benzopyrene, alkylating agents, platinum compounds and psoralens), which can produce numerous forms of DNA damage, including a range of "simple" and helix-distorting base lesions, abasic sites, crosslinks and various types of phosphodiester strand breaks. More significant in terms of frequency are endogenous mechanisms of modification, which include hydrolytic disintegration of DNA chemical bonds, attack by reactive oxygen species and other byproducts of normal cellular metabolism, or incomplete or necessary enzymatic reactions (such as topoisomerases or repair nucleases). Both exogenous and endogenous mechanisms are associated with a high risk of single strand breakage, either produced directly or generated as intermediates of DNA repair. This review will focus upon the creation, consequences and resolution of single strand breaks, with a particular focus on two major coordinating repair proteins: poly(ADP-ribose) polymerase 1 (PARP1) and X-ray repair cross-complementing protein 1 (XRCC1).

Cytogenetic biomarkers in detection of genotoxic effects of gestagens in peripheral blood lymphocytes in vitro and in vivo

Gestagens are the most frequently used steroid hormones in hormone-replacement therapy in the treatment of threatened miscarriage during the first trimester of pregnancy. This therapy has been applied in a large number of women with threatened abortion, despite various degrees of success of its efficacy. Genetic factors play a key role in miscarriages, especially in the initial stages. Cytogenetic biomarkers such as micronucleus (MN) test, chromosomal aberrations (CAs), and sister chromatid exchanges (SCEs) provide information on DNA damage. Cytogenetic markers detecting DNA damage have become very popular and useful in analysing genetic risk associated with hormone-replacement therapy. Cytogenetic studies presented heterogenous information. In many in vitro studies synthetic gestagens have been shown to induce genotoxic effects, and it was evaluated using three cytogenetic biomarkers. Genotoxic effects of gestagens have also been confirmed in in vivo studies that were conducted involving patients who received gestagen therapy during pregnancy and their newborns. However, some studies have shown that hormone-replacement therapy does not have genotoxic effects. In this paper, we summarize the results from previous studies. We also describe the usefulness of these biomarkers in the detection of genotoxic effects of hormone-replacement therapy.

Replication fork stability confers chemoresistance in BRCA-deficient cells

Brca1- and Brca2-deficient cells have reduced capacity to repair DNA double-strand breaks (DSBs) by homologous recombination (HR) and consequently are hypersensitive to DNA damaging agents, including cisplatin and poly(ADP-ribose) polymerase (PARP) inhibitors. Here we show that loss of the MLL3/4 complex protein, PTIP, protects Brca1/2-deficient cells from DNA damage and rescues the lethality of Brca2-deficient embryonic stem cells. However, PTIP deficiency does not restore HR activity at DSBs. Instead, its absence inhibits the recruitment of the MRE11 nuclease to stalled replication forks, which in turn protects nascent DNA strands from extensive degradation. More generally, acquisition of PARPi and cisplatin resistance is associated with replication fork (RF) protection in Brca2-deficient tumor cells that do not develop Brca2 reversion mutations. Disruption of multiple proteins, including PARP1 and CHD4, leads to the same end point of RF protection, highlighting the complexities by which tumor cells evade chemotherapeutic interventions and acquire drug resistance.

The Tumor-Associated Variant RAD51 G151D Induces a Hyper-Recombination Phenotype

The RAD51 protein plays a key role in the homology-directed repair of DNA double-strand breaks and is important for maintaining genome stability. Here we report on a novel human RAD51 variant found in an aggressive and therapy-refractive breast carcinoma. Expression of the RAD51 G151D variant in human breast epithelial cells increases the levels of homology-directed repair. Expression of RAD51 G151D in cells also promotes high levels of chromosomal aberrations and sister chromatid exchanges. In vitro, the purified RAD51 G151D protein directly and significantly enhances DNA strand exchange activity in the presence of RPA. In concordance with this result, co-incubation of G151D with BRCA2 resulted in a much higher level of strand-exchange activity compared to WT RAD51. Strikingly, the RAD51 G151D variant confers resistance to multiple DNA damaging agents, including ionizing radiation, mitomycin C, and doxorubicin. Our findings demonstrate that the RAD51 G151D somatic variant has a novel hyper-recombination phenotype and suggest that this property of the protein is important for the repair of DNA damage, leading to drug resistance.

Therapeutic resistance is a major hurdle for the treatment and eradication of cancer. Furthermore, the development of therapeutic resistance significantly decreases patient survival and negatively impacts the quality of life of patients battling cancer. Cancer cells utilize a number of previously described mechanisms in order to overcome sensitivity to cancer therapeutics, including overexpression of RAD51. However, in this study we report a novel gain-of-function heterozygous somatic variant, RAD51 G151D, identified in a highly refractory and aggressive breast adenocarcinoma. RAD51 G151D induces a hyper-recombination phenotype in human cells resulting in increased resistance to therapeutics via enhanced HDR of DSBs. We further demonstrate enhanced DNA strand exchange activity in the presence of RPA, providing a possible mechanism for the hyper-recombination phenotype observed in cells. Our study presents a novel hyper-recombinant RAD51 tumor-associated variant (RAD51 G151D), providing the first evidence that links altered RAD51 function with therapeutic resistance as well as a novel genetic marker to identify patients at high risk for aggressive and refractory disease.

PARP Inhibitors in Clinical Use Induce Genomic Instability in Normal Human Cells

Poly(ADP-ribose) polymerases (PARPs) are the first proteins involved in cellular DNA repair pathways to be targeted by specific inhibitors for clinical benefit. Tumors harboring genetic defects in homologous recombination (HR), a DNA double-strand break (DSB) repair pathway, are hypersensitive to PARP inhibitors (PARPi). Early phase clinical trials with PARPi have been promising in patients with advanced BRCA1 or BRCA2-associated breast, ovary and prostate cancer and have led to limited approval for treatment of BRCA-deficient ovary cancer. Unlike HR-defective cells, HR-proficient cells manifest very low cytotoxicity when exposed to PARPi, although they mount a DNA damage response. However, the genotoxic effects on normal human cells when agents including PARPi disturb proficient cellular repair processes have not been substantially investigated. We quantified cytogenetic alterations of human cells, including primary lymphoid cells and non-tumorigenic and tumorigenic epithelial cell lines, exposed to PARPi at clinically relevant doses by both sister chromatid exchange (SCE) assays and chromosome spreading. As expected, both olaparib and veliparib effectively inhibited poly-ADP-ribosylation (PAR), and caused marked hypersensitivity in HR-deficient cells. Significant dose-dependent increases in SCEs were observed in normal and non-tumorigenic cells with minimal residual PAR activity. Clinically relevant doses of the FDA-approved olaparib led to a marked increase of SCEs (5-10-fold) and chromatid aberrations (2-6-fold). Furthermore, olaparib potentiated SCE induction by cisplatin in normal human cells. Our data have important implications for therapies with regard to sustained genotoxicity to normal cells. Genomic instability arising from PARPi warrants consideration, especially if these agents will be used in people with early stage cancers, in prevention strategies or for non-oncologic indications.

SIRT7 promotes genome integrity and modulates non-homologous end joining DNA repair

Sirtuins, a family of protein deacetylases, promote cellular homeostasis by mediating communication between cells and environment. The enzymatic activity of the mammalian sirtuin SIRT7 targets acetylated lysine in the N-terminal tail of histone H3 (H3K18Ac), thus modulating chromatin structure and transcriptional competency. SIRT7 deletion is associated with reduced lifespan in mice through unknown mechanisms. Here, we show that SirT7-knockout mice suffer from partial embryonic lethality and a progeroid-like phenotype. Consistently, SIRT7-deficient cells display increased replication stress and impaired DNA repair. SIRT7 is recruited in a PARP1-dependent manner to sites of DNA damage, where it modulates H3K18Ac levels. H3K18Ac in turn affects recruitment of the damage response factor 53BP1 to DNA double-strand breaks (DSBs), thereby influencing the efficiency of non-homologous end joining (NHEJ). These results reveal a direct role for SIRT7 in DSB repair and establish a functional link between SIRT7-mediated H3K18 deacetylation and the maintenance of genome integrity.

Association of Polymorphisms of Phase I Metabolizing Genes with Sister Chromatid Exchanges in Occupational Workers Exposed to Toluene Used in Paint Thinners

This study investigated genetic damage in paint workers mainly exposed to toluene as it is a major solvent used in paint thinners. Sister chromatid exchange (SCE) assay was used as biomarker of genotoxicity. Blood samples were collected from 30 paint workers and 30 control subjects matched with respect to age and other confounding factors except for exposure to toluene. SCE frequency was found to be significantly higher in paint workers (4.81 ± 0.92) as compared to control individuals (1.73 ± 0.54) (p < 0.05). We also investigated influence of polymorphisms of CYP2E1 and CYP1A1m2 genes on SCE frequency. Our results showed that there was significant increase in frequencies of SCE among the mutant genotypes of CYP2E1 and CYP1A1m2 as compared to wild genotypes. Our study indicated that long term exposure of toluene can increase genotoxic risk in paint workers.

Spontaneous sister chromatid exchange in mitotic chromosomes of the chinchilla (Chinchilla lanigera)

Kuchta-Gładysz, M., Wójcik, E., Szeleszczuk, O., Niedbała, P. and Tyblewska, K. 2015. Spontaneous sister chromatid exchange in mitotic chromosomes of the chinchilla (Chinchilla lanigera). Can. J. Anim. Sci. 95: 543–550. The sister chromatid exchange (SCE) test is a cytogenetic tool with applications as a short-term screen. It is used to assess the influence of physical and chemical factors with potential mutagenic and genotoxic properties on the animal organism. The test results make it possible to eliminate mutagens, as well as helping to predict possible genetic consequences in animal cells and assess animal resistance. The mitotic chromosomes were obtained from an in vitro culture of peripheral blood lymphocytes with added bromodeoxyuridine (BrdU), at five different concentrations: 0.25, 0.5, 1.0, 2.5, and 5.0 µg mL−1. The chromosomes were stained according to the FPG method. Our analyses revealed the spontaneous SCE level in the chinchilla at the concentration of 0.5 µg mL−1. Higher concentrations of this substance have a genotoxic effect and cause damage to the DNA structure of the chromosomes by inducing additional SCEs in the chromosomes of this species. The mean SCE/cell incidence in the chinchilla population was 4.34±1.28. We investigated the effects of age on the incidence of SCE and found it significantly affected this phenomenon in both sexes.