DNA Double-strand Breaks Analysis Research Articles

Evaluation of the effect of intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc radiotherapy (VMAT) techniques on survival response in cell lines with a new radiobiological modeling.

The optimal radiobiological model, which assesses the biological effects of novel radiotherapy techniques that concurrently modify multiple physical factors, has not yet been defined. This study aimed to investigate the impact of intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT) on cellular response in head and neck cancer and melanoma models. Clonogenic analysis, DNA double-strand break analysis, apoptosis, and cell cycle analysis were performed on cancer stem cell models, cancer models, and normal tissue cell models to assess radiation sensitivity. The segmented radiation approach used in IMRT applications enhanced radiosensitivity and cytotoxicity in the cancer models, while changes in dose rate had varying effects on cytotoxicity depending on the tumor cell type. VMAT increased cellular resistance, favoring treatment outcomes. The biological processes were influenced differently by dose rate, IMRT, and VMAT depending on the tumor cell type. The selection of the most appropriate technique is crucial in representing new radiotherapy approaches. The obtained data can serve as a model to address clinical questions in daily practice. The integration of non-standard outcomes with standard applications should be considered in clinical settings.

Utilization of DNA double-strand breaks for biodosimetry of ionizing radiation exposure

Analysis of DNA double-strand breaks (DSBs) is an important novel tool to estimate the biological effects of ionizing radiation. Despite the large number of developed methods for assessing DNA damage, each method has its own advantages and disadvantages. In this paper we provide a review of the methods for assessing DSBs in DNA and the possibility of the practical use of such methods for biodosimetry of ionizing radiation exposure. Specifically, they include methods based on assessing the degree of DNA fragmentation (pulsed-field gel electrophoresis, DNA comet assay), enzymatic methods (terminal deoxynucleotidyl transferase dUTP nick end labeling) and methods based on the quantitative analysis of proteins involved in DNA DSBs repair (immunocytochemical analysis of foci of DNA repair proteins using fluorescence microscopy, analysis of DNA repair proteins using fluorescence flow cytometry, imaging flow cytometry). Utilization of DNA DSBs for biodosimetry of ionizing radiation exposure is a new niche for fast screening and is quite sensitive to reflect the biological importance of the radiation exposure.

Increase of DNA Damage and Alteration of the DNA Damage Response in Monoclonal B-Cell Lymphocytosis and Chronic Lymphocytic Leukemia

The increase of DNA damage and the alteration of the DNA damage response (DDR) are critical features of genetic instability presumably implicated in the pathogenesis of monoclonal B-cell lymphocytosis (MBL) and chronic lymphocytic leukemia (CLL). Immunofluorescence microscopy of γH2AX and 53BP1 was performed for the analysis of DNA double-strand breaks (DSB) in CD19+ lymphocytes of 6 healthy individuals, 6 MBL patients, 21 CLL patients and in cells of the CLL cell line HG-3. In addition, immunoblotting of p-ATM, p-ATR, p-CHK1, p-CHK2 and p-TP53 was used for the analysis of the DNA damage response (DDR). As compared to the γH2AX foci levels in healthy individuals (0.1 focus per CD19+ lymphocyte ± 0.0; mean ± standard error of mean) increased γH2AX foci levels were detected in MBL patients (0.3 focus per CD19+ lymphocyte ± 0.1), CLL patients (1.3 foci per CD19+ lymphocyte ± 0.3) and in cells of the cell line HG-3 (1.0 focus per cell). Particularly high γH2AX foci levels were observed in immunoglobulin heavy-chain variable-region (IGHV)-unmutated, 11q-deficient, 17p-deficient and TP53 -mutated CLL. Co-localization of γH2AX and 53BP1 indicated promotion of 53BP1-mediated nonhomologous end-joining (NHEJ) repair mechanisms at sites of DSB. Absent expression of p-CHK1 and p-TP53 suggested impaired G2/M checkpoint control and impaired apoptosis signaling in MBL and CLL. In summary, our results provide evidence for a continuous increase of DNA damage across the spectrum from MBL to CLL in conjunction with an impaired DDR. Particularly high γH2AX foci levels were detected in IGHV -unmutated, 11q-deficient, 17p-deficient and TP53 -mutated CLL. Moreover, abundant γH2AX/53BP1 foci suggested a critical role for (in)effective NHEJ repair mechanisms at sites of DSB in MBL and CLL.Figure legendsFig. 1. Analysis of γH2AX foci in MBL and CLL patient samples. (A) Fluorescence microscopic image of γH2AX foci (green, Alexa 488) in nuclei (blue, DAPI) of the sample CLL8. (B) γH2AX foci levels in CD19+ lymphocytes of healthy individuals, MBL and CLL patients. (C) γH2AX foci levels in CLL samples according to CD38 and ZAP-70 expression. (D) γH2AX foci levels in CLL samples according to the immunoglobulin heavy-chain variable-region mutational status. (E) γH2AX foci levels according to cytogenetic risk categories. The categories were defined by (1) harboring a normal karyotype, (2) a 13q deletion as sole aberration, (3) a 12q trisomy but not an 11q or 17p deletion, (4) an 11q deletion but not a 17p deletion and (5) a 17p deletion. (F) γH2AX foci levels according to gene mutation categories. The categories were defined (irrespective of the karyotype) by harboring (1) no mutations in SF3B1, NOTCH1 and TP53, (2) a SF3B1 mutation but not a TP53 mutation, (3) a NOTCH1 mutation but not a TP53 or SF3B1 mutation and (4) a TP53 mutation (irrespective of other mutations). Note: Each dot in the graphs B - F represents the mean γH2AX foci level of one sample. MBL, monoclonal B-cell lymphocytosis; CLL, chronic lymphocytic leukemia. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

DeepFoci: Deep learning-based algorithm for fast automatic analysis of DNA double-strand break ionizing radiation-induced foci

DNA double-strand breaks (DSBs), marked by ionizing radiation-induced (repair) foci (IRIFs), are the most serious DNA lesions and are dangerous to human health. IRIF quantification based on confocal microscopy represents the most sensitive and gold-standard method in radiation biodosimetry and allows research on DSB induction and repair at the molecular and single-cell levels. In this study, we introduce DeepFoci – a deep learning-based fully automatic method for IRIF counting and morphometric analysis. DeepFoci is designed to work with 3D multichannel data (trained for 53BP1 and γH2AX) and uses U-Net for nucleus segmentation and IRIF detection, together with maximally stable extremal region-based IRIF segmentation.The proposed method was trained and tested on challenging datasets consisting of mixtures of nonirradiated and irradiated cells of different types and IRIF characteristics – permanent cell lines (NHDFs, U-87) and primary cell cultures prepared from tumors and adjacent normal tissues of head and neck cancer patients. The cells were dosed with 0.5–8 Gy γ-rays and fixed at multiple (0–24 h) postirradiation times. Under all circumstances, DeepFoci quantified the number of IRIFs with the highest accuracy among current advanced algorithms. Moreover, while the detection error of DeepFoci remained comparable to the variability between two experienced experts, the software maintained its sensitivity and fidelity across dramatically different IRIF counts per nucleus. In addition, information was extracted on IRIF 3D morphometric features and repair protein colocalization within IRIFs. This approach allowed multiparameter IRIF categorization of single- or multichannel data, thereby refining the analysis of DSB repair processes and classification of patient tumors, with the potential to identify specific cell subclones.The developed software improves IRIF quantification for various practical applications (radiotherapy monitoring, biodosimetry, etc.) and opens the door to advanced DSB focus analysis and, in turn, a better understanding of (radiation-induced) DNA damage and repair.

Quantitative \u03b3-H2AX immunofluorescence method for DNA double-strand break analysis in testis and liver after intravenous administration of 111InCl3

BackgroundIt is well known that a severe cell injury after exposure to ionizing radiation is the induction of DNA double-strand breaks (DSBs). After exposure, an early response to DSBs is the phosphorylation of the histone H2AX molecule regions adjacent to the DSBs, referred to as γ-H2AX foci. The γ-H2AX assay after external exposure is a good tool for investigating the link between the absorbed dose and biological effect. However, less is known about DNA DSBs and γ-H2AX foci within the tissue microarchitecture after internal irradiation from radiopharmaceuticals. Therefore, in this study, we aimed to develop and validate a quantitative ex vivo model using γ-H2AX immunofluorescence staining and confocal laser scanning microscopy (CLSM) to investigate its applicability in nuclear medicine dosimetry research. Liver and testis were selected as the organs to study after intravenous administration of 111InCl3.ResultsIn this study, we developed and validated a method that combines ex vivo γ-H2AX foci labeling of tissue sections with in vivo systemically irradiated mouse testis and liver tissues. The method includes CLSM imaging for intracellular cell-specific γ-H2AX foci detection and quantification and absorbed dose calculations. After exposure to ionizing radiation from 111InCl3, both hepatocytes and non-hepatocytes within the liver showed an absorbed dose-dependent elevation of γ-H2AX foci, whereas no such correlation was seen for the testis tissue.ConclusionIt is possible to detect and quantify the radiation-induced γ-H2AX foci within the tissues of organs at risk after internal irradiation. We conclude that our method developed is an appropriate tool to study dose–response relationships in animal organs and human tissue biopsies after internal exposure to radiation.

Parameters Affecting the Antimicrobial Properties of Cold Atmospheric Plasma Jet.

Using the Taguchi method to narrow experimental parameters, the antimicrobial efficiency of a cold atmospheric plasma jet (CAPJ) treatment was investigated. An L9 array with four parameters of CAPJ treatments, including the application voltage, CAPJ-sample distance, argon (Ar) gas flow rate, and CAPJ treatment time, were applied to examine the antimicrobial activity against Escherichia coli (E. coli). CAPJ treatment time was found to be the most influential parameter in its antimicrobial ability by evaluation of signal to noise ratios and analysis of variance. 100% bactericidal activity was achieved under the optimal bactericidal activity parameters including the application voltage of 8.5 kV, CAPJ-sample distance of 10 mm, Ar gas flow rate of 500 sccm, and CAPJ treatment time of 300 s, which confirms the efficacy of the Taguchi method in this design. In terms of the mechanism of CAPJ’s antimicrobial ability, the intensity of hydroxyl radical produced by CAPJ positively correlated to its antimicrobial efficiency. The CAPJ antimicrobial efficiency was further evaluated by both DNA double-strand breaks analysis and scanning electron microscopy examination of CAPJ treated bacteria. CAPJ destroyed the cell wall of E. coli and further damaged its DNA structure, thus leading to successful killing of bacteria. This study suggests that optimal conditions of CPAJ can provide effective antimicrobial activity and may be grounds for a novel approach for eradicating bacterial infections.

Assessment of 213Bi-anti-EGFR MAb treatment efficacy in malignant cancer cells with [1-13C]pyruvate and [18F]FDG

Evaluation of response to therapy is among the key objectives of oncology. A new method to evaluate this response includes magnetic resonance spectroscopy (MRS) with hyperpolarized 13C-labelled metabolites, which holds promise to provide new insights in terms of both therapeutic efficacy and tumor cell metabolism. Human EJ28Luc urothelial carcinoma and LN18 glioma cells were treated with lethal activity concentrations of a 213Bi-anti-EGFR immunoconjugate. Treatment efficacy was controlled via analysis of DNA double-strand breaks (immunofluorescence γH2AX staining) and clonogenic survival of cells. To investigate changes in metabolism of treated cells vs controls we analyzed conversion of hyperpolarized [1-13C]pyruvate to [1-13C]lactate via MRS as well as viability of cells, lactate formation and lactate dehydrogenase activity in the cellular supernatants and [18F]FDG uptake in treated cells vs controls, respectively. Treatment of malignant cancer cells with 213Bi-anti-EGFR-MAb induced intense DNA double-strand breaks, resulting in cell death as monitored via clonogenic survival. Moreover, treatment of EJ28Luc bladder cancer cells resulted in decreased cell viability, [18F]FDG-uptake and an increased lactate export. In both EJ28Luc and LN18 carcinoma cells treatment with 213Bi-anti-EGFR-MAb triggered a significant increase in lactate/pyruvate ratios, as measured with hyperpolarized [1-13C]pyruvate. Treatment with 213Bi-anti-EGFR-MAb resulted in an effective induction of cell death in EJ28Luc and LN18 cells. Lactate/pyruvate ratios of hyperpolarized [1-13C]pyruvate proved to detect early treatment response effects, holding promise for future clinical applications in early therapy monitoring.

Detection of DNA Double-Strand Breaks Using Pulsed-Field Gel Electrophoresis.

DNA is one of the most biologically important targets of exogenous and endogenous toxicants as well as carcinogens. Damage to DNA can be of different types (e.g., DNA adducts, DNA protein cross-links, single-strand breaks, oxidized bases, abasic sites, and double-strand breaks (DSBs)). DSBs are considered the most lethal form of DNA damage for eukaryotic cells, and if left unrepaired or misrepaired, can cause cell death, chromosome instability, and cancer. DSBs can arise in the cells through different sources and can be distinguished as endogenous or exogenous DSBs. Exogenous sources can be chemotherapeutic drugs, irradiation, and environmental chemicals. The endogenous causes of DNA DSBs in the cells are mainly reactive oxygen species and faulty repair of oxidative clustered DNA lesions. Qualitative and quantitative analysis of DNA DSBs is of utmost importance to understand physiologically relevant cellular processes as well as to investigate the genotoxic or clastogenic effects of toxicants. Pulsed-field gel electrophoresis (PFGE) is a widely used method for direct quantification of DNA DSBs. In this method, the cells exposed to DSB-inducing agents are embedded in the agarose blocks and lysed. These agarose blocks containing DNA are then run under multiple electric fields which are at 120° angle, to aid in the movement of large DNA strands. It gives a direct and specific measure of DSBs unlike the foci-based assays. This chapter provides a brief overview of the various commonly used approaches to analyze DNA DSBs and describes the theory, advantages and method of PFGE, for use in cells exposed to DNA DSB inducing agents.

Higher Initial DNA Damage and Persistent Cell Cycle Arrest after Carbon Ion Irradiation Compared to X-irradiation in Prostate and Colon Cancer Cells.

The use of charged-particle beams, such as carbon ions, is becoming a more and more attractive treatment option for cancer therapy. Given the precise absorbed dose-localization and an increased biological effectiveness, this form of therapy is much more advantageous compared to conventional radiotherapy, and is currently being used for treatment of specific cancer types. The high ballistic accuracy of particle beams deposits the maximal dose to the tumor, while damage to the surrounding healthy tissue is limited. In order to better understand the underlying mechanisms responsible for the increased biological effectiveness, we investigated the DNA damage and repair kinetics and cell cycle progression in two p53 mutant cell lines, more specifically a prostate (PC3) and colon (Caco-2) cancer cell line, after exposure to different radiation qualities. Cells were irradiated with various absorbed doses (0, 0.5, and 2 Gy) of accelerated 13C-ions at the Grand Accélérateur National d’Ions Lourds facility (Caen, France) or with X-rays (0, 0.1, 0.5, 1, 2, and 5 Gy). Microscopic analysis of DNA double-strand breaks showed dose-dependent increases in γ-H2AX foci numbers and foci occupancy after exposure to both types of irradiation, in both cell lines. However, 24 h after exposure, residual damage was more pronounced after lower doses of carbon ion irradiation compared to X-irradiation. Flow cytometric analysis showed that carbon ion irradiation induced a permanent G2/M arrest in PC3 cells at lower doses (2 Gy) compared to X-rays (5 Gy), while in Caco-2 cells the G2/M arrest was transient after irradiation with X-rays (2 and 5 Gy) but persistent after exposure to carbon ions (2 Gy).

A multiparameter platform for the analysis of DNA double-strand breaks and associated biomarkers after genome editing

A multiparameter platform for the analysis of DNA double-strand breaks and associated biomarkers after genome editing

Analysis of DNA Double-Strand Breaks and Cytotoxicity after 7 Tesla Magnetic Resonance Imaging of Isolated Human Lymphocytes.

The global use of magnetic resonance imaging (MRI) is constantly growing and the field strengths increasing. Yet, only little data about harmful biological effects caused by MRI exposure are available and published research analyzing the impact of MRI on DNA integrity reported controversial results. This in vitro study aimed to investigate the genotoxic and cytotoxic potential of 7 T ultra-high-field MRI on isolated human peripheral blood mononuclear cells. Hence, unstimulated mononuclear blood cells were exposed to 7 T static magnetic field alone or in combination with maximum permissible imaging gradients and radiofrequency pulses as well as to ionizing radiation during computed tomography and γ-ray exposure. DNA double-strand breaks were quantified by flow cytometry and automated microscopy analysis of immunofluorescence stained γH2AX. Cytotoxicity was studied by CellTiter-Blue viability assay and [3H]-thymidine proliferation assay. Exposure of unstimulated mononuclear blood cells to 7 T static magnetic field alone or combined with varying gradient magnetic fields and pulsed radiofrequency fields did not induce DNA double-strand breaks, whereas irradiation with X- and γ-rays led to a dose-dependent induction of γH2AX foci. The viability assay revealed a time- and dose-dependent decrease in metabolic activity only among samples exposed to γ-radiation. Further, there was no evidence for altered proliferation response after cells were exposed to 7 T MRI or low doses of ionizing radiation (≤ 0.2 Gy). These findings confirm the acceptance of MRI as a safe non-invasive diagnostic imaging tool, but whether MRI can induce other types of DNA lesions or DNA double-strand breaks during altered conditions still needs to be investigated.

Suppression of radiation-induced DNA double-strand break repair by MyD88 is accompanied by apoptosis and crypt loss in mouse colon

Intestinal microbes promote the injurious effects of radiation on those tissues. However, the molecular factors mediating this effect are largely unknown. In this work, we explored the effects of orally administered antibiotics and MyD88, a key adapter molecule in toll-like receptor signaling, on molecular and cellular responses of mouse colon to radiation. Results show that oral antibiotics lowered radiation-induced colonic damage by protecting epithelial cells against radiation-induced apoptosis, leading to increased survival of crypts. MyD88 deficiency partially phenocopied the effects of oral antibiotics on apoptosis and crypt survival, suggesting that colonic microbes exert their injurious effects in part via that molecule. Analysis of DNA double-strand breaks, the primary genotoxic lesions induced by radiation, showed that their early induction in mouse colon was unaffected by MyD88. However, MyD88 deficiency resulted in the later disappearance of DNA double-strand breaks. Loss of DNA double-strand breaks was accompanied by the evidence of increased activation of both the non-homologous end-joining and homologous recombination pathways of DNA repair in MyD88-deficient mice. These results show that colonic microbes and MyD88 regulate DNA double-strand break repair in irradiated mouse colon, effects which exert significant control over radiation-induced apoptosis and crypt survival.

DNA Double-Strand Break Analysis by γ-H2AX Foci: A Useful Method for Determining the Overreactors to Radiation-Induced Acute Reactions Among Head-and-Neck Cancer Patients

Interindividual variability in normal tissue toxicity during radiation therapy is a limiting factor for successful treatment. Predicting the risk of developing acute reactions before initiation of radiation therapy may have the benefit of opting for altered radiation therapy regimens to achieve minimal adverse effects with improved tumor cure. DNA double-strand break (DSB) induction and its repair kinetics in lymphocytes of head-and-neck cancer patients undergoing chemoradiation therapy was analyzed by counting γ-H2AX foci, neutral comet assay, and a modified version of neutral filter elution assay. Acute normal tissue reactions were assessed by Radiation Therapy Oncology Group criteria. The correlation between residual DSBs and the severity of acute reactions demonstrated that residual γ-H2AX foci in head-and-neck cancer patients increased with the severity of oral mucositis and skin reaction. Our results suggest that γ-H2AX analysis may have predictive implications for identifying the overreactors to mucositis and skin reactions among head-and-neck cancer patients prior to initiation of radiation therapy.

Abstract LB-101: A novel role of semaphorin4a (sema4a) in genotoxin-induced DNA damage response in human lung fibroblasts

Abstract Dysregulation of DNA repair signaling after genotoxin exposure contributes to genomic instability and carcinogenesis. Hexavalent chromium [Cr(VI)] is a genotoxin of occupational and environmental concern. Protein tyrosine phosphatase (PTP) inhibitors (i.e., sodium orthovanadate (SOV)) activate key survival pathways. We reported that SOV enhances clonogenic survival after Cr(VI) exposure by overriding Cr-induced growth arrest in human lung fibroblasts (HLFs). PTP inhibition with SOV increased expression of DNA damage/repair genes as determined by microarray analysis. Kinetic analysis of DNA double-strand breaks (DSBs) by comet assay showed equal DSB formation 15 min after Cr(VI) exposure in the absence and presence of SOV. However, PTP inhibition significantly decreased DSBs 0.5-24 hr after Cr(VI) treatment. Aim of the present study was to determine the molecular mechanism(s) by which PTP inhibition affects DNA damage response during genotoxic stress. Gene expression was examined by DNA Damage Signaling Pathway PCR Array after 1 μM Cr(VI) treatment for 24 hr in the absence or presence of SOV. The PTP inhibitor reversed Cr-mediated changes in expression of several unique genes. Interestingly, the sema4a gene, known to be involved in T cell activation and endothelial cell proliferation and migration, was strongly induced by co-treatment of SOV and Cr(VI). Gene expression correlated with increased sema4a protein expression after co-treatment of SOV and Cr(VI). A potential role of sema4a in Cr-induced DNA DSB formation/repair in the absence or presence of SOV was assessed after sema4a siRNA transfection. Silencing of sema4a did not alter the effect of SOV on Cr-induced DSBs. However, sema4a silencing completely blocked Cr-induced DSBs 4 hr after exposure. These results suggest a novel role of sema4a in DNA DSB formation/repair in normal HLFs. Taken together, these data shed light on the emerging role of semaphorins as mediators of cell survival as well as potential therapeutic targets in carcinogenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-101.

DNA Double-strand Break Analysis by CHEF Electrophoresis

Pulsed-field gel electrophoresis (PFGE) has become a powerful tool for the study of high-molecular-weight DNA. In this technical note the application of clamped homogeneous electrical field (CHEF) electrophoresis for the determination of DNA double-strand breaks is described, and a number of parameters that influence the sensitivity of the assay are discussed. They include the concentration of the cell sample, agarose concentration in the plug and the electrophoresis gel, lysis conditions, pulse time, electric field gradient and the temperature of electrophoresis.

Eluting solution composition affects DNA double-strand break analysis by filter elution.

The filter elution technique was used to assay for 137Cs-induced DNA double-strand breaks (dsb) in V79 Chinese hamster cells. The elutions were performed using two different sets of lysing and eluting solutions at pH 7.2 and 9.6. The data agree with those of others who have demonstrated differences in elution profiles at pH 7.2 and 9.6. In addition, the data indicate that solution composition has a significant effect on elution.