Mechanisms of induction and repair of DNA double-strand breaks by ionizing radiation: some contradictions

The out-of-field dose in radiation therapy induces delayed tumorigenesis by senescence evasion

A rare but severe complication of curative-intent radiation therapy is the induction of second primary cancers. These cancers preferentially develop not inside the planning target volume (PTV) but around, over several centimeters, after a latency period of 1–40 years. We show here that normal human or mouse dermal fibroblasts submitted to the out-of-field dose scattering at the margin of a PTV receiving a mimicked patient’s treatment do not die but enter in a long-lived senescent state resulting from the accumulation of unrepaired DNA single-strand breaks, in the almost absence of double-strand breaks. Importantly, a few of these senescent cells systematically and spontaneously escape from the cell cycle arrest after a while to generate daughter cells harboring mutations and invasive capacities. These findings highlight single-strand break-induced senescence as the mechanism of second primary cancer initiation, with clinically relevant spatiotemporal specificities. Senescence being pharmacologically targetable, they open the avenue for second primary cancer prevention.

Effects of Low-Dose X-Ray on Cell Growth, Membrane Permeability, DNA Damage and Gene Transfer Efficiency

Background

We aimed to reveal if low dose X-rays would induce harmful or beneficial effect or dual response on biological cells and whether there are conditions the radiation can enhance gene transfer efficiency and promote cell growth but without damage to the cells.

Method

A systematic study was performed on the effects of Kilo-V and Mega-V X-rays on the cell morphology, viability, membrane permeability, DNA damage, and gene transfection of 293 T and CHO cells.

Results

The Kilo-V X-rays of very low doses from 0.01 to 0.04 Gray in principle didn't induce any significant change in cell morphology, growth, membrane permeability, and cause DNA damage. The Mega-V X-ray had a damage threshold between 1.0 and 1.5 Gray. The 0.25 Gray Mega-V-X-ray could promote cell growth and gene transfer, while the 1.5 Gray Mega-V X-ray damaged cells.

Conclusion

The very low dose of KV X-rays is safe to cells, while the effects of Mega-V-X-rays are dose-dependent. Mega-V-X-rays with a dose higher than the damage threshold would be harmful, that between 1.0 -1.5 Gray can evoke dual effects, whereas 0.25 Gray MV X-ray is beneficial for both cell growth and gene transfer, thus would be suitable for radiation-enhanced gene transfection.

Regulation of DNA Damage Response and Homologous Recombination Repair by microRNA in Human Cells Exposed to Ionizing Radiation

Ionizing radiation may be of both artificial and natural origin and causes cellular damage in living organisms. Radioactive isotopes have been used significantly in cancer therapy for many years. The formation of DNA double-strand breaks (DSBs) is the most dangerous effect of ionizing radiation on the cellular level. After irradiation, cells activate a DNA damage response, the molecular path that determines the fate of the cell. As an important element of this, homologous recombination repair is a crucial pathway for the error-free repair of DNA lesions. All components of DNA damage response are regulated by specific microRNAs. MicroRNAs are single-stranded short noncoding RNAs of 20–25 nt in length. They are directly involved in the regulation of gene expression by repressing translation or by cleaving target mRNA. In the present review, we analyze the biological mechanisms by which miRNAs regulate cell response to ionizing radiation-induced double-stranded breaks with an emphasis on DNA repair by homologous recombination, and its main component, the RAD51 recombinase. On the other hand, we discuss the ability of DNA damage response proteins to launch particular miRNA expression and modulate the course of this process. A full understanding of cell response processes to radiation-induced DNA damage will allow us to develop new and more effective methods of ionizing radiation therapy for cancers, and may help to develop methods for preventing the harmful effects of ionizing radiation on healthy organisms.

Radiobiology at the forefront: Hanns Langendorff and two of his disciples

Hanns Langendorff (1902-1974) was an eminent radiobiologist and a visionary, who not only helped found the field, but also made significant scientific contributions. He was a member of the first editorial board of IJRB and actually published a paper in its first issue about the radio-protector 5-hydroxytryptamine. Langendorff started working in the field of radiobiology in 1929 and became director of the 'Radiologisches Institut' of Freiburg University in 1936. His studies impressively show the development of radiobiology over decades in areas such as radiation-induced cell death at various stages of development, as well as radiosensitivity of sea urchin, yeast and mammals. Using mice, Langendorff made many early discoveries about spermatogenesis, hematopoiesis, prenatal development, chromosomal damage and metabolic pathways after exposures to X-rays and neutrons. He also investigated aspects of target theory and dosimetry and developed personal dosimeters using films. After the atomic bomb catastrophes in Japan, Langendorff and his collaborators soon began research in mice related to acute radiation sickness and stimulated the development of radioprotectors by studying their mechanisms of action associated with cell death, as well as cellular and metabolic changes involved. Langendorff also trained a cadre of young scientists who advanced the field and brought it to its golden age in the seventies and the eighties. Research activities of two of his disciples are reviewed: Ulrich Hagen and the author. Both made significant contributions: Hagen mainly studying DNA-damage and repair in vitro as well in cells and the author investigating metabolic processes, cellular and chromosomal damage, prenatal effects, genomic instability, individual radio-sensitivity and their connections to cancer therapy.

Untargeted metabolite profiling reveals that nitric oxide bioynthesis is an endogenous modulator of carotenoid biosynthesis in Deinococcus radiodurans and is required for extreme ionizing radiation resistance

Deinococcus radiodurans (Drad) is the most radioresistant organism known. Although mechanisms that underlie the extreme radioresistance of Drad are incompletely defined, resistance to UV irradiation-induced killing was found to be greatly attenuated in an NO synthase (NOS) knockout strain of Drad (Δnos). We now show that endogenous NO production is also critical for protection of Drad against γ-irradiation (3000 Gy), a result of accelerated growth recovery, not protection against killing. NO-donor treatment rescued radiosensitization in Δnos Drad but did not influence radiosensitivity in wild type Drad. To discover molecular mechanisms by which endogenous NO confers radioresistance, metabolite profiling studies were performed. Untargeted LC-MS-based metabolite profiling in Drad quantified relative abundances of 1425 molecules and levels of 294 of these were altered by >5-fold (p < 0.01). Unexpectedly, these studies identified a dramatic perturbation in carotenoid biosynthetic intermediates in Δnos Drad, including a reciprocal switch in the pathway end-products from deoxydeinoxanthin to deinoxanthin. NO supplementation rescued these nos deletion-associated changes in carotenoid biosynthesis, and fully-restored radioresistance to wildtype levels. Because carotenoids were shown to be important contributors to radioprotection in Drad, our findings suggest that endogenously-produced NO serves to maintain a spectrum of carotenoids critical for Drad's ability to withstand radiation insult.

Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1

Adaptation of D. radiodurans cells to extreme irradiation environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans.

GammaH2AX and cancer

Histone H2AX phosphorylation on a serine four residues from the carboxyl terminus (producing gammaH2AX) is a sensitive marker for DNA double-strand breaks (DSBs). DSBs may lead to cancer but, paradoxically, are also used to kill cancer cells. Using gammaH2AX detection to determine the extent of DSB induction may help to detect precancerous cells, to stage cancers, to monitor the effectiveness of cancer therapies and to develop novel anticancer drugs.

Mutation rate and novel tt mutants of Arabidopsis thaliana induced by carbon ions

Irradiation of Arabidopsis thaliana by carbon ions was carried out to investigate the mutational effect of ion particles in higher plants. Frequencies of embryonic lethals and chlorophyll-deficient mutants were found to be significantly higher after carbon-ion irradiation than after electron irradiation (11-fold and 7.8-fold per unit dose, respectively). To estimate the mutation rate of carbon ions, mutants with no pigments on leaves and stems (tt) and no trichomes on leaves (gl) were isolated at the M2 generation and subjected to analysis. Averaged segregation rate of the backcrossed mutants was 0.25, which suggested that large deletions reducing the viability of the gametophytes were not transmitted, if generated, in most cases. During the isolation of mutants, two new classes of flavonoid mutants (tt18, tt19) were isolated from carbon-ion-mutagenized M2 plants. From PCR and sequence analysis, two of the three tt18 mutant alleles were found to have a small deletion within the LDOX gene and the other was revealed to contain a rearrangement. Using the segregation rates, the mutation rate of carbon ions was estimated to be 17-fold higher than that of electrons. The isolation of novel mutants and the high mutation rate suggest that ion particles can be used as a valuable mutagen for plant genetics.

Heavy ion-induced DNA double-strand breaks in yeast

Induction of DSBs in the diploid yeast, Saccharomyces cerevisiae, was measured by pulsed-field gel electrophoresis (PFGE) after the cells had been exposed on membrane filters to a variety of energetic heavy ions with values of linear energy transfer (LET) ranging from about 2 to 11,500 keV/microm, (241)Am alpha particles, and 80 keV X rays. After irradiation, the cells were lysed, and the chromosomes were separated by PFGE. The gels were stained with ethidium bromide, placed on a UV transilluminator, and analyzed using a computer-coupled camera. The fluorescence intensities of the larger bands were found to decrease exponentially with dose or particle fluence. The slope of this line corresponds to the cross section for at least one double-strand break (DSB), but closely spaced multiple breaks cannot be discriminated. Based on the known size of the native DNA molecules, breakage cross sections per base pair were calculated. They increased with LET until they reached a transient plateau value of about 6 x 10(-7) microm(2) at about 300-2000 keV/microm; they then rose for the higher LETs, probably reflecting the influence of delta electrons. The relative biological effectiveness for DNA breakage displays a maximum of about 2.5 around 100-200 keV/microm and falls below unity for LET values above 10(3) keV/microm. For these yeast cells, comparison of the derived breakage cross sections with the corresponding cross section for inactivation derived from the terminal slope of the survival curves shows a strong linear relationship between these cross sections, extending over several orders of magnitude.

Time-dose relationships in radiation-enhanced integration

PURPOSE

We have shown that ionizing radiation increases recombination, as manifested by increased stable transduction of both plasmid and adenoviral vectors. This paper reports the duration of increased recombination after irradiation.

MATERIALS AND METHODS

A549 or NIH/3T3 cells were transfected at various times after irradiation. Cells were also irradiated with several fractionation schemes and then transfected.

RESULTS

Enhanced integration (EI) is a very long-lived process, lasting at least 2-3 days after single radiation fractions. The duration of EI activation is radiation dose-dependent. The efficiency of EI is dependent on radiation dose and independent of fractionation, such that low dose-rate, fractionated and single radiation doses result in similar levels of EI when corrected for differences in cytotoxicity.

CONCLUSIONS

Radiation, given with fraction sizes and dose-rates used in clinical radiation therapy, induces a long-lived hyper-recombination state. Since radiotherapy is already a component of treatment for many malignancies and is integrated into radiation-gene therapy trials, an understanding of recombination events that improve gene delivery is important and timely.

Assessment of DNA damage induced by high-LET ions in human lymphocytes using the comet assay

The alkaline single-cell gel electrophoresis assay (comet assay) was used to analyze DNA damage induced in human lymphocytes by irradiation with high linear energy transfer (LET) ions. Our aim was to measure DNA breaks and to demonstrate the heterogeneity of the damage levels in a lymphocyte population irradiated with ions of different energies and LETs. Four experiments with heavy ions (Ar, C and U), as well as gamma-ray exposure, were conducted to enable comparisons. We demonstrated that the comet assay is able to assess the variability in DNA damage induced at the single cell level. The amount of DNA damage and its heterogeneity increased with particle fluence and LET, but saturated at high LETs. However, when expressed in terms of the mean dose, gamma-rays were more efficient than most of the ions used. The comet assay also allowed the detection of highly damaged cells (HDC), which were previously described as cells in late apoptotic stages. The rapid emergence of HDC in this study suggests that they were generated following ion irradiation-induced creation of DNA break clusters induced by ion exposure. Another clue was that the proportion of HDC increased with LET and fluence. We hypothesized that the LET threshold observed and the higher efficiency of low-LET radiation might be linked to the impossibility of measuring small DNA fragments in HDC.

A comparison of gamma and neutron irradiation on Raji cells: effects on DNA damage, repair, cell cycle distribution and lethality

The Comet assay (microgel electrophoresis) was used to study DNA damage in Raji cells, a B-lymphoblastoid cell line, after treatment with different doses of neutrons (0.5 to 16 Gy) or gamma rays (1.4 to 44.8 Gy). A better growth recovery was observed in cells after gamma-ray treatments compared with neutron treatments. The relative biological effectiveness (RBE) of neutron in cell killing was determined to be 2.5. Initially, the number of damaged cells per unit dose was approximately the same after neutron and gamma-ray irradiation. One hour after treatment, however, the number of normal cells per unit dose was much lower for neutrons than for gamma rays, suggesting a more efficient initial repair for gamma rays. Twenty-four hours after treatment, the numbers of damaged cells per unit dose of neutrons or gamma rays were again at comparable level. Cell cycle kinetic studies showed a strong G2/M arrest at equivalent unit dose (neutrons up to 8 Gy; gamma rays up to 5.6 Gy), suggesting a period in cell cycle for DNA repair. However, only cells treated with low doses (up to 2 Gy) seemed to be capable of returning into normal cell cycle within 4 days. For the highest dose of neutrons, decline in the number of normal cells seen at already 3 days after treatment was deeper compared with equivalent unit doses of gamma rays. Our present results support different mechanisms of action by these two irradiations and suggest the generation of locally multiply damaged sites (LMDS) for high linear energy transfer (LET) radiation which are known to be repaired at lower efficiency.

Molecular analysis of carbon ion-induced mutations in Arabidopsis thaliana

In order to elucidate the characteristics of the mutations induced by ion particles at the molecular level in plants, mutated loci in carbon ion-induced mutants of Arabidopsis were investigated by PCR and Southern blot analyses. In the present study, two lines of gl1 mutant and two lines of tt4 mutant were isolated after carbon ion-irradiation. Out of four mutants, one had a deletion, other two contained rearrangements, and one had a point-like mutation. From the present result, it was suggested that ion particles induced different kinds of alterations of the DNA and therefore they could produce various types of mutant alleles in plants.

The Drosophila grapes gene is related to checkpoint gene chk1/rad27 and is required for late syncytial division fidelity

BACKGROUND

Cell cycle checkpoints maintain the fidelity of the somatic cell cycle by ensuring that one step in the cell cycle is not initiated until a previous step has been completed. The extent to which cell cycle checkpoints play a role in the initial rapid embryonic divisions of higher eukaryotes is unclear. The initial syncytial divisions of Drosophila embryogenesis provide an excellent opportunity to address this issue as they are amenable to both genetic and cellular analysis. In order to study the relevance of cell cycle checkpoints in early Drosophila embryogenesis, we have characterized the maternal-effect grapes (grp) mutation, which may affect feedback control during early syncytial divisions.

RESULTS

The Drosophila grp gene encodes a predicted serine/threonine kinase and has significant homology to chk1/rad27, a gene required for a DNA damage checkpoint in Schizosaccharomyces pombe. Relative to normal embryos, embryos derived from grp-mutant mothers exhibit elevated levels of DNA damage. During nuclear cycles 12 and 13, alignment of the chromosomes on the metaphase plate was disrupted in grp-derived embryos, and the embryos underwent a progression of cytological events that were indistinguishable from those observed in normal syncytial embryos exposed to X-irradiation. The mutant embryos also failed to progress through a regulatory transition in Cdc2 activity that normally occurs during interphase of nuclear cycle 14.

CONCLUSION

We propose that the primary defect in grp-derived embryos is a failure to replicate or repair DNA completely before mitotic entry during the late syncytial divisions. This suggests that wild-type grp functions in a developmentally regulated DNA replication/damage checkpoint operating during the late syncytial divisions. These results are discussed with respect to the proposed function of the chk1/rad27 gene.

A discrete cell survival model including repair after high dose-rate of ionizing radiation

A discrete cell survival model has been developed that is represented by six parameters (gamma, delta, alpha, epsilon, kappa, and t0). It is assumed that, linearly with the dose, two types of lesions are generated, with the number per unit dose described by the parameters gamma and delta. The two types of lesions, irreparable (lethal damage abbreviated as LD) damage and reparable (potentially lethal damage abbreviated as PLD) damage, follow a Poisson statistic. The PLD can be either repaired by an enzymatic process or converted into a lethal damage by a time- and dose-dependent process. For repair of PLD a Michaelis-Menten kinetics has been assumed, described by the maximum velocity alpha of the process and the Michaelis-Menten constant, kappa. The unrepaired PLD are fixed and become lethal after replating. The applicability of the model was tested by fitting 11 experimental data sets obtained with different cell lines and variable repair times simulated by delayed plating recovery or inhibition of repair processes by different agents. It has been concluded from the results that the repair process is rather totally than partially saturated. Therefore, the model was adapted by assuming a zero-order reaction for the repair process. Good agreement between model assumptions and molecular mechanisms is obtained by assuming PLD and LD to be double-strand breaks. The model and the results obtained are discussed and compared with published results and experimental data.

Migration patterns in pulsed-field electrophoresis of DNA restriction fragments from log-phase mammalian cells after irradiation and incubation for repair

An assay system was developed to detect changes of restriction fragment profiles obtained after pulsed-field gel electrophoresis (PFGE) for DNA from mammalian cells that were irradiated and incubated for repair. DNA was prepared from irradiated log-phase human melanoma cells (MRI 221) after incubation for repair (6 h) and was digested with the rare-cutting restriction enzyme NotI (RE) prior to PFGE separation. DNA-fragment size distributions were compared to the respective PFGE profiles from unirradiated controls. After doses of 5 and 10 Gy (plus a 6-h incubation for repair), the relative amount of DNA retained in the plug during PFGE was increased. For higher doses (30 and 60 Gy), this phenomenon was superimposed by the residual fragmentation (25-30% of the initial breakage of 0.42 dsb/100 Mbp/Gy). Since irradiated cells accumulated in S phase during incubation for repair, a correction for the reduced electrophoretic migration of DNA from S-phase cells was necessary, and a 0.5% increase in DNA retention per 1% S-phase increment was found. However, the % retention for the 5 Gy plus repair sample was significantly higher than for the S-phase adjusted control (p < 0.01). Radiation induced DNA-protein crosslinks cannot account for the observed phenomenon because of the extensive proteolysis in DNA preparation, and also a loss of restriction enzyme recognition sites appear to be an unlikely explanation from simple quantitative considerations. Based on the recent observation of misrejoining during dsb repair, it is proposed that the incorrect joining of DNA ends also causes a more random distribution of replicating DNA in restriction fragments derived from cells in S phase after incubation for repair. This process would necessarily increase the proportion of DNA unable to migrate in PFGE.

Radiation-induced DNA damage in canine hemopoietic cells and stromal cells as measured by the comet assay

Stromal cell progenitors (fibroblastoid colony-forming unit; CFU-Fs) are representative of the progenitor cell population of the hemopoietic microenvironment in bone marrow (BM). Previous studies of the radiation dose-effect relationships for colony formation have shown that canine CFU-Fs are relatively radioresistant as characterized by a D0 value of about 2.4 Gy. In contrast, hemopoietic progenitors are particularly radiosensitive (D0 values= 0.12-0.60 Gy. In the present study, the alkaline single-cell gel electrophoresis technique for the in situ quantitation of DNA strand breaks and alkali-labile sites was employed. Canine buffy coat cells from BM aspirates and cells harvested from CFU-F colonies or from mixed populations of adherent BM stomal cell (SC) layers were exposed to increasing doses of X-rays, embedded in agarose gel on slides, lysed with detergents, and placed in an electric field. DNA migrating from single cells in the gel was made visible as "comets" by ethidium bromide staining. Immediate DNA damage was much less in cultured stromal cells than in hemopoietic cells in BM aspirates. These results suggest that the observed differences in clonogenic survival could be partly due to differences in the type of the initial DNA damage between stromal cells and hemopoietic cells.

The quality of DNA double-strand breaks: a Monte Carlo simulation of the end-structure of strand breaks produced by protons and alpha particles

The quality of DNA damage induced by protons and alpha-particles of various linear energy transfer (LET) was studied. The aim was to single out specific lesions in the DNA molecule that might lead to biological endpoints such as inactivation. A DNA model coupled with a track structure code (MOCA-15) were used to simulate the lesions induced on the two helixes. Four categories of DNA breaks were considered: single-strand breaks (ssb), blunt-ended double-strand breaks (dsb, with no or few overlapping bases), sticky-ended double-strand breaks (with cohesive free ends of many bases), and deletions (complex lesions which involve at least two dsb within a small number of base pairs). Calculations were carried out assuming various sets of parameters characterizing the production of these different DNA breaks. No large variations in the yields of ssb and blunt- or sticky-ended dsb were found in the LET range between 10 and 200 keV/mu m. On the other hand, the yield of deletions increases up to about 100 keV/mu m and seems to reach a plateau at higher LET values. In the LET interval from 30 to 60 keV/mu m, protons proved to be more efficient than alpha-particles in inducing deletions. The induction of these complex lesions is thus dependent not simply on LET but also on the characteristics of the track structure. Comparison with RBE values for cell killing shows that this special class of dsb might play an important role in radiation-induced cell inactivation.

Induction of DNA double-strand breaks in CHO-K1 cells by carbon ions

Radiation-induced DNA double-strand breaks (dsbs) were measured in CHO-K1 cells by means of an experimental approach involving constant-field gel electrophoresis and densitometric scanning of ethidium bromide stained gels. For X-irradiation, an induction efficiency of 36 +/- 5 dsbs (Gy x cell)-1 was determined. With this set-up, the induction of dsbs was investigated in CHO-K1 cells after irradiation with accelerated carbon ions with specific energies ranging from 2.7 to 261 MeV/u. This set of particle beams covers the important linear energy transfer (LET) range between 17 and 400 keV/microns, where maximum efficiencies have been reported for other cellular endpoints like inactivation or mutation induction. For LETs up to 100 keV/microns, RBEs of approximately 1 have been determined, while efficiencies per unit dose decline for higher LETs. No RBE maximum > 1 was found. Data are compared with published results on dsb induction in mammalian cells by radiations of comparable LET.

Simple and complex double-strand breaks induced by electrons

Biophysical modelling of DNA damage based on Monte Carlo simulation of charged particle tracks allows to describe radiation induced double-strand breaks (dsb) in a quantitative and qualitative way. Experimental and calculated data suggest that in the electron energy range from 50 eV to 1 MeV dsb can be grouped in simple and complex dsb. Complex dsb are mainly produced by low energy electrons with initial energies between approximately 200 and approximately 500 eV, whereas simple dsb are preferentially induced by energy transfers < 200 eV, which produce at least two ionizations.