Explanation for excessive DNA single-strand breaks and endogenous repair foci in pluripotent mouse embryonic stem cells.

Pluripotent mouse embryonic stem cells (mES cells) exhibit approximately 100 large gammaH2AX repair foci in the absence of measurable numbers of DNA double-strand breaks. Many of these cells also show excessive numbers of DNA single-strand breaks (>10,000 per cell) when analyzed using the alkaline comet assay. To understand the reasons for these unexpected observations, various methods for detecting DNA strand breaks were applied to wild-type mES cells and to mES cells lacking H2AX, ATM, or DNA-PKcs. H2AX phosphorylation and expression of other repair complexes were measured using flow and image analysis of antibody-stained cells. Results indicate that high numbers of endogenous gammaH2AX foci and single-strand breaks in pluripotent mES cells do not require ATM or DNA-PK kinase activity and appear to be associated with global chromatin decondensation rather than pre-existing DNA damage. This will limit applications of gammaH2AX foci analysis in mES cells to relatively high levels of initial or residual DNA damage. Excessive numbers of single-strand breaks in the alkaline comet assay can be explained by the vulnerability of replicating chromatin in mES cells to osmotic shock. This suggests that caution is needed in interpreting results with the alkaline comet assay when applied to certain cell types or after treatment with agents that make chromatin vulnerable to osmotic changes. Differentiation of mES cells caused a reduction in histone acetylation, gammaH2AX foci intensity, and DNA single-strand breakage, providing a link between chromatin structural organization, excessive gammaH2AX foci, and sensitivity of replicating mES cell chromatin to osmotic shock.

Mouse but not human embryonic stem cells are deficient in rejoining of ionizing radiation-induced DNA double-strand breaks.

Mouse embryonic stem (mES) cells will give rise to all of the cells of the adult mouse, but they failed to rejoin half of the DNA double-strand breaks (dsb) produced by high doses of ionizing radiation. A deficiency in DNA-PK(cs) appears to be responsible since mES cells expressed <10% of the level of mouse embryo fibroblasts (MEFs) although Ku70/80 protein levels were higher than MEFs. However, the low level of DNA-PK(cs) found in wild-type cells appeared sufficient to allow rejoining of dsb after doses <20Gy even in G1 phase cells. Inhibition of DNA-PK(cs) with wortmannin and NU7026 still sensitized mES cells to radiation confirming the importance of the residual DNA-PK(cs) at low doses. In contrast to wild-type cells, mES cells lacking H2AX, a histone protein involved in the DNA damage response, were radiosensitive but they rejoined double-strand breaks more rapidly. Consistent with more rapid dsb rejoining, H2AX(-/-) mES cells also expressed 6 times more DNA-PK(cs) than wild-type mES cells. Similar results were obtained for ATM(-/-) mES cells. Differentiation of mES cells led to an increase in DNA-PK(cs), an increase in dsb rejoining rate, and a decrease in Ku70/80. Unlike mouse ES, human ES cells were proficient in rejoining of dsb and expressed high levels of DNA-PK(cs). These results confirm the importance of homologous recombination in the accurate repair of double-strand breaks in mES cells, they help explain the chromosome abnormalities associated with deficiencies in H2AX and ATM, and they add to the growing list of differences in the way rodent and human cells deal with DNA damage.

Endogenous expression of phosphorylated histone H2AX in tumors in relation to DNA double-strand breaks and genomic instability.

Microscopically visible gammaH2AX foci signify the presence of DNA double-strand breaks (dsbs) in irradiated cells. However, large foci are also observed in untreated tumour cells, and high numbers reduce the sensitivity for detecting drug or radiation-induced DNA breaks. SW756 cervical carcinoma cells that express about 50 gammaH2AX foci per cell (i.e., equivalent to the number of breaks produced by about 2Gy) showed similar numbers of dsbs as C33A cells that exhibit fewer than three foci per cell. The possibility that differences in numbers of these endogenous foci could be explained by genomic instability perhaps related to misrepair was examined. For 17cell lines selected from the panel of NCI-60 tumor cells previously characterized for karyotypic complexity [A.V. Roschke, G. Tonon, K.S. Gehlhaus, N. McTyre, K.J. Bussey, S. Lababidi, D.A. Scudiero, J.N. Weinstein, I.R. Kirsch, Karyotypic complexity of the NCI-60 drug-screening panel, Cancer Res. 63 (2003) 8634-8647], there was a significant trend (r=0.6) for cell lines with greater numbers of structural or numerical chromosomal rearrangements to show a higher background expression of gammaH2AX. Moreover, cells from this panel with wild-type p53 showed a significantly lower background level of gammaH2AX than cells with mutant p53. To confirm the importance of p53 expression, endogenous and radiation-induced gammaH2AX expression were analyzed using four isogenic SKOV3 cell lines varying in p53 function. Again, higher gammaH2AX expression was found in SKOV3 cell lines expressing mutant p53 compared to wild-type p53. HFL-1 primary lung fibroblasts showed a progressive increase in gammaH2AX as they moved towards senescence, confirming the importance of telomere instability in the development of at least some gammaH2AX foci. Therefore, the explanation for high endogenous levels of gammaH2AX in some tumor cells appears to be multifactorial and may be best described as a consequence of chromatin instability.

Comparison between pimonidazole binding, oxygen electrode measurements, and expression of endogenous hypoxia markers in cancer of the uterine cervix.

BACKGROUND: Although tumor hypoxia has been associated with a more aggressive phenotype and lower cure rate, there is no consensus as to the method best suited for routine measurement. Binding of the chemical hypoxia marker, pimonidazole, and expression of the endogenous hypoxia markers HIF-1alpha and CAIX were compared for their ability to detect hypoxia in tumor biopsies from 67 patients with advanced carcinoma of the cervix. METHODS: Two biopsies were taken one day after administration of pimonidazole and were analyzed for pimonidazole binding using flow cytometry or immunohistochemistry. CAIX and HIF-1alpha expression and degree of colocalization were measured in sequential antibody-stained sections. Patient subsets were examined for tumor oxygen tension using an Eppendorf electrode, S phase DNA content, or change in HIF-1alpha expression over the course of treatment. RESULTS: Approximately 6% of the tumor area stained positive for pimonidazole, HIF-1alpha, or CAIX. The CAIX positive fraction correlated with the pimonidazole positive fraction (r = 0.60). Weaker but significant correlations were observed between pimonidazole and HIF-1alpha (r = 0.31) and CAIX and HIF-1alpha (r = 0.41). Taking the extent of marker colocalization into consideration increased the confidence that all markers were identifying hypoxic regions. Over 65% of stained areas showed a high degree of colocalization with the other markers. Oxygen microelectrode measurements and S phase fraction were not correlated with the hypoxic fraction measured using the three hypoxia markers. HIF-1alpha levels tended to decrease with time after the start of therapy. CONCLUSIONS: Endogenous hypoxia marker binding shows reasonable agreement, in extent and location, with binding of pimonidazole. CAIX staining pattern is a better match to the pimonidazole staining pattern than is HIF-1alpha, and high CAIX expression in the absence (or low levels) of HIF-1alpha may indicate a different biology.

Detection of etoposide resistance by measuring DNA damage in individual Chinese hamster cells.

The comet assay, which measures DNA strand breakage in individual cells, was used to examine the relation between DNA damage, cell survival, and resistance to the topoisomerase II inhibitor etoposide (VP-16). Chinese hamster V79-171b cells and a VP-16-resistant subline (VPr) were exposed to VP-16 as monolayers or spheroids. The comet assay was comparable in sensitivity to the DNA precipitation and alkali unwinding assays for detecting DNA strand breaks induced by VP-16. However, unlike conventional DNA damage assays, the comet assay also indicated heterogeneity in cell response. For V79 multicell spheroids exposed to VP-16, the external cycling cells were 50 times more sensitive to killing and DNA damage than the internal noncycling cells; the comet assay indicated the fraction of cells resistant to the drug. VPr cells, which were 10 times more resistant to killing and DNA damage by VP-16 than the parent cell line, could also be identified in mixed populations with the use of this method. These results suggest that the comet assay could be useful in predicting tumor cell response to DNA-damaging agents.

Multicell spheroid response to drugs predicted with the comet assay.

Multicell spheroids were exposed to DNA-damaging agents with the aim of determining whether prompt DNA damage could be predictive for cell killing and drug resistance. Chinese hamster V79 cells, SiHa human cervical carcinoma cells, and WiDr human colon carcinoma cells were grown as spheroids and exposed to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), 4-nitroquinoline-1-oxide (4NQO), doxorubicin, etoposide, actinomycin D, 1-(2-nitro-1-imidazolyl)-3-aziridino-2-propanol (RSU 1069), 3-amino-1,2,4-benzotriazine-1,4-dioxide (tirapazamine), and nitrogen mustard. Average DNA damage measured using the alkali comet assay generally correlated with cell killing irrespective of exposure times or drug concentration. However, better predictive power was achieved by using DNA damage levels in individual cells to identify the fraction of cells containing sufficient numbers of DNA strand breaks to cause death. Using this concept of a "threshold" for DNA damage, cell survival could be predicted for exposure to 4NQO, tirapazamine, nitrogen mustard, RSU 1069, and actinomycin D and was largely independent of cell type. The threshold value varied for each drug. For 4NQO, tirapazamine, and RSU 1069, DNA damage equivalent to about 10,000 strand breaks/cell was not toxic to cells of any spheroid type. Conversely, for actinomycin D, any DNA damage above background levels (approximately 100 breaks) was toxic for all three cell types. For some DNA-damaging drugs, the lack of correlation between DNA damage and cell killing was also informative. For etoposide and doxorubicin, no common threshold for cell killing could be determined, consistent with the hypothesis that DNA damage is only one of the actions of these drugs leading to cell death. For MNNG, the tail moment threshold varied significantly for the different spheroid types, probably indicating differences in repair. Overall, for five of the eight drugs, DNA damage measured using the comet assay was an effective and quantitative method of predicting drug cytotoxicity in complex multicelled systems.

DNA double-strand breaks measured in individual cells subjected to gel electrophoresis.

Microscopic examination of individual mammalian cells embedded in agarose, subjected to electrophoresis, and stained with a fluorescent DNA-binding dye provides a novel way of measuring DNA damage and more importantly, of assessing heterogeneity in DNA damage within a mixed population of cells. With this method, DNA double-strand breaks can be detected in populations of cells exposed to X-ray doses as low as 5 Gy. The radiation dose-response relationship for initial formation of double-strand breaks was identical for cell lines irradiated in G1, regardless of their sensitivity to killing by ionizing radiation. However, for cells irradiated in S phase, DNA migration was significantly reduced. For Chinese hamster V79 cells, Chinese hamster ovary cells, WiDr human colon carcinoma cells, and L5178Y-R mouse lymphoblastoid cells, S-phase DNA appeared to be about 3 times less sensitive to X-ray damage than DNA from other phases of the cell cycle. However, for the very radiosensitive L5178Y-S cells, the migration of replicating DNA was reduced only slightly. For Chinese hamster V79 and Chinese hamster ovary cells, damage was repaired at a similar rate in all cells of the population, and 85% of the breaks were rejoined within 2 h after irradiation. The radiosensitive L5178Y-S cells repaired damage more slowly than V79 or Chinese hamster ovary cells; 2 h after exposure to 50 Gy, approximately 50% of the damage was still present.

Lack of a correlation between radiosensitivity and DNA double-strand break induction or rejoining in six human tumor cell lines.

The neutral filter elution method and the neutral comet assay have been used to analyze radiation-induced DNA damage and repair in 6 human tumor cell lines: HT-144 melanoma; DU-145 prostate carcinoma; U-87 glioma; WiDr and HT-29 colon adenocarcinomas; and SiHa cervical carcinoma. In spite of large differences in intrinsic radiosensitivity measured using a clonogenic assay, double-strand break induction, rejoining rate, and amount of residual DNA damage 4 h after irradiation were similar among these cell lines when measured using the neutral comet assay. Differences in initial numbers of double-strand breaks were observed using the neutral filter elution method; however, there was no correlation with radiosensitivity, nor did the rejoining rate or amount of residual DNA damage measured using filter elution correlate with radiation sensitivity. We conclude that neither double-strand break assay is able to reliably rank cells according to clonogenic survival following irradiation.

Use of the comet assay to identify cells sensitive to tirapazamine in multicell spheroids and tumors in mice.

Tirapazamine, a bioreductive drug preferentially toxic to hypoxic cells, produces significant numbers of DNA single-strand breaks that can be detected using the alkaline comet assay. Our goal was to determine whether single-strand breaks measured using this assay could act as a surrogate end point for cell killing in multicell spheroids and solid tumors in mice. In spheroids composed of Chinese hamster V79 cells, WiDr human colon carcinoma cells, or SiHa human cervical carcinoma cells, histograms of tail moments (indicators of DNA damage in the comet assay) could be used to identify the percentage of cells that sustained sufficient DNA damage to cause cell death after treatment with tirapazamine. The proportion of comets with tail moments

Changes in subcellular distribution of topoisomerase IIalpha correlate with etoposide resistance in multicell spheroids and xenograft tumors.

The outer cells of Chinese hamster V79 spheroids are about 10 times more resistant than monolayers to DNA damage and cell killing by the topoisomerase (topo) II inhibitor etoposide. Although the amount and catalytic activity of topo IIalpha are identical for monolayers or the outer cells of spheroids, and the cell proliferation rate is the same, our previous results indicated that phosphorylation of topo IIalpha is at least 10 times higher in V79 monolayers than in spheroids. Because phosphorylation of topo IIalpha has been associated with nuclear translocation, we examined subcellular distribution of Topo IIalpha in monolayers, spheroids, and xenograft tumors using immunohistochemistry. Topo IIalpha was located predominantly in the nucleus of V79, human SiHa, and rat C6 monolayers but was found mainly in the cytoplasm of the proliferating outer cells of spheroids formed from these cell lines. Conversely, the outer cells of WiDr human colon carcinoma spheroids showed predominantly nuclear localization of topo IIalpha, and only WiDr cells showed no increase in resistance to etoposide when grown as spheroids. Cells sorted from xenografts resembled the spheroids in terms of sensitivity to etoposide and location of topo IIalpha. When the outer cells of V79 spheroids were returned to monolayer growth, the rate of redistribution of topo IIalpha to the nucleus occurred with similar kinetics as the increase in sensitivity to killing by etoposide. Removal and return of individual outer V79 spheroid cells to suspension culture resulted in the translocation of topo IIalpha to the nucleus for the first 24 h, accompanied by an increase in sensitivity to DNA damage by etoposide. Therefore, the cytoplasmic topo IIalpha distribution in outer spheroid cells and tumors appears to correlate not with morphological changes associated with growth in suspension but rather with the presence of neighboring, noncycling cells.

Growth of V79 cells as xenograft tumors promotes multicellular resistance but does not increase spontaneous or radiation-induced mutant frequency.

A Chinese hamster V79 xenograft model was developed to determine whether cells subjected to a hypoxic tumor microenvironment would be more likely to undergo mutation at the HPRT locus. V79-171b cells stably transfected with VEGF and EGFP were grown subcutaneously in immunodeficient NOD/ SCID mice. V79-VE tumors were characterized for host cell infiltration, doubling time, hypoxic fraction, vascular perfusion, and response to ionizing radiation. When irradiated in vitro, the mutant frequency for a given surviving fraction did not differ for cells grown in vivo or in vitro. Similar results were obtained using HCT116 human colorectal carcinoma cells grown as xenografts. However, V79-VE cells grown as xenografts were significantly more resistant to killing than monolayers. The background mutant frequency and the radiation-induced mutant frequency did not differ for tumor cells close to or distant from blood vessels. Similarly, tumor cells from well-perfused regions showed the same rate of strand break rejoining and the same rate of loss of phosphorylated histone H2AX as cells sorted from poorly perfused regions. Therefore, deleterious effects of the tumor microenvironment on DNA repair efficiency or mutation induction could not be demonstrated in these tumors. Rather, development of multicellular resistance in V79-VE tumors acted to reduce mutant frequency for a given dose of radiation.

Growth fraction measured using the comet assay.

Growth fraction, an important determinant of tumour response to therapy, was measured using a novel assay in WiDr human colon carcinoma cells grown as monolayers, spheroids, or xenografts. The assay is based on the fact that the anticancer agent etoposide produces DNA strand breaks in proliferating but not non-proliferating cells. Strand breaks were detected in individual cells using the alkaline 'comet' assay, and growth fraction was defined as the fraction of cells containing elevated numbers of DNA strand breaks. The specificity of the method for detecting proliferating cells was verified directly by allowing cells to incorporate bromodeoxyuridine (BrdUrd) into DNA, followed by exposure to etoposide and treatment of the comets with anti-BrdUrd antibodies. All cells stained with anti-BrdUrd antibodies were also damaged by etoposide. Similarly, growth fraction measured using Ki-67 correlated well with the new assay. The accuracy, speed and convenience of the comet assay for measuring growth fraction suggest that it may be useful for predicting response of human cancers to therapy.

Radiation-induced DNA double-strand breaks produced in histone-depleted tumor cell nuclei measured using the neutral comet assay.

Removal of histones and other nuclear proteins greatly enhances the sensitivity of mammalian cells to DNA damage by ionizing radiation. We examined the possibility that the ease of dissociation of histones, or the association of other nuclear proteins with DNA, may differ between radioresistant and sensitive human tumor cells. Cells embedded in agarose were exposed to increasing salt concentrations prior to irradiation and examination using a microscopic gel electrophoresis method, the neutral comet assay. Induction of double-strand breaks increased by a factor of about 20 when cells of four human tumor cell lines, HT144 melanoma, HT29 adenocarcinoma, DU145 prostate carcinoma and U87 glioma, were exposed to 2 M NaCl prior to irradiation. Subtle differences in sensitivity to induction of double-strand breaks by radiation between cells of the four cell lines were also observed after extraction with 0.7-1.1 M NaCl; however, no correlation with radiosensitivity was apparent. While a significant number of histone and non-histone proteins are present after extraction with 1.2 M NaCl, these proteins apparently have only a minor influence on radiosensitivity. However, if they are allowed to remain with DNA during electrophoresis, about 15 times more strand breaks are required to produce a similar amount of DNA migration in both DU145 and HT144 cells. These results suggest that the association between proteins and DNA within the nucleus, as probed by extraction with sodium chloride, does not help to explain differences in intrinsic radiosensitivity among cells of these diverse tumor cell lines.

Overnight lysis improves the efficiency of detection of DNA damage in the alkaline comet assay.

The ability to detect DNA damage using the alkaline comet assay depends on pH, lysis time and temperature during lysis. However, it is not known whether different lysis conditions identify different types of DNA damage or simply measure the same damage with different efficiencies. Results support the latter interpretation for radiation, but not for the alkylating agent MNNG. For X-ray-induced damage, cells showed the same amount of damage, regardless of lysis pH (12.3 compared to >13). However, increasing the duration of lysis at 5 degrees C from 1 h to more than 6 h increased the amount of DNA damage detected by almost twofold. Another twofold increase in apparent damage was observed by conducting lysis at room temperature (22 degrees C) for 6 h, but at the expense of a higher background level of DNA damage. The oxygen enhancement ratio and the rate of rejoining of single-strand breaks after irradiation were similar regardless of pH and lysis time, consistent with more efficient detection of strand breaks rather than detection of damage to the DNA bases. Conversely, after MNNG treatment, DNA damage was dependent on both lysis time and pH. With the higher-pH lysis, there was a reduction in the ratio of oxidative base damage to strand breaks as revealed using treatment with endonuclease III and formamidopyrimidine glycosylase. Therefore, our current results support the hypothesis that the increased sensitivity of longer lysis at higher pH for detecting radiation-induced DNA damage is due primarily to an increase in efficiency for detecting strand breaks, probably by allowing more time for DNA unwinding and diffusion before electrophoresis.

Radiation-induced apoptosis measured in TK6 human B lymphoblast cells using the comet assay.

The comet assay, a sensitive method of measuring DNA strand breaks in individual cells, is also capable of identifying apoptotic cells which contain highly fragmented DNA. This method requires embedding cells in agarose, lysing cells to remove proteins, and providing a brief exposure to an electric field to allow broken pieces of DNA to migrate. TK6 human B lymphoblast cells undergo fragmentation which is dependent on both time after irradiation and radiation dose. While some TK6 cells undergo apoptosis within 2 h after irradiation, the fragmentation rate increases approximately 10 h after exposure to radiation doses of 2.5 to 15 Gy. Results confirm that apoptosis is a very rapid event since few cells with intermediate amounts of DNA damage were detected. The comet assay detected apoptotic TK6 cells much earlier than a flow cytometry method.

Development of apoptosis and polyploidy in human lymphoblast cells as a function of position in the cell cycle at the time of irradiation.

The TK6 and WI-L2-NS human lymphoblast cell lines are derived from the same donor, but WI-L2-NS cells are more resistant to killing by ionizing radiation and also contain a mutation in the coding region of the p53 gene which delays the appearance of apoptosis. To determine whether the difference in radiosensitivity is a result of the slower rate of appearance of apoptosis (referred to as the rate of apoptosis) or to other factors related to the function of p53 such as the G1-phase checkpoint, we have examined the clonogenicity and rates of apoptosis in synchronous populations of these two cell lines as a function of time after exposure to x-rays. The greater radiosensitivity of G1-phase TK6 cells compared to G1-phase WI-L2-NS cells appeared adequate to explain the difference in radiosensitivity of asynchronous cultures. However, TK6 cells irradiated in G1 phase underwent apoptosis about three times more slowly than cells irradiated in other phases of the cycle, cautioning against equating more rapid apoptosis with greater radiosensitivity. The slower rate of apoptosis of G1-phase TK6 cells could not be explained by a radiation-induced block in G1 phase since there was only a short delay in exit of cells from G1 phase. Giant cells (primarily polyploid) were formed after irradiation of WI-L2-NS but not TK6 cells, and fewer giant cells were observed 3-4 days after irradiation in WI-L2-NS cells irradiated in S phase than cells irradiated in other phases. Giant cells were lost from the population through apoptosis which occurred in a synchronous fashion in the multiple nuclei. These results highlight interesting differences in the pattern of cell death between the two cell lines and suggest that the response of TK6 cells in G1 phase, which has the slowest rate of appearance of apoptosis in spite of the fact that it is the most radiosensitive phase for clonogenic survival, may be largely responsible for the reduced shoulder on the radiation survival curve for TK6 cells compared with WI-L2-NS cells.

Radiation-induced DNA base damage detected in individual aerobic and hypoxic cells with endonuclease III and formamidopyrimidine-glycosylase.

X-ray-induced DNA base damage can be detected using endonuclease III and formamidopyrimidine-glycosylase, which create DNA strand breaks at enzyme-sensitive sites. Strand breaks can then be measured with excellent sensitivity using the alkaline comet assay, a single-cell gel electrophoresis method that detects DNA damage in individual cells. In using this approach to measure the oxygen enhancement ratio (OER) for radiation-induced base damage, we observed that the number of enzyme-sensitive sites increased with dose up to 4 Gy in air and 12 Gy in hypoxic WIL2NS cells. After rejoining of radiation-induced strand breaks, base damage was detected more easily after higher doses. The number of radiation-induced enzyme-sensitive sites was similar under both air and nitrogen. Base damage produced by hydrogen peroxide and 4-nitroquinoline-N-oxide (4NQO) was also measured. Results with hydrogen peroxide (20 min at 4 degrees C) were similar to those observed for X rays, indicating that enzyme-sensitive sites could be detected most efficiently when few direct strand breaks were present. Removing DNA-associated proteins before irradiation did not affect the ability to detect base damage. Base damage produced by 4NQO (30 min at 37 degrees C) was readily apparent after treatment with low concentrations of the drug when few 4NQO-induced strand breaks were present, but the detection sensitivity decreased rapidly as direct strand breaks increased after treatment with higher concentrations. We conclude that: (1) the OER for base damage is approximately 1.0, and (2) the presence of direct DNA strand breaks (>2000-4000 per cell) prevents accurate detection of base damage measured as enzyme-sensitive sites with the alkaline comet method.

Heterogeneity in radiation-induced DNA damage and repair in tumor and normal cells measured using the "comet" assay.

A method for measuring DNA damage to individual cells, based on the technique of microelectrophoresis, was described by Ostling and Johanson in 1984 (Biochem. Biophys. Res. Commun. 123, 291-298). Cells embedded in agarose are lysed, subjected briefly to an electric field, stained with a fluorescent DNA-binding stain, and viewed using a fluorescence microscope. Broken DNA migrates farther in the electric field, and the cell then resembles a "comet" with a brightly fluorescent head and a tail region which increases as damage increases. We have used video image analysis to define appropriate "features" of the comet as a measure of DNA damage, and have quantified damage and repair by ionizing radiation. The assay was optimized for lysing solution, lysing time, electrophoresis time, and propidium iodide concentration using Chinese hamster V79 cells. To assess heterogeneity of response of normal versus malignant cells, damage to both tumor cells and normal cells within mouse SCC-VII tumors was assessed. Tumor cells were separated from macrophages using a cell-sorting method based on differential binding of FITC-conjugated goat anti-mouse IgG. The "tail moment", the product of the amount of DNA in the tail and the mean distance of migration in the tail, was the most informative feature of the comet image. Tumor and normal cells showed significant heterogeneity in damage produced by ionizing radiation, although the average amount of damage increased linearly with dose (0-15 Gy) and suggested similar net radiosensitivities for the two cell types. Similarly, DNA repair rate was not significantly different for tumor and normal cells, and most of the cells had repaired the damage by 30 min following exposure to 15 Gy. The heterogeneity in response did not appear to be a result of differences in response through the cell cycle.

Higher-order chromatin structure-dependent repair of DNA double-strand breaks: factors affecting elution of DNA from nucleoids.

The nuclear matrix is increasingly identified with the processing of DNA damage. Previous work has suggested that association of DNA with the matrix can influence the repair of DNA double-strand breaks (DSBs) and the sensitivity of mammalian cells to ionizing radiation. By selectively examining DSBs that occur as multiples (multiple DSBs) within looped DNA structures, we have identified a subset of DSBs that repair with slow kinetics through the V(D)J recombination-associated DSB repair pathway. Enrichment of S-phase populations by centrifugal elutriation and selective examination of nascent DNA by pulse-labeling were used to demonstrate that elution of DNA from nucleoids is retarded by the presence of replicating DNA. Previously, application of a Poisson-based model of induction of multiple DSBs and DNA elution to a panel of mammalian cell lines indicated that the size of the looped chromatin domains varied between cell lines. The data presented here explain the range in domain sizes between cells as the result of differences in the percentage of cells actively replicating their DNA. Correction of the model to account for S-phase populations results in a looped domain size of 2.9 Mbp independent of cell type. Single-cell gel electrophoresis of nucleoids provides additional evidence for such sized structures. Stabilization of DNA to elution during S phase does not permit repair of DSBs in the DSB repair mutants xrs5 and St.SCID, both defective for the DSB repair pathway associated with V(D)J recombination.