From DNA damage to chromosome aberrations: joining the break.

Despite many years of experimental studies on radiation-induced chromosomal aberrations, and the recent progress in elucidating the molecular mechanisms of the DNA damage response, the link between DNA double-strand break repair and its expression as microscopically visible chromosomal rearrangements remains, in many ways, obscure. Some long standing controversies have partially been resolved to the satisfaction of most investigators, including the linearity of the dose-response for DNA double-strand break induction, the necessity of pairwise interaction of radiogenic damaged sites in the formation of exchange aberrations, and the importance of proximity between lesions in misrejoining. However, the contribution of different molecular DNA repair mechanisms (e.g., alternative end-joining pathways) and their impact on the kinetics of aberration formation is still unclear, as is the definition of "complex" radiogenic damaged sites - in either the chemical or spatial sense - which ostensibly lead to chromosome rearrangements. These topics have been recently debated by molecular biologists and cytogeneticists, whose opinions are summarized in this paper.

Telomeres and DNA double-strand breaks: ever the twain shall meet?

Telomeres were first recognized as a bona fide constituent of the chromosome based on their inability to rejoin with broken chromosome ends produced by radiation. Today, we recognize two essential and interrelated properties of telomeres. They circumvent the so-called end-replication problem faced by genomes composed of linear chromosomes, which erode from their termini with each successive cell division. Equally vital is the end-capping function that telomeres provide, which is necessary to deter chromosome ends from illicit recombination. This latter property is critical in facilitating the distinction between the naturally occurring DNA double-strand breaks (DSBs) found at chromosome ends (i.e., telomeres) and DSBs produced by exogenous agents. Here we discuss, in a brief historical narrative, key discoveries that led investigators to appreciate the unique properties of telomeres in protecting chromosome ends, and the consequences of telomere dysfunction, particularly as related to recombination involving radiation-induced DSBs.

Strand-specific fluorescence in situ hybridization: the CO-FISH family.

The ability to prepare single-stranded chromosomal target DNA allows innovative uses of FISH technology for studies of chromosome organization. Standard FISH methodologies require functionally single-stranded DNAs in order to facilitate hybridization between the probe and the complementary chromosomal target sequence. This usually involves denaturation of double-stranded probes to induce temporary separation of the DNA strands. Strand-specific FISH (CO-FISH; Chromosome Orientation-FISH) involves selective removal of newly replicated strands from DNA of metaphase chromosomes which results in single-stranded target DNA. When single-stranded probes are then hybridized to such targets, the resulting strand-specific hybridization is capable of revealing a level of information previously unattainable at the cytogenetic level. Mammalian telomeric DNA consists of tandem repeats of the (TTAGGG) sequence, oriented 5'-->3' towards the termini of all vertebrate chromosomes. Based on this conserved structural organization, CO-FISH with a telomere probe reveals the absolute 5'-->3' orientation of DNA sequences with respect to the pter-->qter direction of chromosomes. Development and various applications of CO-FISH will be discussed: detection of cryptic inversions, discrimination between telomeres produced by leading- versus lagging-strand synthesis, and replication timing of mammalian telomeres.

Complex chromatid-isochromatid exchanges following irradiation with heavy ions?

We describe a peculiar and relatively rare type of chromosomal rearrangement induced in human peripheral lymphocytes that were ostensibly irradiated in G(0) phase of the cell cycle by accelerated heavy ions, and which, to the best of our knowledge, have not been previously described. The novel rearrangements which were detected using mFISH following exposure to 500 MeV/nucleon and 5 GeV/n 56Fe particles, but were not induced by either 137Cs gamma rays or 238Pu alpha particles, can alternatively be described as either complex chromatid-isochromatid or complex chromatid-chromosome exchanges. Different mechanisms potentially responsible for their formation are discussed.

Computer analysis of mFISH chromosome aberration data uncovers an excess of very complicated metaphases.

PURPOSE: To analyse spectra of chromosome aberrations induced in vitro by low LET radiation, in order to characterize radiation damage mechanisms quantitatively. METHODS: Multiplex fluorescence in situ hybridization (mFISH) allows the simultaneous identification of each homologous chromosome pair by its own colour. mFISH data, specifying number distributions for colour junctions in metaphases of human peripheral blood lymphocytes 72 hours after exposure in vitro to a 3 Gy gamma-ray dose, were combined with similar, previously published results. Monte Carlo computer implementations of radiobiological models for chromosome aberration production guided quantitative analyses, which took into account distribution of cells among different metaphases and lethal effects or preferential elimination of some aberrations at cell division. RESULTS AND CONCLUSIONS: Standard models of DNA damage induction/repair/misrepair explain the main trends of the data as regards the fraction of metaphases having a particular number of colours involved in colour junctions. However, all standard models systematically under-predict the observed fraction of metaphases where a large number of different chromosomes participate in aberrations. An early appearance of chromosomal instability could explain most of the discrepancies.

Strand-specific postreplicative processing of mammalian telomeres.

Telomeres are specialized nucleoprotein structures that stabilize the ends of linear eukaryotic chromosomes. In mammalian cells, abrogation of telomeric repeat binding factor TRF2 or DNA-dependent protein kinase (DNA-PK) activity causes end-to-end chromosomal fusion, thus establishing an essential role for these proteins in telomere function. Here we show that TRF2-mediated end-capping occurs after telomere replication. The postreplicative requirement for TRF2 and DNA-PKcs, the catalytic subunit of DNA-PK, is confined to only half of the telomeres, namely, those that were produced by leading-strand DNA synthesis. These results demonstrate a crucial difference in postreplicative processing of telomeres that is linked to their mode of replication.

Complex chromosome exchanges induced by gamma rays in human lymphocytes: an mFISH study.

Loucas, B. D. and Cornforth, M. N. Complex Chromosome Exchanges Induced by Gamma Rays in Human Lymphocytes: An mFISH Study. Radiat. Res. 155, 660-671 (2001). Combinatorial multi-fluor fluorescence in situ hybridization (mFISH) allows the simultaneous painting of each pair of homologous chromosomes, thereby eliminating many of the difficulties previously associated with the analysis of complex rearrangements. We employed mFISH to visualize exchanges in human lymphocytes and found significant frequencies of these aberrations after gamma-ray doses of 2 and 4 Gy. At 4 Gy, roughly half of the cells contained at least one complex exchange that required anywhere from 3 to 11 initial chromosome breaks. At this dose, more than 40% of gross cytogenetic damage, as measured by the total number of exchange breakpoints, was complex in origin. Both simple and complex exchanges were found to have nonlinear dose responses, although the latter showed significantly more upward curvature. In many cases, it could be deduced that the initial breaks leading to a particular complex exchange were proximate, meaning that the resulting broken chromosome ends all must have been capable of interacting freely during the exchange process. For other complex exchanges, the rearrangement could just as well have resulted from two or more simpler exchanges that occurred sequentially. The results demonstrate the utility of mFISH in visualizing intricacies of the exchange process, but also highlight the various sources of ambiguity concerning cytogenetic analysis that remain despite the power of this approach.

Analyzing radiation-induced complex chromosome rearrangements by combinatorial painting.

Cornforth, M. N. Analyzing Radiation-Induced Complex Chromosome Rearrangements by Combinatorial Painting. Radiat. Res. 155, 643-659 (2001). Prior to the advent of whole-chromosome painting, it was universally assumed that virtually all radiation-induced exchanges represented a simple rejoining between pairs of chromosome breaks. It is now known that a substantial proportion of such exchanges are actually complex, meaning that they involve the interaction of three (or more) breaks distributed among two (or more) chromosomes. The purpose of this review is to discuss some of the implications of aberration analysis using whole-chromosome painting, with emphasis given to newer combinatorial painting schemes that allow for the unambiguous identification of all homologous chromosome pairs. Such analysis requires reconsideration of how resulting information is to be handled for the purposes of tabulating and communicating raw data, quantifying aberration yields, and presenting experimental results in a cogent manner. Facilitating these objectives requires the introduction of certain concepts and terminologies that have no counterpart in conventional cytogenetic analyses.

Termini of human chromosomes display elevated rates of mitotic recombination.

The strand-specific in situ hybridization technique of CO-FISH was used to probe telomeres of human mitotic cells in order to determine the spontaneous frequency of crossover. This approach allowed the detection of recombinational crossovers occurring anywhere along the length of individual chromosomes, including reciprocal events taking place between sister chromatids. Although the process of sister chromatid exchange (SCE) is the most prominent type of recombination in somatic mammalian cells, our results show that SCEs accounted for less than a third of the recombinational events revealed by CO-FISH. It is concluded that chromosomal regions near the termini of chromosome arms undergo extraordinarily high rates of spontaneous recombination, producing terminal crossovers whose small size precludes detection by standard cytogenetic methods. That similar results were observed for transformed epithelial cells, as well as primary fibroblasts, suggests that the phenomenon is a common characteristic of human cells. These findings are noteworthy because, although telomeric and subtelomeric DNA is known to be preferentially involved in certain types of recombination, the tips of somatic mammalian chromosomes have not previously been identified as preferred sites for crossover. Implications of these results are discussed in terms of limitations imposed on CO-FISH for its proposed use in directional hybridization mapping.

Random breakage and reunion chromosome aberration formation model; an interaction-distance version based on chromatin geometry.

PURPOSE: Using published FISH data for chromosome aberration production in human fibroblasts by hard X-rays to test a breakage-and-reunion model. METHODS: The model assumed pairwise misrejoining, random apart from proximity effects, of DNA double-strand break (DSB) free ends. CAS (chromosome aberration simulator) Monte Carlo computer software implementing the model was modified to use a distance algorithm for misrejoining instead of using DSB interaction sites. The modification (called CAS2) allowed a somewhat more realistic approach to large-scale chromatin geometry, chromosome territories and proximity effects. It required adding a third adjustable parameter, the chromosome territory intersection factor, quantifying the amount of intertwining among different chromosomes. RESULTS: CAS2 gave somewhat better results than CAS. A reasonable fit with a few discrepancies was obtained for the frequencies at three different radiation doses of many different aberration types and of aberrations involving various specific chromosomes in a large data set using one-paint FISH scoring. The optimal average chromosome territory intersection factor was approximately 1.1, indicating that, for an arbitrarily chosen location in the nucleus, on average slightly more than two chromosomes have very nearby loci. Without changing the three parameter values, a fit was also obtained for a corresponding, smaller, two-paint data set. CONCLUSIONS: A random breakage-and-reunion model incorporating proximity effects by using a distance algorithm gave acceptable approximations for many details of hard X-ray aberration patterns. However, enough discrepancies were found that the possibility of an additional or alternate formation mechanism remains.

Postirradiation growth in HAT medium fails to eliminate the delayed appearance of 6-thioguanine-resistant clones in EJ30 human epithelial cells.

The latent effects of radiation-induced damage include "delayed" mutations that arise de novo in the progeny of nonmutant cells. We investigated the early stages of delayed mutagenesis at the HPRT locus of EJ30 human epithelial cells that were exposed to 4 Gy of 137Cs gamma rays. To eliminate directly induced "prompt" HPRT- mutants, cultures were grown in HAT medium before selection in 6-thioguanine was applied. Although irradiated cells were grown in HAT medium throughout the phenotypic expression period, mutant fractions some tenfold above spontaneous levels were observed subsequently; incubation in HAT medium did not cause an increase in mutations in unirradiated cells. We conclude that, in our experimental system, a significant proportion of induced mutation is of a delayed type. We speculate that the delayed induction is caused by an instability process that is a frequent and (typically) transient consequence of exposure of cells to ionizing radiation. The connection, if any, between this process and other manifestations of instability, including the acquisition of a "mutator phenotype," remains to be established.

Induction of chromosomal instability in human mammary cells by neutrons and gamma rays.

There is now substantial evidence that ionizing radiations can induce genomic instability in the form of chromosomal aberrations that appear several cell generations after irradiation. However, questions remain concerning the influence of radiation quality on this phenomenon. In this study, progeny of either gamma- or neutron-irradiated human epithelial MCF-10A cells were examined for chromosomal aberrations between 5 and 40 population doublings postirradiation. Exposure to either type of radiation resulted in an increase in chromatid-type gaps and breaks several doublings after the irradiation; no such effect was observed for chromosome-type aberrations. Neutron-irradiated cells showed consistently elevated frequencies of aberrations compared to nonirradiated controls at all times examined. Aberration frequencies for gamma-irradiated cells were not significantly different from controls until 20 to 35 population doublings postirradiation, where they increased 2-fold above background before returning to near control levels. To our knowledge these data represent the first evidence of chromosomal instability caused by neutron exposure. Results show that while either gamma rays or neutrons are capable of inducing similar types of delayed aberrations, the time course of their appearance can differ markedly.

Radiation-induced chromosomal instability in BALB/c and C57BL/6 mice: the difference is as clear as black and white.

Genomic instability has been proposed to be the earliest step in radiation-induced tumorigenesis. It follows from this hypothesis that individuals highly susceptible to induction of tumors by radiation should exhibit enhanced radiation-induced instability. BALB/c white mice are considerably more sensitive to radiation-induced mammary cancer than C57BL/6 black mice. In this study, primary mammary epithelial cell cultures from these two strains were examined for the "delayed" appearance of chromosomal aberrations after exposure to 137Cs gamma radiation, as a measure of radiation-induced genomic instability. As expected, actively dividing cultures from both strains showed a rapid decline of initial asymmetrical aberrations with time postirradiation. However, after 16 population doublings, cells from BALB/c mice exhibited a marked increase in the frequency of chromatid-type breaks and gaps which remained elevated throughout the time course of the experiment (28 doublings). No such effect was observed for the cells of C57BL/6 mice; after the rapid clearance of initial aberrations, the frequency of chromatid-type aberrations in the irradiated population remained at or near those of nonirradiated controls. These results demonstrate a correlation between the latent expression of chromosomal damage in vitro and susceptibility for mammary tumors, and provide further support for the central role of radiation-induced instability in the process of tumorigenesis.

CO-FISH reveals inversions associated with isochromosome formation.

Despite the likely prevalence and documented biological impact of inverted DNA sequences in humans and other species, our ability to detect them on a routine basis is limited. The technique of chromosome orientation fluorescence in situ hybridization (CO-FISH) was used to detect obligate chromosome inversions associated with isochromosome formation in two human cell lines. Simultaneous hybridization of a strand-specific telomeric probe allowed us to deduce the absolute orientation of repetitive DNA sequences associated with the inverted region. These results show that, in principle, CO-FISH could be used to detect virtually any type of inversion, including those likely to escape detection by other methods. Prospective applications of the technique are discussed in relation to its principal limitation, the present availability of suitable single-stranded DNA probes.

The effect of track structure on cell inactivation and chromosome damage at a constant LET of 120 keV/micrometer.

The influence of track structure on chromosome damage and cell inactivation are being investigated. Plateau-phase normal human fibroblast cultures were irradiated with gamma rays, and He, Ne and Ar ions. Particle velocities were chosen so that all beams had an LET of 120 keV/micrometer. In this constant-LET experimental design, the radial distribution of excitations and ionizations about the particle track is the most significant variable. Using premature chromosome condensation, chromatin breaks were measured at two time points, promptly after irradiation and after a prolonged incubation to allow for repair. These measurements give an indication of both initial chromosomal damage and also residual damage that is either not repaired or is misrepaired. Survival was measured under the same conditions. Results indicate that the RBEs for both cell inactivation and, to a lesser extent, chromosome damage decrease as particle energy increases.

A new method for detecting pericentric inversions using COD-FISH.

A new approach for detecting chromosomal inversions, based on the recently developed technique of chromosome orientation and direction fluorescence in situ hybridization (COD-FISH), is presented. COD-FISH is a strand-specific modification of standard FISH technology which allows the hybridization of single-stranded probes to one, and only one, chromatid of a metaphase chromosome. It can be used to determine the absolute 5'-to-3' direction of DNA target sequences with respect to the short-to-long arm direction of a given chromosome. Since an inversion reverses the orientation of DNA sequences within the inverted region, an inversion becomes detectable as a "switch" in probe signal from one chromatid to the other, when compared to a reference probe outside of the inverted region. Pericentric inversions in chromosomes 1, 8, 10, and X, which had previously been identified by chromosome banding, were analyzed by the COD-FISH technique. The results presented here demonstrate that COD-FISH can be used for the detection of pericentric inversions and that, in some instances, it provides additional information not obtainable by more conventional methods of cytogenetic analysis. Practical limitations of the COD-FISH technique are also discussed.

Latent expression of p53 mutations and radiation-induced mammary cancer.

EF42 is a clonally derived preneoplastic cell lineage from irradiated mouse mammary tissue, which becomes neoplastic with time in vitro or in vivo. We now report that multiple mutations in p53 occur before the acquisition of the neoplastic phenotype. The selective expansion of mutant cells is accompanied by loss of heterozygosity at the p53 locus and c-myc amplification. Although p53 mutations represent critical early events, our data argue these mutations were not directly induced by radiation but arose in the progeny of irradiated cells several cell generations later. The data are consistent with a multistep model of carcinogenesis that identifies genomic instability as the earliest step.

A proposed system for scoring structural aberrations detected by chromosome painting.

The advent of chromosome painting has brought the realization that structural aberrations can be far more complicated than previously imagined. Various investigators have devised their own nomenclature systems to deal with this difficulty, with the result that the terminology has become inconsistent and confusing. Recently, an international group of cytogeneticists experienced in chromosome painting gathered to address this issue. Results of the meeting are presented in this report, which provides a nomenclature system capable of describing chromosome aberrations that occur between painted and unpainted chromosomes, as well as aberrations involving only painted chromosomes. The nomenclature is flexible enough to describe accurately even the extensively rearranged chromosomes. As a consequence of this flexibility, the scheme upon which the nomenclature is based differs substantially from other systems of aberration classification. We call this system the Protocol for Aberration Identification and Nomenclature Terminology (PAINT).

RBE: mechanisms inferred from cytogenetics.

Cyclotron-accelerated heavy ion beams provide a fine degree of control over the physical parameters of radiation. Cytogenetics affords a view into the irradiated cell at the resolution of chromosomes. Combined they form a powerful means to probe the mechanisms of RBE. Cytogenetic studies with high energy heavy ion beams reveal three LET-dependent trends for 1) level of initial damage, 2) distribution of damage among cells, and 3) lesion severity. The number of initial breaks per unit dose increases from a low-LET plateau to a peak at approximately 180 keV/micrometer and declines thereafter. Overdispersion of breaks is significant above approximately 100 keV/micrometer. Lesion severity, indicated by the level of chromosomal fragments that have not restituted even after long repair times, increases with LET. Similar studies with very low energy 238Pu alpha particles (120 keV/micrometer) reveal higher levels of initial breakage per unit dose, fewer residual fragments and a higher level of misrepair when compared to high energy heavy ions at the same LET. These observations would suggest that track structure is an important factor in genetic damage in addition to LET.