Simulation of exon deletion mutations induced by low-LET radiation at the HPRT locus

Molecular Configuration of Human Genome Neighboring Megabase-Sized Large Deletions Induced by X-Ray Irradiation

The genomic landscape neighboring large deletions including the hypoxanthine-guanine phosphoribosyl transferase (HPRT) locus on human X chromosome in 6-thioguanine-resistant mutants originating from immortalized human fibroblast cells exposed to X rays was characterized by real-time quantitative PCR (qPCR)-based analyses. Among the 13 mutant clones with large deletions extending over several Mb, including the HPRT locus, revealed by 10 conventional sequence-tagged site (STS) markers, three clones bearing the largest deletions were selected for further qPCR analysis using another 21 STS markers and 15 newly designed PCR primer pairs. The results indicated that the major deletions were in very specific regions between the 130-Mb and 140-Mb positions containing the HPRT locus on the X chromosome and, contrary to our initial expectations, additional minor deletions were distributed in a patchwork pattern. These findings strongly indicate that the complex deletion patterns in the affected chromosome are related to the radiation track structure with spatially heterogeneous energy deposition and the specific structure of the chromatin-nuclear membrane complex. The uncovered complex deletion patterns are in agreement with the idea of complex chromatin damage, which is frequently associated with carcinogenesis.

A New Standard DNA Damage (SDD) Data Format

Our understanding of radiation-induced cellular damage has greatly improved over the past few decades. Despite this progress, there are still many obstacles to fully understand how radiation interacts with biologically relevant cellular components, such as DNA, to cause observable end points such as cell killing. Damage in DNA is identified as a major route of cell killing. One hurdle when modeling biological effects is the difficulty in directly comparing results generated by members of different research groups. Multiple Monte Carlo codes have been developed to simulate damage induction at the DNA scale, while at the same time various groups have developed models that describe DNA repair processes with varying levels of detail. These repair models are intrinsically linked to the damage model employed in their development, making it difficult to disentangle systematic effects in either part of the modeling chain. These modeling chains typically consist of track-structure Monte Carlo simulations of the physical interactions creating direct damages to DNA, followed by simulations of the production and initial reactions of chemical species causing so-called "indirect" damages. After the induction of DNA damage, DNA repair models combine the simulated damage patterns with biological models to determine the biological consequences of the damage. To date, the effect of the environment, such as molecular oxygen (normoxic vs. hypoxic), has been poorly considered. We propose a new standard DNA damage (SDD) data format to unify the interface between the simulation of damage induction in DNA and the biological modeling of DNA repair processes, and introduce the effect of the environment (molecular oxygen or other compounds) as a flexible parameter. Such a standard greatly facilitates inter-model comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter-model comparisons, this unified standard has the potential to greatly advance our understanding of the underlying mechanisms of radiation-induced DNA damage and the resulting observable biological effects when radiation parameters and/or environmental conditions change.

Ionizing radiation and genetic risks. XVII. Formation mechanisms underlying naturally occurring DNA deletions in the human genome and their potential relevance for bridging the gap between induced DNA double-strand breaks and deletions in irradiated germ cells

While much is known about radiation-induced DNA double-strand breaks (DSBs) and their repair, the question of how deletions of different sizes arise as a result of the processing of DSBs by the cell's repair systems has not been fully answered. In order to bridge this gap between DSBs and deletions, we critically reviewed published data on mechanisms pertaining to: (a) repair of DNA DSBs (from basic studies in this area); (b) formation of naturally occurring structural variation (SV) - especially of deletions - in the human genome (from genomic studies) and (c) radiation-induced mutations and structural chromosomal aberrations in mammalian somatic cells (from radiation mutagenesis and radiation cytogenetic studies). The specific aim was to assess the relative importance of the postulated mechanisms in generating deletions in the human genome and examine whether empirical data on radiation-induced deletions in mouse germ cells are consistent with predictions of these mechanisms. The mechanisms include (a) NHEJ, a DSB repair process that does not require any homology and which functions in all stages of the cell cycle (and is of particular relevance in G0/G1); (b) MMEJ, also a DSB repair process but which requires microhomology and which presumably functions in all cell cycle stages; (c) NAHR, a recombination-based DSB repair mechanism which operates in prophase I of meiosis in germ cells; (d) MMBIR, a microhomology-mediated, replication-based mechanism which operates in the S phase of the cell cycle, and (e) strand slippage during replication (involved in the origin of small insertions and deletions (INDELs). Our analysis permits the inference that, between them, these five mechanisms can explain nearly all naturally occurring deletions of different sizes identified in the human genome, NAHR and MMBIR being potentially more versatile in this regard. With respect to radiation-induced deletions, the basic studies suggest that those arising as a result of the operation of NHEJ/MMEJ processes, as currently formulated, are expected to be relatively small. However, data on induced mutations in mouse spermatogonial stem cells (irradiation in G0/G1 phase of the cell cycle and DSB repair presumed to be via NHEJ predominantly) show that most are associated with deletions of different sizes, some in the megabase range. There is thus a 'discrepancy' between what the basic studies suggest and the empirical observations in mutagenesis studies. This discrepancy, however, is only an apparent but not a real one. It can be resolved by considering the issue of deletions in the broader context of and in conjunction with the organization of chromatin in chromosomes and nuclear architecture, the conceptual framework for which already exists in studies carried out during the past fifteen years or so. In this paper, we specifically hypothesize that repair of DSBs induced in chromatin loops may offer a basis to explain the induction of deletions of different sizes and suggest an approach to test the hypothesis. We emphasize that the bridging of the gap between induced DSB and resulting deletions of different sizes is critical for current efforts in computational modeling of genetic risks.

Stochastic properties of radiation-induced DSB: DSB distributions in large scale chromatin loops, the HPRT gene and within the visible volumes of DNA repair foci

PURPOSE

We computed probabilities to have multiple double-strand breaks (DSB), which are produced in DNA on a regional scale, and not in close vicinity, in volumes matching the size of DNA damage foci, of a large chromatin loop, and in the physical volume of DNA containing the HPRT (human hypoxanthine phosphoribosyltransferase) locus.

MATERIALS AND METHODS

The model is based on a Monte Carlo description of DSB formation by heavy ions in the spatial context of the entire human genome contained within the cell nucleus, as well as at the gene sequence level.

RESULTS

We showed that a finite physical volume corresponding to a visible DNA repair focus, believed to be associated with one DSB, can contain multiple DSB due to heavy ion track structure and the DNA supercoiled topography. A corrective distribution was introduced, which was a conditional probability to have excess DSB in a focus volume, given that there was already one present. The corrective distribution was calculated for 19.5 MeV/amu N ions, 3.77 MeV/amu alpha-particles, 1000 MeV/amu Fe ions, and X-rays. The corrected initial DSB yield from the experimental data on DNA repair foci was calculated. The DSB yield based on the corrective function converts the focus yield into the DSB yield, which is comparable with the DSB yield based on the earlier PFGE experiments. The distribution of DSB within the physical limits of the HPRT gene was analyzed by a similar method as well.

CONCLUSION

This corrective procedure shows the applicability of the model and empowers the researcher with a tool to better analyze focus statistics. The model enables researchers to analyze the DSB yield based on focus statistics in real experimental situations that lack one-to-one focus-to-DSB correspondance.

hTERT-immortalized cells useful for analyzing effects of low-dose-rate radiation on human cells

To establish immortal human cells, we introduced the cDNA of the human telomere reverse transcriptase (hTERT) gene into skin fibroblast cells obtained from normal and ataxia telangiectasia (AT) individuals of Japanese origin. hTERT-immortalized cells retained their original characteristics and radiosensitivity except for immortalization, suggesting that these cells might be useful for analyzing the effects of radiation on human cells.hTERT-immortalized cells from a normal individual showed a greater resistance after low-dose-rate irradiation than after high-dose-rate irradiation. In contrast, cells from AT patients irradiated at a low-dose rate showed virtually the same survival as those irradiated at a high-dose rate. In hTERT-immortalized normal cells, the genetic effects of low-dose-rate radiation were quantitatively and qualitatively less severe than those of high-dose-rate radiation. In hTERT-immortalized AT cells, some fraction of DNA damage such as DNA double-strand breaks might not be repaired, and AT cells were severely affected by low-dose-rate radiation. The activation of ataxia telangiectasia mutated (ATM) protein was confirmed during low-dose-rate radiation, and may play an important role in repair of DNA damage induced by low-dose-rate radiation. This paper reviews briefly the current research at our laboratory. The hTERT-immortalized cells may be useful in determining the effects of low-dose and low-dose-rate radiation on human cells.

Cytotoxic and Mutagenic Effects of Chronic Low-Dose-Rate Irradiation onTERT-Immortalized Human Cells

To analyze the genetic effects of low-dose-rate radiation on human cells, we used human telomere reverse transcriptase (TERT)-immortalized fibroblast cells obtained from normal individuals. We studied the effect of low-dose-rate (0.3 mGy/ min) and high-dose-rate (2 Gy/min) radiation on cells in a confluent state. Survival and micronucleus induction frequency showed higher resistance after irradiation at low dose rate than at high dose rate. The survival after 5 Gy of high-dose-rate radiation was 0.01 compared to 0.3 after low-dose-rate irradiation at the same dose. In accordance with this, the level of HPRT mutation induction by low-dose-rate radiation decreased to approximately one-eighth that for high-dose-rate radiation. We then characterized the mutants by multiplex PCR analysis, which showed that the fraction of deletion mutations was lower in the mutant cells induced at low dose rate than at high dose rate. Furthermore, the size of the deletions in mutant cells induced by low-dose-rate radiation appeared to be smaller than those in mutant cells irradiated at high dose rate. Only a few exons were deleted in the former mutants while all exons were deleted in most of the latter mutants. The present study indicates that the genetic effects of low-dose-rate radiation on nonproliferating normal human cells are quantitatively and qualitatively less severe than the effect of high-dose-rate radiation.

Radiation research society 1952-2002. Physics as an element of radiation research

Since its inception in 1954, Radiation Research has published an estimated total of about 8700 scientific articles up to August 2001, about 520, or roughly 6%, of which are primarily related to physics. This average of about 11 articles per year indicates steadily continuing contributions by physicists, though there are appreciable fluctuations from year to year. These works of physicists concern radiation sources, dosimetry, instrumentation for measurements of radiation effects, fundamentals of radiation physics, mechanisms of radiation actions, and applications. In this review, we have selected some notable accomplishments for discussion and present an outlook for the future.