NSF Award
9630735
The recent development of FISH (chromosome painting) technology has revolutionized radiobiology. The interpretation of the large amount of FISH data now being collected on chromosome aberrations can be greatly facilitated by computer codes modeling the mechanisms involved. Chromosome aberrations are molecular rearrangements following DNA double strand breakage. They are relevant to cell death, DNA damage repair, carcinogenesis, biological dosimetry and most other aspects of radiobiology. Significantly for this grant, aberration yields are influenced by large-scale chromosome geometry during cell-cycle interphase, and act as probes for the geometry. The geometry dependence is in the form of "proximity" effects, i.e. effects caused by chromosome localization within a cell nucleus and by spatial limitations on DNA double strand break induction or interactions. With the advent of (FISH), a rich spectrum of detail has become available in the 90's on various kinds of aberrations, including quite complicated ones. It is non-trivial to evaluate systematically the implications of the yield pattern for chromatin geometry and for the mechanics of double strand break reactions, because of multiple DNA double strand break interactions, of the dependence of yields on individual chromosome arm lengths, and of influence of radiation track geometry. In addition, different experiments often use different painting schemes, making more difficult intercomparisons or comparisons to older, non-FISH experiments. However, Monte Carlo methods are well-suited for analyzing the molecular reshufffling problems involved, and a code has been developed by members of our team and coworkers which gives methods for interpreting data, comparing experiments, and predicting; it uses only one adjustable parameter (corresponding to the radiation dose), and gives good results for some experimentally observed ratios, e.g. when comparing chromosomes of different lengths for aberration yields. Thi s algorithm does not incorporate the proximity effects discussed above, although there is clear experimental evidence, involving the ratio of ring aberrations to exchange aberrations or the ratio of complex aberrations to simple aberrations, that such a generalization is needed. Moreover, the code is applicable only to sparsely ionizing radiation, not to densely ionizing radiation, whose known geometric properties can lead to additional geometric information about the biological target. Consequently the code is not yet useful for analyzing the relations between aberration yields and chromosome geometry. The object of the grant is to develop better algorithms, which do incorporate geometric effects, and check them experimentally. The simplest new algorithm will incorporate proximity effects by an extension of the present code with just one extra adjustable parameter (for a total of two). Further extensions of the algorithms will use recently published data and quantitative models for large-scale interphase chromosome structure and cell nucleus ultrastructure. In addition, up-to-date algorithms for simulating ionizing radiation tracks will be developed and included, as will a number of technical refinements. The resulting algorithms will be tested by chromosome aberration experiments which use different cell types and different FISH painting schemes in a controlled comparison. The code will also be compared to experiments using sparsely or densely ionizing radiation reported in the literature from various laboratories, world wide. The algorithms will be used to critically test and extend modern models, including polymer models, for large-scale chromatin geometry during the Gl phase of the cell cycle. The work will be a joint effort by scientists with primary training in radiobiology, mathematics, cytogenetics, or radiation biophysics. Individual team members have extensive interdisciplinary experience in programming for biology. The algorithms developed will be important for the increasing number of scientists using FISH technology to study DNA damage processing, to probe chromosomal structure, or in applications.
