Biologic Basis of Radiation Oncology

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Chapter 1 Biologic Basis of Radiation Oncology

What Is Radiation Biology?

In the most general sense, radiation biology is the study of the effects of electromagnetic radiation on biologic systems. Three aspects of this definition deserve special mention. First, “effects” may include everything from DNA damage to genetic mutations, chromosome aberrations, cell killing, disturbances in cell cycle transit and cell proliferation, neoplastic transformation, early and late effects in normal tissues, teratogenesis, cataractogenesis, and carcinogenesis, to name but a few. Second, “electromagnetic radiation” refers to any type of radiant energy in motion with wave and/or particulate characteristics that has the capacity to impart some or all of its energy to the medium through which it passes. The amount of energy deposited can vary over some 25 orders of magnitude, depending on the type of electromagnetic radiation. For example, 1-kHz radio waves have energies in the range of 10−11 to 10−12 eV, whereas x rays or gamma rays may have energies of 10 MeV or more. The more energetic forms of electromagnetic radiation, the so-called ionizing radiations, deposit energy as they traverse the medium by setting secondary particles in motion that can go on to produce further ionizations. Finally, “biologic systems” may be, for example, simple cell-free extracts of biomolecules or increasingly complex, from prokaryotes to single-celled eukaryotes, to mammalian cells in culture, to tissues and tumors in laboratory animals or humans, to entire ecosystems.

Radiotherapy-oriented radiobiology focuses on that portion of the electromagnetic spectrum energetic enough to cause ionization of atoms. This ultimately results in the breaking of chemical bonds that can lead to damage to important biomolecules. The most significant effect of ionizing radiation in this context is cell killing, which directly or indirectly is at the root of nearly all of the normal tissue and tumor responses noted in patients.

Cytotoxicity is not the only significant biologic effect caused by radiation exposure, although it will be the main focus of this chapter. Other important radiation effects, carcinogenesis, for example, will also be mentioned, although the reader should be aware that this aspect of radiation biology is a large discipline in and of itself, involving investigators from fields as diverse as biochemistry, toxicology, epidemiology, environmental sciences, molecular biology, tumor biology, and health and medical physics, in addition to those from the radiobiology field. Most radiation protection standards are based on minimizing the risks associated with mutagenic and carcinogenic events. Radiologic health professionals therefore are de facto educators of and advocates for the general public when it comes to ionizing radiation and need to be fully conversant in the potential risks and benefits of medical procedures involving radiation.

Most of this chapter will be devoted to so-called classical radiobiology, that is, studies that largely predate the revolution in molecular biology of the 1980s and 1990s. Although the reader might be tempted to view this body of knowledge as rather primitive by today’s standards, relying too heavily on phenomenology, empiricism, and simplistic, descriptive models and theories, the real challenge is to integrate the new biology into the already-existing framework of classical radiobiology; this will be discussed in detail in Chapter 2.

Radiotherapy-Oriented Radiobiology: A Conceptual Framework

Before examining any one aspect of radiobiology in depth, it is important to introduce several general concepts to provide a framework for putting the information in its proper perspective.

Therapeutic Ratio

The most fundamental of these concepts is what is termed the therapeutic ratio, in essence a risk-versus-benefit approach to planning a radiotherapy treatment regimen. Many of the radiobiologic phenomena to be discussed in this chapter are thought to play important roles in optimizing, or at least fine-tuning, the therapeutic ratio. In theory, it should be possible to eradicate any and all malignant tumors simply by delivering sufficiently high doses of radiation. Of course, in practice, the biologic consequences for normal tissues that are necessarily irradiated along with the tumor tissue limit the total dose that can be safely administered. As such, a balance must be struck between what is deemed an acceptable probability of a radiation-induced complication in a normal tissue and the probability of tumor control. Ideally, one would hope to achieve the maximum likelihood of tumor control that does not produce unacceptable normal tissue damage.

The concept of therapeutic ratio is best illustrated graphically, by making a direct comparison of dose-response curves for both tumor control and normal tissue complication rates plotted as a function of dose. Examples of this approach are shown in Figure 1-1, for cases in which the therapeutic ratio is either “unfavorable,” “favorable,” or “optimal,” bearing in mind that these are theoretical curves. Actual dose-response curves derived from experimental or clinical data are much more variable, particularly for tumors, which tend to show much shallower dose responses.1 This serves to underscore how difficult it can be in practice to assign a single numerical value to the therapeutic ratio in any given situation.

Many of the radiobiologic properties of cells (and, therefore, tissues) can have either a favorable or an adverse effect on the therapeutic ratio. Therefore, in planning a course of radiation therapy, the goal should be to optimize the therapeutic ratio as much as possible, in other words, using our graphical approach, increase the separation between the tumor control and the normal tissue complication curves. This can be accomplished either by shifting the tumor control curve to the left with respect to the dose axis (toward lower doses for the same level of tumor control, that is, tumor radiosensitization) or by shifting the normal tissue complication curve to the right (toward higher doses for the same level of normal tissue complications, that is, normal tissue radioprotection) or perhaps a combination of both. The key is to shift these curves differentially, not necessarily an easy task given that there are precious few exploitable differences in the radiobiology of cells derived from tumors and those derived from normal tissues.

Radiation Biology “Continuum”

There is a surprising continuity between the physical events that occur in the first picosecond (or less) after ionizing radiation interacts with biologic material and the ultimate consequences of that interaction on tissues. The consequences themselves may not become apparent until days, weeks, months, or even years after the radiation exposure. Some of the important steps in this radiobiology “continuum” are listed in Table 1-1. The orderly progression from one stage of the continuum to the next—from physical to physicochemical to biochemical to biologic—is particularly noteworthy not only because of the vastly different time scales over which the critical events occur, but also because of the increasing biologic complexity associated with each of the endpoints or outcomes. Each stage of the continuum also offers a unique radiobiologic window of opportunity: the potential to intervene in the process and thereby modify all the events and outcomes that follow.

Levels of Complexity in Radiobiologic Systems

Another important consideration in all radiobiologic studies is the nature of the experimental system used to study a particular phenomenon, the assays used, and the endpoints assessed. For example, one investigator may be interested in studying DNA damage caused by ionizing radiation and, in particular, the frequency of DNA double-strand breaks (DSBs) produced per unit dose. As an experimental system, he or she might choose DNA extracted from mammalian cells. Then, using a DNA elution assay, the rate at which the irradiated DNA passes through a semipermeable membrane is measured as an endpoint and compared with the rate of elution of DNA extracted from cells that had not been previously irradiated. DNA containing more DSBs elutes faster than DNA containing fewer breaks, allowing a calibration curve to be generated that relates the dose received to the elution rate.

A second investigator, on the other hand, may be interested in improving the control rate of head and neck cancers with radiation therapy by employing a nonstandard fractionation schedule. In this case, the type of experiment would be a clinical trial. The “experimental system” would be a cohort of patients, some of whom are randomized to receive nonstandard fractionation, and the rest, standard fractionation. The endpoints assessed could be one or more of the following: locoregional control, long-term survival, disease-free survival, or normal tissue complication frequency, evaluated at specific times after completion of the radiation therapy.

In considering both the strengths and weaknesses of these two investigators’ studies, any number of pertinent questions may be asked. Which is the more complex or heterogeneous system? Which is the more easily manipulated and controlled system? Which is more relevant for the day-to-day practice of radiation therapy? What kinds of results are gleaned from each, and can these results be obtained in a timely manner? In this example, it is clear that human patients with spontaneously arising tumors represent a far more heterogeneous and complex experimental system than an extract of mammalian DNA. On the other hand, the DNA system is much more easily manipulated, possible confounding factors can be more easily controlled, and the measurement of the desired endpoint (elution rate) plus the data analysis can be completed within a day or two. Obviously, this is not the case with the human studies, where numerous confounding factors can and do influence results, manipulation of the system can be difficult if not impossible, and the experimental results typically take years to obtain.

The issue of relevance is an even thornier one. Arguably, both studies are relevant to the practice of radiation therapy insofar as the killing of cells is at the root of normal tissue and tumor toxicity caused by radiation exposure, and as cell killing usually is, either directly or indirectly, a consequence of irreparable damage to DNA. As such, any laboratory findings that contribute to the knowledge base of radiation-induced DNA damage are relevant. Clearly, however, clinical trials with human patients are not only a more familiar experimental system to clinicians but, also, their efficacy in cancer patients is, ultimately, the “gold standard” against which all new therapeutic strategies are judged.

All things considered, then, there is a time and place for both relatively simple systems and more complex ones. The relatively simple, homogeneous, and easily manipulated systems are best suited for the study of the mechanisms of radiation action, such as measuring DNA or chromosomal damage, changes in gene expression, perturbations of the cell cycle, or the clonogenic survival of cells maintained in culture. The more complicated and heterogeneous systems, with their unique endpoints, are more clinically relevant, such as assays of tumor control or normal tissue complication rates. Both types of assay systems have inherent strengths and weaknesses, yet both are critically important for hoped-for improvement in the practice of radiation therapy based on sound biologic principles.

Tissue Heterogeneity

Why is radiation therapy successful at controlling one patient’s tumor but not another’s, even when the two tumors seem identical? Why are we generally more successful at controlling certain types of cancers than others? The short answer to such questions is that although the tumors may appear identical “macroscopically,” their component cells may be quite different phenotypically and/or genotypically. Also, there may be important differences between the two patients’ normal tissues.

Normal tissues, being composed of more than one type of cell, are somewhat heterogeneous, and tumors, owing both to the genetic instability of individual tumor cells and to microenvironmental differences, are very heterogeneous. Different subpopulations of cells have been isolated from many types of human and experimental cancers, and these may differ in antigenicity, metastatic potential, sensitivity to radiation therapy and chemotherapy, and so on.2,3 This heterogeneity is manifest within a particular patient, and to a much greater extent, between patients with otherwise similar tumors.

Both intrinsic and extrinsic factors contribute to this heterogeneity. Intrinsic factors may include the following: inherent radiosensitivity, gene expression, biochemical repair processes, modes of cell death (clonogenic versus apoptotic, for example), genomic instability, cell cycle kinetics, and the structural and functional arrangement of the tissue. Extrinsic factors, on the other hand, tend to be related to physiologic differences between tissues, such as the degree of vascularity, availability of oxygen and nutrients, pH level, energy charge, and proximity of, and degree of contact between, normal host tissue and the tumor.

What are the practical implications of normal tissue and tumor heterogeneity? First, if one assumes that normal tissues are the more uniform and predictable in behavior of the two, then tumor heterogeneity is responsible, either directly or indirectly, for most radiotherapy failures. If so, this suggests that a valid clinical strategy might be to identify the radioresistant subpopulation(s) of tumor cells and then tailor therapy specifically to cope with them. This approach is much easier said than done. Some prospective clinical studies now include one or more pretreatment determinations of, for example, the extent of tumor hypoxia4 or the potential doubling time of tumor clonogens5 as criteria for assigning patients to different treatment groups.

Another consequence of tissue heterogeneity is that any radiobiologic endpoint measured in an intact tissue is necessarily related to the radiosensitivities of all the subsets of cells, plus all the other intrinsic and extrinsic factors contributing to the overall response of the tissue. And, because data on normal tissue tolerances and tumor control probabilities are also averaged among a number of patients, heterogeneity is even more pronounced.

“Powers of Ten”

Tumor control is achieved only when all clonogenic cells are killed or otherwise rendered unable to sustain tumor growth indefinitely. To estimate the likelihood of cure, it is necessary to know—or at least have an appreciation for—approximately how many clonogenic cells the tumor contains, how radiosensitive these cells are (i.e., some measure of killing efficiency per unit radiation dose), and what the relationship is between the number of clonogenic cells remaining after treatment and the probability of recurrence. The latter is perhaps the easiest to ascertain, given our knowledge of both the random and discrete nature of radiation damage and the general shape of dose-response curves for mammalian cells and tissues (approximately exponential for multifraction irradiation).

For a given number of surviving cells per tumor, the probability of local control can be derived from Poisson statistics using the equation P = en, where P is the tumor control probability and n is the average number of surviving clonogenic tumor cells. For example, when, for a large number of tumors, an average of two clonogenic cells remain per tumor at the end of radiation therapy, the tumor control rate will be about 10%, that is, that nine out of ten tumors of the same size and relative radiosensitivity will recur. Should the treatment reduce clonogenic cell numbers to an average of 0.1 per tumor, the tumor control probability would increase to 90%; for 0.05 surviving cells per tumor, control would be 95%; and for 0.01 surviving cells per tumor, control would be 99%.

The tumor control probability for a given fraction of surviving cells is not particularly helpful if the total number of cells at risk is unknown, however, and this is where an understanding of logarithmic relationships and exponential cell killing is useful. Based on the resolution of existing tools and technology for cancer detection, let us assume that a 1-cm3 (1-g) tumor mass can be identified reliably. A tumor of this size has been estimated to contain approximately 109 cells,6 admittedly a theoretical value that assumes all cells are perfectly “packed” and uniformly sized and that the tumor contains no stroma. A further assumption, that all such cells are clonogenic (rarely, if ever, the case), suggests that at least 9 logs of cell killing would be necessary before any appreciable tumor control (about 37%) would be achieved, and 10 logs of cell killing would be required for a high degree of tumor control (i.e., 90%).

After the first log or two of cell killing, however, some tumors respond by shrinking, a partial response. After two to three logs of cell killing, the tumor may shrink to a size below the current limits of clinical detection, that is, a complete response. Although partial and complete responses are valid clinical endpoints, a complete response does not necessarily mean tumor cure. At least six more logs of cell killing would be required before any significant probability of cure would be expected. This explains why radiation therapy is not halted if the tumor “disappears” during the course of treatment; this concept is illustrated graphically in Figure 1-2.

Finally, it should be noted that while the goal of curative radiation therapy is to reduce tumor cell survival by at least nine logs, even for the smallest tumor likely to be encountered, it is much less clear how many logs of cell killing a particular normal tissue can tolerate before it loses its structural and/or functional integrity. This would depend on how the tissue is organized structurally, functionally, and proliferatively; which constituent cells are the most and least radiosensitive; and which cells are the most important to the integrity of the tissue. It is unlikely, however, that many normal tissues could tolerate a depletion of two logs (99%) of their cells, let alone nine or more logs.

Radiation Biology and Therapy: The First 50 Years

In less than 4 years after the discovery of x rays by Roentgen,7 radioactivity by Becquerel,8 and radium by the Curies,9 the new modality of cancer treatment known as radiation therapy claimed its first apparent cure of skin cancer.10 Today, more than a century later, radiotherapy is most commonly given as a series of small daily dose fractions of approximately 1.8 to 2 Gy each, 5 days per week, over a period of 5 to 7 weeks, to a total dose of 50 to 70 Gy. Although it is true that the historical development of this conventional radiotherapy schedule was empirically based, there were a number of early radiobiologic experiments that suggested this approach.

In the earliest days of radiotherapy, both x rays and radium were used for cancer treatment. Because of the greater availability and convenience of using x-ray tubes and the higher intensities of radiation output achievable, it was fairly easy to deliver large single doses in short overall treatment times. Thus, from about 1900 into the 1920s, this “massive dose technique”11 was a common way of administering radiation therapy. Unfortunately, normal tissue complications were quite severe. To make matters worse, the rate of local tumor recurrence was still unacceptably high.

Radium therapy was used more extensively in France. Because of the low activities available, radium applications involved longer overall treatment times to reach comparable total doses. Although extended treatments were less convenient, clinical results were often superior. Perceiving that the change in overall time was the critical factor, physicians began to experiment with the use of multiple smaller x-ray doses delivered over extended periods. At that time, there was already a radiobiologic precedent for expecting improvement in tumor control when radiation treatments were protracted.

As early as 1906, Bergonié and Tribondeau12 observed histologically that the immature dividing cells of the rat testis showed evidence of damage at lower radiation doses than the mature nondividing cells. Based on these observations, the two researchers put forth some basic “laws” stating that x rays were more effective on cells that were: (1) actively dividing, (2) likely to continue to divide indefinitely, and (3) poorly differentiated.12 Because tumors were already known to contain cells that not only were less differentiated but also exhibited greater mitotic activity, Bergonié and Tribondeau reasoned that several radiation exposures might preferentially kill these tumor cells but not their slowly proliferating, differentiated counterparts in the surrounding normal tissues.

The end of common usage of the single-dose technique in favor of fractionated treatment came during the 1920s as a consequence of the pioneering experiments of Claude Regaud and colleagues.13 Using the testis of the rabbit as a model tumor system (because the rapid and unlimited proliferation of spermatogenic cells simulated to some extent the pattern of cell proliferation in malignant tumors), Regaud14 showed that only through the use of multiple radiation exposures could animals be completely sterilized without producing severe injury to the scrotum. Regaud15 suggested that the superior results afforded the multifraction irradiation scheme were related to alternating periods of relative radioresistance and sensitivity in the rapidly proliferating germ cells. These principles were soon tested in the clinic by Henri Coutard,16,17 who used fractionated radiotherapy for the treatment of head and neck cancers, with spectacularly improved results. Mainly as a result of these and related experiments, fractionated treatment subsequently became the standard form of radiation therapy.

Time-dose equivalents for skin erythema published by Reisner,18 Quimby and MacComb,19 and others20,21 formed the basis for the calculation of equivalents for other tissue and tumor responses. By plotting the total doses required for each of these “equivalents” for a given level of effect in a particular tissue, as a function of a treatment parameter such as overall treatment time, number of fractions, dose per fraction, and so on, an isoeffect curve could be derived. All time-dose combinations that fell along such a curve would, theoretically, produce tissue responses of equal magnitude. Isoeffect curves, relating the total dose to the overall treatment time, derived in later years from some of these data,22 are shown in Figure 1-3.

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Figure 1-3 Isoeffect curves relating the log of the total dose to the log of the overall treatment time for various levels of skin reaction and the cure of skin cancer. A, Isoeffect curves were constructed by Cohen on the basis of a survey of earlier published data on radiotherapy equivalents.2126 The slope of the curves for skin complications was 0.33, and the slope for tumor control was 0.22. B, The Strandqvist28 isoeffect curves were first published in 1944. All lines were drawn parallel and had a common slope of 0.33.

A, Adapted from Cohen L: Radiation response and recovery: Radiobiological principles and their relation to clinical practice. In Schwartz E, editor: The Biological Basis of Radiation Therapy, Philadelphia, 1966, JB Lippincott, p 208; B, adapted from Strandqvist M: Studien uber die kumulative Wirkung der Roentgenstrahlen bei Fraktionierung, Acta Radiol Suppl 55:1, 1944.

The first published isoeffect curves were produced by Strandqvist23 in 1944, and are also shown in Figure 1-3. When transformed on log-log coordinates, isoeffect curves for a variety of skin reactions, and the cure of skin cancer, were drawn as parallel lines, with common slopes of 0.33. These results implied that there would be no therapeutic advantage to using prolonged treatment times (i.e., multiple small fractions versus one or a few large doses) for the preferential eradication of tumors while simultaneously sparing normal tissues.24 It was somewhat ironic that the Strandqvist curves were so popular in the years that followed, when it was already known that the therapeutic ratio did increase (at least to a point) with prolonged, as opposed to very short, overall treatment times. However, the overarching advantage was that these isoeffect curves were quite reliable at predicting skin reactions, which were the dose-limiting factors at that time.

The “Golden Age” of Radiation Biology and Therapy: The Second 50 Years

Perhaps the defining event that ushered in the golden age of radiation biology was the publication of the first survival curve for mammalian cells exposed to graded doses of ionizing radiation.25 This first report of a quantitative measure of intrinsic radiosensitivity of a human cell line (HeLa, derived from a cervical carcinoma26) was published by Puck and Marcus25 in 1956. To put this seminal work in the proper perspective, however, it is first necessary to review the physicochemical basis for why ionizing radiation is toxic to biologic materials.

The Interaction of Ionizing Radiation with Biologic Materials

As mentioned in the introductory section of this chapter, ionizing radiation deposits energy as it traverses the absorbing medium through which it passes. The most important feature of the interaction of ionizing radiation with biologic materials is the random and discrete nature of the energy deposition. Energy is deposited in increasingly energetic packets referred to as “spurs” (100 eV or less deposited), “blobs” (100 to 500 eV), or “short tracks” (500 to 5000 eV), each of which can leave from approximately three to several dozen ionized atoms in its wake. This is illustrated in Figure 1-4, along with a segment of (interphase) chromatin shown to scale. The frequency distribution and density of the different types of energy deposition events along the track of the incident photon or particle are measures of the radiation’s linear energy transfer or LET (see also the “Relative Biologic Effectiveness” section, later). Because these energy deposition events are discrete, it follows that although the average amount of energy deposited in a macroscopic volume of biologic material may be rather modest, the distribution of this energy on a microscopic scale may be quite large. This explains why ionizing radiation is so efficient at producing biologic damage; the total amount of energy deposited in a 70-kg human that will result in a 50% probability of death is only about 70 calories, about as much energy as is absorbed by drinking one sip of hot coffee.27 The key difference is that the energy contained in the sip of coffee is uniformly distributed, not random and discrete.

image

Figure 1-4 Hypothetical alpha particle track through an absorbing medium, illustrating the random and discrete energy-deposition events along the track. Each event can be classified according to the amount of energy deposited locally, which determines how many ionized atoms will be produced. A segment of a DNA double helix is shown approximately to scale.

Adapted from Goodhead D: Physics of radiation action: microscopic features that determine biological consequences. In Hagen U, Harder D, Jung H, et al, editors: Radiation research 1895-1995, proceedings of the 10th international congress of radiation research, vol. 2. congress lectures, Wurzburg, 1995, Universitatsdruckerei H Sturtz, p 43.

Those biomolecules receiving a direct hit from a spur or blob, receive, relatively speaking, a huge radiation dose, that is, a large deposition of energy in a very small volume. For photons and charged particles, this energy deposition results in the ejection of orbital electrons causing the target molecule to be converted first into an ion pair and then into a free radical. Further, the ejected electrons—themselves energetic charged particles—can go on to produce additional ionizations. For uncharged particles such as neutrons, the interaction is between the incident particles and the nuclei of the atoms in the absorbing medium, causing the ejection of recoil protons (charged) and lower-energy neutrons. The cycle of ionization, free radical production, and release of secondary charged particles continues until all the energy of the incident photon or particle is expended. These interactions are complete within a picosecond after the initial energy transfer. After that time, the chemical reactions of the resulting free radicals predominate the radiation response (discussed later).

Any and all cellular molecules are potential targets for the localized energy deposition events that occur in spurs, blobs, or short tracks. Whether the ionization of a particular biomolecule results in a measurable biologic effect depends on a number of factors, including how probable a target the molecule represents from the point of view of the ionizing particle, how important the molecule is to the continued health of the cell, how many copies of the molecule are normally present in the cell and to what extent the cell can react to the loss of “working copies,” and how important the cell is to the structure or function of its corresponding tissue or organ. DNA, for example, is obviously an important cellular macromolecule and one that is present only as a single double-stranded copy. On the other hand, other molecules in the cell may be less crucial to survival yet are much more abundant than DNA, and therefore have a much higher probability of being hit and ionized. The most abundant molecule in the cell by far is water, comprising some 80% to 90% of the cell on a per weight basis. The highly reactive free radicals formed by the radiolysis of water are capable of adding to the DNA damage resulting from direct energy absorption by migrating to the DNA and damaging it indirectly. This mechanism is referred to as “indirect radiation action” to distinguish it from the aforementioned “direct radiation action.”28 The direct and indirect action pathways for ionizing radiation are illustrated below.

Direct effect

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Indirect effect

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The most highly reactive and damaging species produced by the radiolysis of water is the hydroxyl radical (OH), although other free radical species are also produced in varying yields.29,30 Ultimately, it has been determined that cell killing by indirect action constitutes some 70% of the total damage produced in DNA for low LET radiation.

How do the free radicals produced by the direct and indirect action of ionizing radiation go on to cause the myriad lesions that have been identified in irradiated DNA? Because they contain unpaired electrons, free radicals are highly reactive chemically and will undergo any number of reactions in an attempt to either acquire new electrons or rid themselves of remaining unpaired ones. These reactions are considered quite slow compared with the speed of initial ionization events but are still quite fast relative to normal enzymatic processes in a typical mammalian cell. For all intents and purposes, free radical reactions are complete in less than a second after irradiation.

The OH radical is capable of both abstraction of hydrogen atoms from other molecules and addition across carbon-carbon or other double bonds. More complex macromolecules that have been converted to free radicals can undergo a series of transmutations in an attempt to rid themselves of unpaired electrons, many of which result in the breakage of nearby chemical bonds. In the case of DNA, these broken bonds may result in the loss of a base or an entire nucleotide or in frank scission of the sugar phosphate backbone, involving one or both DNA strands. In some cases, chemical bonds are first broken but then rearranged, exchanged, or rejoined in inappropriate ways. Bases in DNA may be modified by the addition of one or more hydroxyl groups (e.g., the base thymine converted to thymine glycol), pyrimidines may become dimerized, and/or the DNA may become cross-linked to itself or to associated protein components. And again, because the initial energy deposition events are discrete, the free radicals produced also are clustered and therefore undergo their multiple chemical reactions and produce multiple damages in a highly localized area. This has been termed the “multiply-damaged site”31 or “cluster”32 hypothesis. Examples of the types of damage found in irradiated DNA are shown in Figure 1-5.

Biochemical Repair of DNA Damage

DNA is unique insofar as it is the only cellular macromolecule with its own repair system. Until relatively recently, little was known about DNA repair processes in mammalian cells, particularly because of the complexities involved and the relative lack of spontaneously occurring mutants defective in genes involved with DNA repair. As a consequence, most studies of DNA repair were carried out either in bacteria or yeasts and usually employed UV radiation as the tool for producing DNA damage. Although these were rather simple and relatively “clean” systems in which to study DNA repair, their relevance to mammalian repair systems and to the broader spectrum of DNA damage produced by ionizing radiation ultimately limited their usefulness.

The study of DNA repair in mammalian cells received a significant boost during the late 1960s with publications by Cleaver33,34 that identified the molecular defect responsible for the human disease xeroderma pigmentosum (XP). Patients with XP are exquisitely sensitive to sunlight and highly cancer-prone (particularly to skin cancers). Cleaver showed that cells derived from such patients were likewise sensitive to UV radiation and defective in the nucleotide excision repair pathway (discussed later). These cells were not especially sensitive to ionizing radiation, however. Several years later, Taylor and colleagues35 reported that cells derived from patients with a second cancer-prone disorder called ataxia telangiectasia (AT) were extremely sensitive to ionizing radiation and radiation-mimetic drugs but not to UV radiation. In the years that followed, cell cultures derived from patients with these two conditions were used to help elucidate the complicated processes of DNA repair in mammalian cells.

Today, many rodent and human genes involved in DNA repair have been cloned.36 Nearly 20 distinct gene products participate in excision repair of base damage, and even more are involved in the repair of strand breaks. Many of these proteins function as component parts of larger repair complexes; some of these parts are interchangeable and participate in other DNA repair and replication pathways as well. It is also noteworthy that some are not involved with the repair process per se but rather link DNA repair to other cellular functions, including transcription, cell cycle arrest, chromatin remodeling, and apoptosis.37 This attests to the fact that the maintenance of genomic integrity results from a complex interplay between not only the repair proteins themselves but between others that serve as damage sensors, signaling mediators and transducers, and effectors.

For example, the defect responsible for the disease AT is not in a gene that codes for a repair protein but rather in a gene that participates in damage recognition and in a related pathway that normally prevents cells from entering S phase of the cell cycle and beginning DNA synthesis while residual DNA damage is present. This was termed the G1/S checkpoint response.38 Because of this genetic defect, AT cells do not experience the normal G1 arrest after irradiation and enter S phase with residual DNA damage. This accounts both for the exquisite radiosensitivity of AT cells and the resulting genomic instability that can lead to carcinogenesis.

What is known about the various types of DNA repair in mammalian cells is outlined below.

Base Excision Repair

The repair of base damage is initiated by DNA repair enzymes called DNA glycosylases, which recognize specific types of damaged bases and excise them without otherwise disturbing the DNA strand.39 The action of the glycosylase itself results in the formation of another type of damage observed in irradiated DNA—an apurinic or apyrimidinic (AP) site. The AP site is then recognized by another repair enzyme, an AP endonuclease, which nicks the DNA adjacent to the lesion. The resulting strand break becomes the substrate for an exonuclease, which removes the abasic site, along with a few additional bases. The small gap that results is patched by DNA polymerase, which uses the opposite, hopefully undamaged, DNA strand as a template. Finally, DNA ligase seals the patch in place.

Nucleotide Excision Repair

The DNA glycosylases that begin the process of base excision repair do not recognize all known forms of base damage, however, particularly bulky or complex lesions.39 In such cases, another group of enzymes, termed structure-specific endonucleases, initiate the excision repair process. These repair proteins do not recognize the specific lesion but are thought instead to recognize more generalized structural distortions in DNA that necessarily accompany a complex base lesion. The structure-specific endonucleases incise the affected DNA strand on both sides of the lesion, releasing an oligonucleotide fragment made up of the damage site and several bases on either side of it. Because a longer segment of excised DNA—including both bases and the sugar phosphate backbone—is generated, this type of excision repair is referred to as nucleotide excision repair to distinguish it from base excision repair (described earlier), where the initial step in the repair process is removal of the damaged base only. After this step, the remainder of the nucleotide excision repair process is similar to that of base excision repair; the gap is then filled in by DNA polymerase and sealed by DNA ligase. Overall, however, nucleotide excision repair is a much slower process, with a half-time of approximately 12 hours.

For both types of excision repair, active genes in the process of transcription are repaired preferentially and more quickly. This has been termed transcription-coupled repair.40

Strand Break Repair

Despite the fact that unrepaired or mis-rejoined strand breaks, particularly DSBs, often have the most catastrophic consequences for the cell in terms of loss of reproductive integrity,41 the way in which mammalian cells repair strand breaks has been more difficult to elucidate than the way in which they repair base damage. Much of what was originally discovered about these repair processes is derived from studies of x ray–sensitive rodent cells and microorganisms that were subsequently discovered to harbor specific defects in strand break repair. Since then, other human genetic diseases characterized by DNA repair defects have been identified and are also used to help probe these fundamental processes.

A genetic technique known as complementation analysis allows further characterization of genes involved in DNA repair. Complementation analysis involves the fusion of different strains of cells possessing the same phenotypic defect and subsequent testing of the hybrid cell for the presence or absence of this phenotype. Should two cell types bearing the defect yield a phenotypically normal hybrid cell, this implies that the defect has been “complemented” and that the defective phenotype must result from mutations in at least two different genes. With respect to DNA strand break repair, eight different genetic complementation groups have been identified in rodent cell mutants. For example, a mutant Chinese hamster cell line, designated EM9, seems especially radiosensitive owing to delayed repair of DNA single-strand breaks, a process that is normally complete within minutes of irradiation.42

With respect to the repair of DNA DSBs, the situation is more complicated in that the damage on each strand of DNA may be different, and, therefore, no intact template would be available to guide the repair process. Under these circumstances, cells depend on genetic recombination (nonhomologous end joining or homologous recombination43) to cope with the damage.

Nonhomologous end joining (NHEJ) is a repair mechanism that directly ligates broken ends of DNA DSBs using a heterodimeric enzyme complex consisting of the proteins Ku-70 and Ku-80, the catalytic subunit of DNA protein kinase (DNA-PKCS), and XRCC4/ligase IV. Because no intact complementary strand is available as a template, this process is error-prone and generally results in minor deletions in the DNA sequence. NHEJ predominates during the G1 phase of the cell cycle. Homologous recombination (HR), on the other hand, involves digestion and “cleaning up” of the broken DNA ends followed by assembly of a nucleoprotein filament that contains, among others, the proteins Rad51 and Rad52. This filament then invades the homologous DNA sequence of a sister chromatid, which becomes the template for essentially error-free repair of the broken ends by DNA synthesis. HR is active during S and G2 phases of the cell cycle, that is, after DNA replication, when an identical copy of the DNA strand—the sister chromatid—is available.

The BRCA1 and BRCA2 gene products are also implicated in HR (and, possibly, NHEJ as well) because they interact with the Rad51 protein. Defects in these genes are associated with hereditary breast and ovarian cancer.44

Mismatch Repair

The primary role of mismatch repair (MMR) is to eliminate from newly synthesized DNA errors such as base/base mismatches and insertion/deletion loops caused by DNA polymerase.45 Descriptively, this process consists of three steps: mismatch recognition and assembly of the repair complex, degradation of the error-containing strand, and repair synthesis. In humans, MMR involves at least five proteins, including hMSH2, hMSH3, hMSH6, hMLH1, and hPMS2, as well as other members of the DNA repair and replication machinery.

One manifestation of a defect in mismatch repair is microsatellite instability, mutations observed in DNA segments containing repeated sequence motifs.46 Collectively, this causes the cell to assume a hypermutable state (“mutator phenotype”) that has been associated with certain cancer predisposition syndromes, in particular, hereditary nonpolyposis colon cancer (HNPCC, sometimes called Lynch syndrome).47,48

Cytogenetic Effects of Ionizing Radiation

When cells divide following radiation exposure, chromosomes frequently contain visible structural aberrations, most of which are lethal to the cell. In some cases, these aberrations physically interfere with the processes of mitosis and cytokinesis and result in prompt cell death. In other cases, cell division can occur, but the loss or uneven distribution of genetic material between the cell’s progeny is ultimately lethal as well, although the affected cells may linger for several days before they die (some may even be able to go through a few more cell divisions in the interim). It is clear that these aberrations are the result of any unrepaired or mis-rejoined DNA damage that persists from the time of irradiation until the time of the next cell division. What is not known, however, is how an unrepaired DSB in essentially “naked” DNA is transformed into such a large lesion—a broken arm of a chromosome, for example—given that the chromosome has undergone many levels of modification, folding and packaging, association with chromatin and other proteins, and condensation in preparation for mitosis.

Most chromosome aberrations result from an interaction between two (or more; discussed later) damage sites, and, therefore, can be grouped into three different types of “exchange” categories. A fourth category is reserved for chromosome aberrations thought to result from a single damage site.49 These categories are described below, and representative types of aberrations from each category are shown in Figure 1-6:

These four categories can be further subdivided according to whether the initial radiation damage occurred before or after the DNA is replicated during S phase of the cell cycle (a chromosome-type vs. a chromatid-type of aberration, respectively) and, for the three exchange categories, whether the lesion interaction was symmetric or asymmetric. Asymmetric exchanges always lead to the formation of acentric fragments that are usually lost in subsequent cell divisions and therefore are nearly always fatal to the cell. These fragments may be retained transiently in the cell’s progeny as extranuclear chromatin bodies called micronuclei. Symmetric exchanges are more insidious in that they do not lead to the formation of acentric fragments and the accompanying loss of genetic material at the next cell division, they are sometimes difficult to detect cytologically, and they are not invariably lethal to the cell. As such, they will be transmitted to all the progeny of the original cell. Some types of symmetric exchanges (a reciprocal translocation, for example) have been implicated in radiation carcinogenesis, insofar as they have the net effect of either bringing new combinations of genes together or of separating preexisting groups of genes.27 Depending on where in the genome the translocation takes place, genes normally on could be turned off, or vice versa, possibly with adverse consequences.

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