DNA supercoiling changes and nuclear matrix-associated proteins: possible role in oncogene-mediated radioresistance

Transformation-induced changes in the DNA-nuclear matrix interface, revealed by high-throughput analysis of DNA halos

In higher eukaryotic nuclei, DNA is periodically anchored to an extraction-resistant protein structure, via matrix attachment regions. We describe a refined and accessible method to non-subjectively, rapidly and reproducibly measure both size and stability of the intervening chromatin loops, and use it to demonstrate that malignant transformation compromises the DNA-nuclear matrix interface.

Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography

The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships.

Twilight effects of low doses of ionizing radiation on cellular systems: a bird's eye view on current concepts and research

The debate about the health risks from low doses of radiation is vigorous and often acrimonious since many years and does not appear to weaken. Being far from completeness, this review presents only a bird's eye view on current concepts and research in the field. It is organized and divided in two parts. The first is dedicated to molecular responses determined by radiation-induced DNA ruptures. It focuses its attention on molecular pathways that are activated by ATM and tries to describe the variegated functions and specific roles of Chk2 and p53 and other proteins in sensing, promoting and executing DNA repair. The second part is more concerned with the risk associated with exposure to low dose radiation and possible effects that the radiation-affected cell may undergo. These effects include induction of apoptosis and mitotic catastrophe, bystander effect and genomic instability, senescence and hormetic response. Current hypotheses and research on these issues are briefly discussed.

Clinical target promiscuity: lessons from ras molecular trials

Mutated ras has been identified in approximately 30% of human tumors, and dysregulation of ras function and signal transduction pathways is a critical step in tumorigenesis. Herein, we review the early data that supports the concept that the intrinsic radiosensitivity of tumor cells can be altered by oncogenic ras expression and that this impacts the PI3K-dependent signaling cascade. This ras-induced radioresistance can be reversed using prenyl transferase inhibitors (PTIs.). We discuss the effects of PTIs as a radiosensitizer in both in vivo and in vitro studies and show that PTIs can lead to increased radiosensitization in vivo through a variety of potential mechanisms that enhance radiation-induced cell kill. We critically evaluate the use of ras biomarkers in predicting the clinical response to PTIs that may explain the mixed results seen thus far in clinical trials using PTIs as a clinical radiosensitizer. We conclude that Ras-mediated radioresistance is the result of multiple intercommunicating pathways functioning against a complex genetic background and a solitary biomarker may not be adequate to predict for PTI-mediated radiosensitization. Nonetheless, our knowledge of the ras-signaling pathway has led to development and testing of specific therapies directed against PI3K-AKT signaling pathways as a future approach towards clinical radiosensitization.

Aggregative organization enhances the DNA end-joining process that is mediated by DNA-dependent protein kinase

The occurrence of DNA double-strand breaks in the nucleus provokes in its structural organization a large-scale alteration whose molecular basis is still mostly unclear. Here, we show that double-strand breaks trigger preferential assembly of nucleoproteins in human cellular fractions and that they mediate the separation of large protein-DNA aggregates from aqueous solution. The interaction among the aggregative nucleoproteins presents a dynamic condition that allows the effective interaction of nucleoproteins with external molecules like free ATP and facilitates intrinsic DNA end-joining activity. This aggregative organization is functionally coacervate-like. The key component is DNA-dependent protein kinase (DNA-PK), which can be characterized as a DNA-specific aggregation factor as well as a nuclear scaffold/matrix-interactive factor. In the context of aggregation, the kinase activity of DNA-PK is essential for efficient DNA end-joining. The massive and functional concentration of nucleoproteins on DNA in vitro may represent a possible status of nuclear dynamics in vivo, which probably includes the DNA-PK-dependent response to multiple double-strand breaks.

Molecular targets for altering radiosensitivity: lessons from Ras as a pre-clinical and clinical model

Ras activation has been correlated with malignant and metastatic cancer phenotypes and poor prognosis for cancer patients. In the preclinical setting, Ras activation by mutation or EGFR amplification results in increased clonogenic cell survival and decreased tumor growth delay following irradiation. Activation of the Ras pathway has also been associated with increased risk of local failure and decreased overall survival in patients receiving radiotherapy. Prenyltransferase inhibitors target the post-translational processing of Ras and have been shown to increase the radiosensitivity of human cancer cell lines. In the clinical setting, these inhibitors have been used with concurrent radiotherapy in a small number of phase I clinical trials with acceptable toxicity. Therefore, inhibiting Ras activation represents a promising molecular approach for radiosensitization in cancer therapy.

DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation

The ATM protein kinase, mutations of which are associated with the human disease ataxia-telangiectasia, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer or higher-order multimer, with the kinase domain bound to a region surrounding serine 1981 that is contained within the previously described 'FAT' domain. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. Most ATM molecules in the cell are rapidly phosphorylated on this site after doses of radiation as low as 0.5 Gy, and binding of a phosphospecific antibody is detectable after the introduction of only a few DNA double-strand breaks in the cell. Activation of the ATM kinase seems to be an initiating event in cellular responses to irradiation, and our data indicate that ATM activation is not dependent on direct binding to DNA strand breaks, but may result from changes in the structure of chromatin.

Cytometric methods to analyze ionizing-radiation effects

Four cytometric assays for the assessment of radiation-induced DNA damage in individual cells are presented. Two of these, the alkaline and neutral comet assays, are useful for the detection of DNA damage due to very low radiation doses and promise to be useful for the quantitation of genomic damage after clinically or environmentally relevant exposures. The other two, the halo and halo-comet assays, reveal aspects of chromatin structure in the presence of DNA damage that reflect differences in intrinsic cellular radiosensitivity. Further development of these assays used alone, or in combination, should eventually lead to the definition of readily measurable cytometric parameters that will be useful as predictive markers for cellular responses to DNA damaging agents.