Nonhomologous DNA end rejoining in chromosomal aberration formation

Formation of carcinogenic chromosomal rearrangements in human thyroid cells after induction of double-strand DNA breaks by restriction endonucleases

Ionizing radiation (IR) exposure increases the risk of thyroid cancer and other cancer types. Chromosomal rearrangements, such as RET/PTC, are characteristic features of radiation-associated thyroid cancer and can be induced by radiation in vitro. IR causes double-strand breaks (DSBs), suggesting that such damage leads to RET/PTC, but the rearrangement mechanism has not been established. To study the mechanism, we explored the possibility of inducing RET/PTC by electroporation of restriction endonucleases (REs) into HTori-3 human thyroid cells. We used five REs, which induced DSB in a dose-dependent manner similar to that seen with IR. Although all but one RE caused DSB in one or more of the three genes involved in RET/PTC, rearrangement was detected only in cells electroporated with either PvuII (25 and 100  U) or StuI (100 and 250  U). The predominant rearrangement type was RET/PTC3, which is characteristic of human thyroid cancer arising early after Chernobyl-related radioactive iodine exposure. Both enzymes that produced RET/PTC had restriction sites only in one of the two fusion partner genes. Moreover, the two enzymes that produced RET/PTC had restriction sites present in clusters, which was not the case for RE that failed to induce RET/PTC. In summary, we establish a model of DSB induction by RE and report for the first time the formation of carcinogenic chromosomal rearrangements, predominantly RET/PTC3, as a result of DSB produced by RE. Our data also raise a possibility that RET/PTC rearrangement can be initiated by a complex DSB that is induced in one of the fusion partner genes.

Intracellular signal transduction and modification of the tumor microenvironment induced by RET/PTCs in papillary thyroid carcinoma

RET gene rearrangements (RET/PTCs) represent together with BRAF point mutations the two major groups of mutations involved in papillary thyroid carcinoma (PTC) initiation and progression. In this review, we will examine the mechanisms involved in RET/PTC-induced thyroid cell transformation. In detail, we will summarize the data on the molecular mechanisms involved in RET/PTC formation and in its function as a dominant oncogene, on the activated signal transduction pathways and on the induced gene expression modifications. Moreover, we will report on the effects of RET/PTCs on the tumor microenvironment. Finally, a short review of the literature on RET/PTC prognostic significance will be presented.

Mechanisms of chromosomal rearrangements in solid tumors: the model of papillary thyroid carcinoma

Thyroid cancer, and its most common type, papillary carcinoma, frequently have chromosomal rearrangements and therefore represent a good model for the understanding of mechanisms of chromosomal rearrangements in solid tumors. Several types of rearrangement known to occur in thyroid cancer, including RET/PTC, NTRK1 and BRAF/AKAP9, are more common in radiation-associated thyroid tumors and RET/PTC can be induced experimentally by exposing human thyroid cells to ionizing radiation. In this review, the molecular mechanisms of generation of RET/PTC and other chromosomal rearrangements are discussed, with the emphasis on the role of nuclear architecture and interphase gene proximity in the generation of intrachromosomal rearrangements in thyroid cells.

Radiosensitivity and double-strand break rejoining in tumorigenic and non-tumorigenic human epithelial cell lines

Radiosensitivity and repair of DNA damage induced by ionizing radiation and restriction enzymes were investigated in three human epithelial cell lines: two tumorigenic squamous carcinoma cell lines (SCC-4 and SCC-25), and a non-tumorigenic epidermal keratinocyte cell line (RHEK-1). Sensitivity to ionizing radiation was determined using a clonogenic cell survival assay, which showed SCC-4 to be more radiosensitive than SCC-25 and RHEK-1, which in turn displayed about equal sensitivity. Using DNA precipitation under alkaline conditions for the analysis of induction and repair of DNA single-strand breaks (ssb), an increased level of ssb induction was found for SCC-4 while the efficiency of ssb repair was about equal in all three cell lines. Using pulsed-field gel electrophoresis (PFGE) for the measurement of induction and repair of DNA double-strand breaks (dsb), no consistent differences were detected between the three cell lines. A plasmid reconstitution assay was used to determine the capacity to rejoin restriction enzyme-induced dsb in whole-cell extracts prepared from the three cell lines. In these experiments, dsb rejoining was shown to be significantly reduced in the most radiosensitive SCC-4 cell line while it was about equal in RHEK-1 and SCC-25. The results indicate that plasmid reconstitution in cell-free extracts is a sufficiently sensitive assay to detect differences in repair capacity among tumour cell lines of different radiosensitivity which remain undetectable by DNA precipitation and PFGE.

Frequencies of polycentric chromosomes following combinational treatments of Chinese hamster ovary cells with restriction endonucleases and X-rays, bleomycin or DNase I

Chinese hamster ovary cells were treated with combinations of the restriction endonucleases AluI, EcoRI or PstI and bleomycin, DNase I or X-rays. With few exceptions the frequencies of polycentric chromosomes calculated as dicentric chromosomes (DIC) were additive or less than additive after combinational treatments when compared with the effects of treatments with the single compounds. Less than additivity was found when the frequencies of DIC were higher than 150 DIC per 100 cells indicating a saturation effect. The data suggest that DNA double-strand breaks (DSB) with different end-structures produce polycentric chromosomes to the same extent as DSB with the same end-structures.

Mechanisms of nonhomologous DNA end-joining in frogs, mice and men

DNA end-joining, a process related to illegitimate recombination and capable of rejoining unrelated pairs of DNA ends in the absence of sequence homology, is considered the major pathway of double-strand break (DSB) repair in mammalian cells. Whole cell and nuclear extracts from three human and one mouse cell line were investigated for their capacities to promote nonhomologous DNA end-joining and their relative activities of DNA-PK, a mammalian DNA end-binding protein complex implicated in DSB-repair. The levels of DNA end-joining and the spectra of junctions of the human systems were identical with the ones of a previously described cell-free joining system derived from Xenopus laevis eggs. Due to the presence of potent 3'-5'-exonuclease activities the mouse system displayed decreased levels of DNA end-joining and larger fractions of junctions containing deletions but otherwise the basic mechanisms of junction formation appeared to be identical with the Xenopus system. DNA-PK activity was found to be equally low in the Xenopus and the mouse system but 4- to 6-fold increased in the human systems. Our results suggest that the mechanisms of DNA end-joining may be modulated by the level of exonuclease activities and/or DNA end-protecting factors but are otherwise highly conserved in vertebrate cells.

Chromosome damage induced by combined treatments with restriction endonucleases introduced into CHO cells by single or double electroporation

The possible recombination between non-homologous termini produced by restriction enzymes (REs) introduced in CHO cells by electroporation was studied. For this purpose, different combinations of REs that produced blunt or 5' overhanging DNA double-strand breaks were electroporated into cells either at the same time or separately by double electroporation experiments. Prior to double electroporation, it was confirmed that, once the cells have been electroporated, they resist a second electroporation, as assessed by cell viability analysis. Besides, the efficient and homogeneous introduction of labelled, non-permeable molecules was assessed by fluorescence microscopy. Our results showed interaction for most of the conditions, mainly when the REs were introduced separately. Differences found in the degree of interaction between the combinations studied are discussed.

Analysis of the joining sequences of the t(15;17) translocation in human acute promyelocytic leukemia: sequence non-specific recombination between the PML and RARA genes within identical short stretches

Molecular analysis of the t(15;17) translocation in 70 patients with acute promyelocytic leukemia (APL) confirmed that the breakpoints of chromosome 15 were located in two regions of the promyelocytic leukemia (PML) gene, mainly introns 3 and 6, whereas the breakpoints of chromosome 17 were consistently in intron 2 of the retinoic acid receptor alpha (RARA) gene. To study the reason for the clustering of the breakpoints and the underlying mechanism of the chromosomal translocation, we characterized the joining sequences of der(15) and der (17) by polymerase chain reaction in samples from eight patients with APL. There was no cluster of the breakpoints within the introns, and no consensus sequence-motif was found around them. One or nine extra nucleotides were inserted into two joining sites. There were identical stretches of one to seven nucleotides between the PML and RARA genes in the majority of the joining sequences. These data provide a potential model of the t(15;17) translocation: random DNA double strand cleavage, modification of DNA ends by enzymes including terminal deoxynucleotidyl transferase, and single strand base-pairing within identical short stretches. Furthermore, APL develops only when the PML and RARA genes are rearranged, within restricted genomic regions and a functional PML-RARA chimeric product is produced, and this might lead to a clustering of the breakpoints.

Modulatory effect of sodium butyrate on AluI-induced chromosomal aberrations in CHO cells

Exponentially growing CHO cells exposed to millimolar concentrations of sodium butyrate (SB) for 24 h were treated with AluI using two methods of cell poration, i.e., electroporation and streptolysin O (SLO). Under both conditions, SB was found to induce a 2-4-fold increase in AluI-induced chromosomal aberrations. When cells in monolayer were treated with AluI/SLO, lower concentrations of SB (2.5 mM) and AluI (1-4 U/ml) were required to produce a similar effect as that observed for electroporated cells, demonstrating the differential sensitivity of the two methods. Furthermore, in AluI/SLO-treated cells, a higher percentage of cells was found to show increased frequencies of aberrations per cell, compared to AluI/electroporated cells. The mechanism by which SB modulates the cell response to AluI treatment might involve changes in chromatin configuration thereby increasing the accessibility of AluI to different parts of chromatin.

Combination treatments of Chinese hamster ovary cells with various restriction endonucleases result in chromosomal aberrations whose frequencies are additive or less than additive

Chinese hamster ovary cells were treated with combinations of different restriction endonucleases (RE). The frequencies of chromosomal aberrations after combination treatments were additive or less than additive when compared with the effects of the single RE. These data indicate that DNA double-strand breaks (DSB) induced by different types of RE in combination treatments lead to chromosomal aberrations in the same way as DSB induced by single RE.