Recombination between separate MYC amplification structures in COLO320 cells

Formation of non-random extrachromosomal elements during development, differentiation and oncogenesis

Extrachromosomal elements (EEs) were first discovered as minute chromatin bodies [Cox et al. Minute chromatin bodies in malignant tumors of childhood. Lancet 1965;62:55-8], and subsequently characterized as small circular DNA molecules physically separated from chromosomes. They include episomes, minichromosomes, small polydispersed DNAs or double minutes. This review focuses on eukaryotic EEs generated by genome rearrangements under physiological or pathological conditions. Some of those rearrangements occur randomly, but others are strictly non-random, highly regulated, and involve specific chromosomal locations (V(D)J-recombination, telomere maintenance mechanisms, c-myc deregulation). The multiple mechanisms of EEs formation are strongly interconnected and frequently linked to gene amplification. Identification of genes located on EEs will undoubtedly allow a better understanding of genome dynamics and oncogenic pathways.

A new role for hypoxia in tumor progression: induction of fragile site triggering genomic rearrangements and formation of complex DMs and HSRs

Genome rearrangements including gene amplification are frequent properties of tumor cells, but how they are related to the tumor microenvironment is unknown. Here, we report direct evidence for a causal relationship between hypoxia, induction of fragile sites, and gene amplification. Recently, we showed that breaks at fragile sites initiate intrachromosomal amplification. We demonstrate here that hypoxia is a potent fragile site inducer and that, like fragile sites inducing drugs, it drives fusion of double minutes (DMs) and their targeted reintegration into chromosomal fragile sites, generating homogeneously staining regions (HSRs). This pathway operates efficiently for DMs bearing different sequences, suggesting a model of hypoxia-driven formation of the HSRs containing nonsyntenic sequences frequently observed in solid tumors.

Use of hydroxyurea to alter drug resistance of human tumor cells

Tumor cell resistance to cancer chemotherapeutic agents is a well-recognized problem for clinicians. Efforts are being made to develop agents that are not affected by cross-resistance to other drugs, as observed with the mdr phenotype. Other efforts are focused on reversing drug resistance to enhance chemotherapeutic intervention. Gene amplification accounts for one mechanism through which tumor cells develop drug resistance. Since amplified genes may be unstable, the elimination of these genes is likely to be a promising new target for cancer chemotherapy. The use of HU at low concentrations either to reestablish tumor sensitivity to chemotherapeutic agents or to decrease tumorigenicity, accomplished by the reduction of oncogene copy number, continues to be investigated. Studies thus far all report similar effects of noncytotoxic concentrations of HU on unstably amplified genes (EC DNA elimination), regardless of what gene is harbored on the EC DNA. The next essential step in the evaluation of HU-induced EC DNA elimination is to study the phenomena in vivo. In spite of extensive tissue distribution, HU appears to have pharmacokinetic properties, due to its short half-life, that may limit investigators' ability to study its use in prototype animal tumor models such as the nude mouse. In contrast, HU's half-life in humans (3.5 to 4.5 hours) [122] is comparatively longer, and therefore clinical trials may prove less troublesome.

Pure chromosome-specific PCR libraries from single sorted chromosomes

Chromosome-specific DNA libraries can be very useful in molecular and cytogenetic genome mapping studies. We have developed a rapid and simple method for the generation of chromosome-specific DNA sequences that relies on polymerase chain reaction (PCR) amplification of a single flow-sorted chromosome or chromosome fragment. Previously reported methods for the development of chromosome libraries require larger numbers of chromosomes, with preparation of pure chromosomes sorted by flow cytometry, generation of somatic cell hybrids containing targeted chromosomes, or a combination of both procedures. These procedures are labor intensive, especially when hybrid cell lines are not already available, and this has limited the generation of chromosome-specific DNA libraries from nonhuman species. In contrast, a single sorted chromosome is a pure source of DNA for library production even when flow cytometric resolution of chromosome populations is poor. Furthermore, any sorting cytometer may be used with this technique. Using this approach, we demonstrate the generation of PCR libraries suitable for both molecular and fluorescence in situ hybridization studies from individual baboon and canine chromosomes, separate human homologues, and a rearranged marker chromosome from a transformed cell line. PCR libraries specific to subchromosomal regions have also been produced by sorting a small chromosome fragment. This simple and rapid technique will allow generation of nonhuman linkage maps and probes for fluorescence in situ hybridization and the characterization of marker chromosomes from solid tumors. In addition, allele-specific libraries generated by this strategy may also be useful for mapping genetic diseases.

Chromosome analysis of non-Hodgkin's lymphomas by fluorescence in situ hybridization

We have recently carried out a cytogenetic survey of a series of non-Hodgkin's lymphomas (NHLs) and identified chromosomal abnormalities in most of the samples studied. A third of these cases, however, had to be recorded as containing derivative or marker chromosomes, whose origins were either partially or completely unknown. In an attempt to further analyse such cases, we have adopted the fluorescence in situ hybridization (FISH) technique. The FISH technique has allowed us to map the myb gene to 6q23, and then to study its position on 6q- derivative chromosomes in the NHL cells. The related FISH technique of chromosome painting has enabled us to identify a marker chromosome in one of our cases as an abnormal X chromosome, and in other cases has allowed 14q+ derivative chromosomes to be further analysed. We have also applied the FISH technique to the analysis of interphase nuclei, and have been able to determine numerical chromosome changes in NHL interphase cells. The application of the FISH technique to the study of NHL cell chromosomes is likely to enable the identification of most chromosomal abnormalities present, and so may reveal the critical events leading to malignant transformation of lymphoid cells.