Nonselective DNA damage induced by a replication inhibitor results in the selective elimination of extrachromosomal double minutes from human cancer cells

Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure

Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model). In the present paper we investigated 10 cell lines from solid tumors showing MYCN amplification as dmin or hsr. Particularly revealing results were provided by the two subclones of the neuroblastoma cell line STA-NB-10, one showing dmin-only and the second hsr-only amplification. Both subclones showed a deletion, at 2p24.3, whose extension matched the amplicon extension. Additionally, the amplicon structure of the dmin and hsr forms was identical. This strongly argues that the episome model, already demonstrated in leukemias, applies to solid tumors as well, and that dmin and hsr are two faces of the same coin. The organization of the duplicated segments varied from very simple (no apparent changes from the normal sequence) to very complex. MYCN was always overexpressed (significantly overexpressed in three cases). The fusion junctions, always mediated by nonhomologous end joining, occasionally juxtaposed truncated genes in the same transcriptional orientation. Fusion transcripts involving NBAS (also known as NAG), FAM49A, BC035112 (also known as NCRNA00276), and SMC6 genes were indeed detected, although their role in the context of the tumor is not clear.

Emergence of micronuclei and their effects on the fate of cells under replication stress

The presence of micronuclei in mammalian cells is related to several mutagenetic stresses. In order to understand how micronuclei emerge, behave in cells, and affect cell fate, we performed extensive time-lapse microscopy of HeLa H2B-GFP cells in the presence of hydroxyurea at low concentration. Micronuclei formed after mitosis from lagging chromatids or chromatin bridges between anaphase chromosomes and were stably maintained in the cells for up to one cell cycle. Nuclear buds also formed from chromatin bridges or during interphase. If the micronuclei-bearing cells entered mitosis, they either produced daughter cells without micronuclei or, more frequently, produced cells with additional micronuclei. Low concentrations of hydroxyurea efficiently induced multipolar mitosis, which generated lagging chromatids or chromatin bridges, and also generated multinuclear cells that were tightly linked to apoptosis. We found that the presence of micronuclei is related to apoptosis but not to multipolar mitosis. Furthermore, the structural heterogeneity among micronuclei, with respect to chromatin condensation or the presence of lamin B, derived from the mechanism of micronuclei formation. Our study reinforces the notion that micronucleation has important implications in the genomic plasticity of tumor cells.

Expulsion of amplified MYCN from homogenously staining chromosomal regions in neuroblastoma cell lines after cultivation with cisplatin, doxorubicin, hydroxyurea, and vincristine

Amplified MYCN, common in neuroblastomas, can be detected as double minutes (dmin) or homogenously staining chromosomal regions (hsr). Expulsion of amplified MYCN has only been described in dmin. We used hydroxyurea (HU), which accelerates the expulsion of amplified genes and cytostatics (used in neuroblastoma therapy), to describe MYCN amplification changes after chemotherapy. We used IMR-32, SK-N-AS, UKF-NB-2, UKF-NB-3, UKF-NB-4, and derived sublines resistant to doxorubicin, cisplatin, and vincristine. The loss of amplified MYCN copies was investigated using comparative genomic hybridization and by fluorescent in situ hybridization. We found expulsion of amplified MYCN from hsr in UKF-NB-4 and IMR-32 cell lines, and determined the exact number of amplified MYCN copies. After the first cultivation with HU, some amplified MYCN was lost. UKF-NB-4 lost 20 copies on average, and IMR-32 lost 15 copies (P<0.001). After the second cultivation, cells without MYCN amplification were found. In comparison to sensitive cell lines, drug-resistant cell lines lost 17 copies on average. Our data show that expulsion of amplified MYCN genes is also possible from hsr and may be induced, not only by HU, but by other cytostatics as well.

Episomal high copy number maintenance of hairpin-capped DNA bearing a replication initiation region in human cells

We previously found that a plasmid bearing a replication initiation region efficiently initiates gene amplification in mammalian cells and that it generates extrachromosomal double minutes and/or chromosomal homogeneously staining regions. During analysis of the underlying mechanism, we serendipitously found that hairpin-capped linear DNA was stably maintained as numerous extrachromosomal tiny episomes for more than a few months in a human cancer cell line. Generation of such episomes depended on the presence of the replication initiation region in the original plasmid. Despite extrachromosomal maintenance, episomal gene expression was epigenetically suppressed. The Southern blot analysis of the DNA of cloned cells revealed that the region around the hairpin end was diversified between the clones. Furthermore, the bisulfite-modified PCR and the sequencing analyses revealed that the palindrome sequence that derived from the original hairpin end or its end-resected structure were well preserved during clonal long term growth. From these data, we propose a model that explains the formation and maintenance of these episomes, in which replication of the hairpin-capped DNA and cruciform formation and its resolution play central roles. Our findings may be relevant for the dissection of mammalian replicator sequences.

How transcription proceeds in a large artificial heterochromatin in human cells

Heterochromatin is critical for genome integrity, and recent studies have suggested the importance of transcription in heterochromatin for maintaining its silent state. We previously developed a method to generate a large homogeneously staining region (HSR) composed of tandem plasmid sequences in human cells that showed typical heterochromatin characteristics. In this study, we examined transcription in the HSR. We found that transcription of genes downstream to no-inducible SRα promoter was restricted to a few specific points inside the large HSR domain. Furthermore, the HSR localized to either to the surface or to the interior of the nucleolus, where it was more actively transcribed. The perinucleolar or intranucleolar locations were biased to late or early S-phase, and the location depended on either RNA polymerase II/III or I transcription, respectively. Strong activation of the inducible TRE promoter resulted in the reversible loosening of the HSR domain and the appearance of transcripts downstream of not only the TRE promoters, but also the SRα promoters. During this process, detection of HP1α or H3K9Me3 suggested that transcription was activated at many specific points dispersed inside large heterochromatin. The transcriptional rules obtained from studying artificial heterochromatin should be useful for understanding natural heterochromatin.

Classification of chromosome segregation errors in cancer

Abnormal chromosome segregation at mitosis is one way by which neoplastic cells accumulate the many genetic abnormalities required for tumour development. In this paper, a straightforward morphology-based classification of chromosome segregation errors in cancer is suggested. This classification distinguishes between abnormalities in spindle symmetry (spindle multipolarity, size-asymmetry of ana-telophase poles) and abnormalities in sister chromatid segregation (chromosome bridges, chromatid bridges, chromosome lagging, acentric fragment lagging). Often, these categories of errors must be combined to accurately describe the events in a single abnormal mitotic cell. The suggested categories can to some extent be distinguished by standard chromatin staining. However, labelling of abnormal mitotic figures by fluorescence in situ hybridization and immunofluorescence enhances the accuracy of classification and also allows visualisation of the segregation of individual chromosomes, making it possible to detect non-disjunction also in the absence of gross alterations in mitotic morphology. Further characterisation of the molecular alterations leading to abnormal chromosome segregation together with the current developments in nano-level and real-time imaging will undoubtedly lead to an improved understanding of chromosome dynamics in cancer cells. Any morphology-based classification of chromosome segregation errors in cancer must therefore be taken as provisional, anticipating a satisfactory integration of morphology and molecular biology.