Double minute chromosomes are not centromeric regions of the host chromosomes

Life of double minutes: generation, maintenance, and elimination

Advances in genome sequencing have revealed a type of extrachromosomal DNA, historically named double minutes (also referred to as ecDNA), to be common in a wide range of cancer types, but not in healthy tissues. These cancer-associated circular DNA molecules contain one or a few genes that are amplified when double minutes accumulate. Double minutes harbor oncogenes or drug resistance genes that contribute to tumor aggressiveness through copy number amplification in combination with favorable epigenetic properties. Unequal distribution of double minutes over daughter cells contributes to intratumoral heterogeneity, thereby increasing tumor adaptability. In this review, we discuss various models delineating the mechanism of generation of double minutes. Furthermore, we highlight how double minutes are maintained, how they evolve, and discuss possible mechanisms driving their elimination.

Extrachromosomal circular DNA in cancer: history, current knowledge, and methods

Extrachromosomal circular DNA (eccDNA) is a closed-circle, nuclear, nonplasmid DNA molecule found in all tested eukaryotes. eccDNA plays important roles in cancer pathogenesis, evolution of tumor heterogeneity, and therapeutic resistance. It is known under many names, including very large cancer-specific circular extrachromosomal DNA (ecDNA), which carries oncogenes and is often amplified in cancer cells. Our understanding of eccDNA has historically been limited and fragmented. To provide better a context of new and previous research on eccDNA, in this review we give an overview of the various names given to eccDNA at different times. We describe the different mechanisms for formation of eccDNA and the methods used to study eccDNA thus far. Finally, we explore the potential clinical value of eccDNA.

Mechanisms Underlying Recurrent Genomic Amplification in Human Cancers

Focal copy-number increases (genomic amplification) pinpoint oncogenic driver genes and therapeutic targets in cancer genomes. With the advent of genomic technologies, recurrent genomic amplification has been mapped throughout the genome. Recurrent amplification could be solely due to positive selection for the tumor-promoting effects of amplified gene products. Alternatively, recurrence could result from the susceptibility of the loci to amplification. Distinguishing between these possibilities requires a full understanding of the amplification mechanisms. Two mechanisms, the formation of double minute (DM) chromosomes and breakage-fusion-bridge (BFB) cycles, have been repeatedly linked to genomic amplification, and the impact of both mechanisms has been confirmed in cancer genomics data. We review the details of these mechanisms and discuss the mechanisms underlying recurrence.

Analysis of ALK, MYCN, and the ALK ligand ALKAL2 (FAM150B/AUGα) in neuroblastoma patient samples with chromosome arm 2p rearrangements

Gain of chromosome arm 2p is a previously described entity in neuroblastoma (NB). This genomic address is home to two important oncogenes in NB-MYCN and anaplastic lymphoma kinase (ALK). MYCN amplification is a critical prognostic factor coupled with poor prognosis in NB. Mutation of the ALK receptor tyrosine kinase has been described in both somatic and familial NB. Here, ALK activation occurs in the context of the full-length receptor, exemplified by activating point mutations in NB. ALK overexpression and activation, in the absence of genetic mutation has also been described in NB. In addition, the recently identified ALK ligand ALKAL2 (previously described as FAM150B and AUGα) is also found on the distal portion of 2p, at 2p25. Here we analyze 356 NB tumor samples and discuss observations indicating that gain of 2p has implications for the development of NB. Finally, we put forward the hypothesis that the effect of 2p gain may result from a combination of MYCN, ALK, and the ALK ligand ALKAL2.

Successful treatment of both double minute of C-MYC and BCL-2 rearrangement containing large B-cell lymphoma with subsequent unfortunate development of therapy-related acute myeloid leukemia with t(3;3)(q26.2;q21)

Double minute chromosomes (DMs), although relatively frequently encountered in solid tumors, are rare in hematologic neoplasms such as acute myeloid leukemia (AML), and even rarer in lymphoid neoplasms. t(3;3)(q26.2;q21) is a very rare genetic alteration observed in myeloid neoplasm. Herein we report an interesting and unique case of concomitant C-MYC DMs and t(14;18)-containing large B-cell lymphoma, which was successfully treated with R-hyper-CVAD; unfortunately, the patient has developed a therapy-related AML (t-AML) 2 years since the start of his lymphoma treatment. His t-AML contains both t(3;3)(q26.2;q21) and monosomy 7, and the patient died of AML 10 months after the initial diagnosis of t-AML despite clinical remission. To the best of our knowledge, this is the first reported case of C-MYC DM-containing de novo large B-cell lymphoma, which was successfully treated with complete remission, but unfortunately died of t-AML harboring t(3;3)(q21;q26).

Binomial mitotic segregation of MYCN-carrying double minutes in neuroblastoma illustrates the role of randomness in oncogene amplification

BACKGROUND

Amplification of the oncogene MYCN in double minutes (DMs) is a common finding in neuroblastoma (NB). Because DMs lack centromeric sequences it has been unclear how NB cells retain and amplify extrachromosomal MYCN copies during tumour development.

PRINCIPAL FINDINGS

We show that MYCN-carrying DMs in NB cells translocate from the nuclear interior to the periphery of the condensing chromatin at transition from interphase to prophase and are preferentially located adjacent to the telomere repeat sequences of the chromosomes throughout cell division. However, DM segregation was not affected by disruption of the telosome nucleoprotein complex and DMs readily migrated from human to murine chromatin in human/mouse cell hybrids, indicating that they do not bind to specific positional elements in human chromosomes. Scoring DM copy-numbers in ana/telophase cells revealed that DM segregation could be closely approximated by a binomial random distribution. Colony-forming assay demonstrated a strong growth-advantage for NB cells with high DM (MYCN) copy-numbers, compared to NB cells with lower copy-numbers. In fact, the overall distribution of DMs in growing NB cell populations could be readily reproduced by a mathematical model assuming binomial segregation at cell division combined with a proliferative advantage for cells with high DM copy-numbers.

CONCLUSION

Binomial segregation at cell division explains the high degree of MYCN copy-number variability in NB. Our findings also provide a proof-of-principle for oncogene amplification through creation of genetic diversity by random events followed by Darwinian selection.

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.

Amplification and overexpression of the hepatocyte growth factor receptor (HGFR/MET) in rat DMBA sarcomas

In the present study subcutaneous fibrosarcomas were induced by the carcinogen 7,12-dimethylbenz(a)anthracene (DMBA) in rats from F1 generation cross breedings of two different inbred strains. Comparative genomic hybridization (CGH) analysis, which allows detection of DNA sequence copy changes, was applied to one of the tumors and it was found that there were increased copy numbers of sequences at chromosome 4q12-q21 in this tumor. We have previously determined that the loci for the hepatocyte growth factor (Hgf) and hepatocyte growth factor receptor (Hgfr/Met), a protooncogene, are situated in this particular chromosome region. Using probes for the two genes in FISH (fluorescence in situ hybridization) and in Southern blots we found that the Hgfr/Met gene was amplified in five of the 19 sarcomas studied, and that the Hgf gene was coamplified in two of them. Northern and Western blots and tyrosine phosphorylation analysis showed that the HGF receptor was overexpressed and functional in all five tumors, as well as in two additional tumors. In summary, both amplification and overexpression of the Hgfr/Met gene was found in about 25% of DMBA-induced experimental rat sarcomas, and HGF receptor overexpression alone was seen in two additional tumors. Possibly this reflects an involvement in paracrine or autocrine stimulation of growth and invasiveness by HGF. Our finding could provide a rodent model system to increased knowledge about causality and therapy, which may be applicable to the sizeable fraction of human musculoskeletal tumors displaying MET overexpression.

Selective entrapment of extrachromosomally amplified DNA by nuclear budding and micronucleation during S phase

Acentric, autonomously replicating extrachromosomal structures called double-minute chromosomes (DMs) frequently mediate oncogene amplification in human tumors. We show that DMs can be removed from the nucleus by a novel micronucleation mechanism that is initiated by budding of the nuclear membrane during S phase. DMs containing c-myc oncogenes in a colon cancer cell line localized to and replicated at the nuclear periphery. Replication inhibitors increased micronucleation; cell synchronization and bromodeoxyuridine-pulse labeling demonstrated de novo formation of buds and micronuclei during S phase. The frequencies of S-phase nuclear budding and micronucleation were increased dramatically in normal human cells by inactivating p53, suggesting that an S-phase function of p53 minimizes the probability of producing the broken chromosome fragments that induce budding and micronucleation. These data have implications for understanding the behavior of acentric DNA in interphase nuclei and for developing chemotherapeutic strategies based on this new mechanism for DM elimination.

Identification of the origin of double minutes in normal human cells by laser-based chromosome microdissection approach

Single copies of tiny chromosome fragments, appearing as double minutes, were observed in a high proportion of cells from amniotic fluid cultures of two mothers undergoing prenatal testing because of advanced age. We applied a laser-based chromosome microdissection method to diagnose the origin of the double minutes. The diagnostic procedures consisted of microdissection of double minutes from a single cell, polymerase chain reaction (PCR) amplification of the dissected DNA, and subsequent fluorescence in situ hybridization (FISH) using the PCR products as a probe pool. Metaphase chromosomes from the patients' cells and from a karyotypically normal individual were probed. Using this strategy, we were able to determine that the double minutes originated from the centromere of chromosome 13 or 21 in one case, and from the chromosome 12 centromere in the other. The characterization of such double minutes helps both in the delineation of the nature of these epichromosomal bodies in normal individuals as well as in the clarification of genetic counselling issues.

Differences in c-myc and pvt-1 amplification in SEWA sarcoma sublines selected for adherent or non-adherent growth

Conversion of solid sarcomas and carcinomas into ascites tumors depends on the in vivo selection of phenotypically altered tumor cell variants that can grow in the dissociated form. Once selected, they retain this property even after prolonged s.c. growth as solid tumors. From an s.c.-passaged subline of an ascites-converted murine sarcoma (SEWA-AS12), we were able to separate cells adapted to the ascites form of growth from cells that can only grow in the solid form on the basis of their differential adherence to plastic. Both c-myc and pvt-1 were amplified approximately 63- to 77-fold in the nonadherent subline (SEWA-AS12-NA), but only 5- to 8-fold in the adherent subline (SEWA-AS12-ADH). This suggests that c-myc and/or pvt-1 amplification may provide a selective advantage to cells that can grow in the dissociated form.

DNA content and structure of (double) minutes of a methotrexate-resistant cell line

We have determined the DNA content of intact double minutes (DMs) and of single minutes (SMs) by fluorometry of the individual chromatin bodies in metaphase spreads after staining with Feulgen-Schiff pararosaniline. We find that the intact DMs and SMs of the methotrexate-resistant mouse cell line 3T6R50 contain 4.4 megabase pairs (Mb) and 2.6 Mb DNA respectively, using the DNA content of E. coli (4.7 Mb) as a reference. As the pulsed field gradient gel electrophoresis experiments by van der Bliek et al. (1988) have indicated that the minutes of 3T6R50 cells contain a homogeneous population of 2.5 Mb DNA circles, we conclude that a SM contains one circular double strand DNA molecule of approximately 2.5 Mb, whereas DMs contain two.

Analysis of the replication mode of double minutes using the PCC technique combined with BrdUrd labeling

A cultured line of neuroblastoma cells (NB) was found to contain double minute chromosomes (DMs) DMs have been reported to be acentric and, therefore, to be segregated randomly into daughter cells without separating their sister elements. When NB cells were fused with Chinese hamster metaphase cells, prematurely condensed chromosomes (PCCs) were induced. DMs seen together with G2 PCCs appeared to be closely paired, dot-like structures resembling DMs observable in metaphase cells. In contrast, DMs in G1 cells showed a tendency to become single as the stage progressed so that the majority of DMs in late G1 cells were actually no longer double. DMs in S-phase cells, however, again appeared double. These results clearly indicate why DMs are invariably double and never assume a quadruple configuration in metaphase cells in spite of their non-disjunctional segregation at anaphase. Such a characteristic mode of DM replication was further confirmed by a 5-bromo-2'-deoxyuridine (BrdUrd) labeling experiment: when NB cells were exposed to BrdUrd for two successive rounds of DNA replication prior to PCC induction, half of the resulting single G1 minutes as well as G1 PCCs stained dark and the other half stained light after staining for sister chromatid differentiation.

Analysis of double minutes and double minute-like chromatin in human and murine tumor cells using antikinetochore antibodies

Antikinetochore antibodies from patients with the calcinosis, Raynaud's phenomenon, esophageal dismobility, sclerodactyly, telangiectasia-(CREST)-syndrome of scleroderma were used as immunofluorescent probes to discriminate between the presence and absence of kinetochores in minute chromosomes not previously seen by conventional banding methods. Double minute chromosomes (DM) consistently lack the antigenic component of the kinetochore, which is direct evidence for the fact that they do not have a centromere. Although somatically stable in malignant cell populations, DM are unable to attach to the mitotic spindle. Conversely, despite their structural similarity to DM, chromosome fragments and supernumerary marker chromosomes exhibit intensely fluorescing kinetochores and, thus, are subject to a precise anaphasic distribution.

Cytogenetic evidence of gene amplification as a mechanism for tumor cell invasion

In order to study the process by which human melanoma cells achieve invasion of basement membranes, a modification of the Membrane Invasion Culture System was developed to allow the in vitro collection of human melanoma cell populations that had invaded acellular human amniotic membranes. A significant increase in the number of double-minute chromosomes (DMs) was observed in metaphase nuclei of A375P human melanoma cells which had passed through two amniotic membranes (A375P-2) over that of control cells. Eighteen percent of the first monolayer of A375P-2 cells contained 1-89 DMs/cell, whereas 3-8.3% of the control A375P cells contained 1-10 DMs/cell. There was a rapid loss of DMs in A375P-2 cells as a function of passage number. After 25 days in tissue culture, the incidence of DMs had essentially dropped below the control range. These data indicate that an unstable gene amplification event may be part of the process by which melanoma cells execute invasion through basement membranes.

Rings and double minutes in a case with blastic phase of chronic myelocytic leukemia

The patient studied was a 33-year-old female in the blastic phase of chronic myelocytic leukemia resistant to busulfan. The results of cytogenetic studies of bone marrow cells were as follows: The abnormal chromosomes were double Ph1, +19, +6, +B, ring D, double ring D, double minutes (DM) of various sizes, etc. The mean number of DM per cell was increased in 4-day culture compared with that in 1-day culture.

Patterns of BrdU incorporation in homogeneously staining regions and double minutes

The replication chronology of two structural chromosome abnormalities linked to the amplification phenomenon of DNA sequences was investigated. Three cell lines containing homogeneously staining region (HSR) chromosomes (IMR-32, MK42, and COLO-320) and one line with double minutes (DM) (SW-613) were examined. Using a bromodeoxyuridine-Hoechst 33258-Giemsa method, the HSR in the three cell lines were shown to be composed of subunits that replicated their DNA throughout all portions of the S-phase of the cell cycle. The double minute chromosomes were observed to replicate randomly throughout the entire S-phase, with no pattern evident. These results are consistent with the suggestion that DNA from HSR and DM are structurally and functionally related. Moreover, this observation that these amplified regions replicate their DNA throughout the entire S-phase favors the idea that, during amplification processes, both early and late replicating sequences are included. The apparent discordance between staining characteristics and replication behavior exhibited by some HSR and DM are also discussed.

Incidence of double minutes, cytogenetic equivalents of gene amplification, in human carcinoma cells

Screening of the occurrence of double minutes (DM) was performed in more than 1,000 metaphases obtained from a total of 22 solid human breast tumours and more than 3,600 metaphases from a total of 55 malignant effusions (45 patients with different types of carcinomas). DM were observed in 15 of these breast tumor cases and in 34 of the effusions (obtained from 29 cancer patients). The percentage of cells exhibiting DM as well as the number of DM per respective cell varied widely. It could be seen that metastatic cells from malignant effusions exhibited on the average more DM per cell than did cells of primary breast carcinomas. Differences in the incidence of DM could be observed between different carcinomas as well as between different age groups. In addition, it did not appear that DM could be induced by mutagenic tumor therapy. DM are thus not a rare finding in human solid tumors but, as cytogenetic equivalents of gene amplification, they rather represent a fundamental biological characteristic of tumor development.

Relationship of amplified dihydrofolate reductase genes to double minute chromosomes in unstably resistant mouse fibroblast cell lines

Murine 3T6 selected in increasing concentrations of methotrexate were unstable with respect to dihydrofolate reductase overproduction and methotrexate resistance when they are cultured in the absence of methotrexate. An analysis of the karyotypes of these resistant cells revealed the presence of numerous double minute chromosomes. We observed essentially identical kinetics of loss of dihydrofolate reductase gene sequences in total deoxyribonucleic acid and in deoxyribonucleic acid from fractions enriched in double minute chromosomes and in the numbers of double minute chromosomes per cell during reversion to methotrexate sensitivity, and this suggested that unstably amplified gene sequences were localized on double minute chromosomes. This conclusion ws also supported by an analysis of cell populations sorted according to dihydrofolate reductase enzyme contents, in which relative gene amplification and double minute chromosome content were related proportionally.

Amplification and loss of dihydrofolate reductase genes in a Chinese hamster ovary cell line

During stepwise increases in the methotrexate concentration in culture medium, we selected Chinese hamster ovary cells that contained elevated dihydrofolate reductase levels which were proportional to the number of dihydrofolate reductase gene copies (i.e., gene amplification). We studied the dihydrofolate reductase levels in individual cells that underwent the initial steps of methotrexate resistance by using the fluorescence-activated cell sorter technique. Such cells constituted a heterogeneous population with differing dihydrofolate reductase levels, and they characteristically lost the elevated enzyme levels when they were grown in the absence of methotrexate. The progeny of individual cells with high enzyme levels behaved differently and could lose all or variable numbers of the amplified genes.

Amplification and loss of dihydrofolate reductase genes in a Chinese hamster ovary cell line

During stepwise increases in the methotrexate concentration in culture medium, we selected Chinese hamster ovary cells that contained elevated dihydrofolate reductase levels which were proportional to the number of dihydrofolate reductase gene copies (i.e., gene amplification). We studied the dihydrofolate reductase levels in individual cells that underwent the initial steps of methotrexate resistance by using the fluorescence-activated cell sorter technique. Such cells constituted a heterogeneous population with differing dihydrofolate reductase levels, and they characteristically lost the elevated enzyme levels when they were grown in the absence of methotrexate. The progeny of individual cells with high enzyme levels behaved differently and could lose all or variable numbers of the amplified genes.

Relationship of amplified dihydrofolate reductase genes to double minute chromosomes in unstably resistant mouse fibroblast cell lines

Murine 3T6 selected in increasing concentrations of methotrexate were unstable with respect to dihydrofolate reductase overproduction and methotrexate resistance when they are cultured in the absence of methotrexate. An analysis of the karyotypes of these resistant cells revealed the presence of numerous double minute chromosomes. We observed essentially identical kinetics of loss of dihydrofolate reductase gene sequences in total deoxyribonucleic acid and in deoxyribonucleic acid from fractions enriched in double minute chromosomes and in the numbers of double minute chromosomes per cell during reversion to methotrexate sensitivity, and this suggested that unstably amplified gene sequences were localized on double minute chromosomes. This conclusion ws also supported by an analysis of cell populations sorted according to dihydrofolate reductase enzyme contents, in which relative gene amplification and double minute chromosome content were related proportionally.

Coincidence of cytogenetic markers in four murine cell lines

Foreign body tumorigenesis was induced by the subcutaneous implantation of a plastic or glass cylinder in BALB/c mice; the inoculation of human neoplastic cells significantly increased the incidence of these anaplastic sarcomas. Of 15 tumors studied, four presented the same markers: one induced with and three without human neoplastic cell inoculation within the foreign body. The markers observed were double minutes (DM), a long acrocentric marker (MLA), and a metacentric marker (MM). The DM are a number of small often tiny chromosomal structures appearing in pairs together with chromosomes of ordinary size. MLA is a long acrocentric derived from a translocation in tandem between chromosomes #1 and #16. MM is due to centric fusion of two chromosomes #10. Numerical anomalies consisted of gains of the same chromosomes types. It is postulated that these coincident findings are related to the foreign-body tumorigenesis.

Stability of C-banded and C-bandless microchromosomes in clonal sublines of the RVP3 mouse tumor grown serially in vivo

Karylogic studies were performed on three monocellular clones derived from mouse RVP3 cells, which had been originally transformed with the Prague strain of Rous sarcoma virus. All clones that had originally contained a stable number of microchromosomes, continues to retain them after prolonged passage in vivo. Centromeric heterochromatin was absent in 32% of the microchromosomes as revealed by C-banding technique. The stability of microchromosomes either positive or negative for centromeric heterochromatin is discussed in relation to double-minute chromatin bodies found in early passages of RVP3 tumor cells.

Chromosomes in solid tumors

Systematic chromosomal studies in solid tumors have been scanty (excepting meningiomas), because of the fact that it is difficult to obtain tumor material at desired times and only in about 10--15% of the cases adequate chromosome preparations are suitable with a direct technique or short term culture. A few facts that emerge from the study of various solid tumors are as follows: 1. modal number of chromosomes in parimary tumors tends to be lower that of metastatic; 2. certain chromosomes and chromosome regions are more susceptible for breakage to oncogenic conditions, hence, there is non-random involvement of certain chromosomes in human neoplasia and 3. certain chromosome changes are more often associated with metastatic spread than others.

Are double minutes chromosomes?

Double minutes of a human breast cancer cell line revealed no centromeres by Cd banding. They cluster at the periphery of metaphase plates, usually encased in a matrix material. They move in anaphase passively with the chromosomes by attaching to the sides or ends of the chromosomes. The two "sister minutes" move to the same pole without separation. Such anomalous mitotic behavior suggests that double minutes are not chromosomes.