Double-minutes--a chromosomal aberration in Rous sarcomas in mice

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells

Extrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. Intercellular differences in ecDNA structure pointed to circular recombination as a mechanism of ecDNA evolution. These results demonstrate scEC&T-seq as an approach to systematically characterize both small and large circular DNA in cancer cells, which will facilitate the analysis of these DNA elements in cancer and beyond.

Chromatin Mechanisms Driving Cancer

The change in cell state from normal to malignant is driven fundamentally by oncogenic mutations in cooperation with epigenetic alterations of chromatin. These alterations in chromatin can be a consequence of environmental stressors or germline and/or somatic mutations that directly alter the structure of chromatin machinery proteins, their levels, or their regulatory function. These changes can result in an inability of the cell to differentiate along a predefined lineage path, or drive a hyperactive, highly proliferative state with addiction to high levels of transcriptional output. We discuss how these genetic alterations hijack the chromatin machinery for the oncogenic process to reveal unique vulnerabilities and novel targets for cancer therapy.

From Human Cytogenetics to Human Chromosomics

BACKGROUND

The concept of "chromosomics" was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a "chromosomic view" of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is dedicated to the memory of Prof. Uwe Claussen (30 April 1945⁻20 July 2008).

RECENT FINDINGS

Chromosomics is the study of chromosomes, their three-dimensional positioning in the interphase nucleus, the consequences from plasticity of chromosomal subregions and gene interactions, the influence of chromatin-modification-mediated events on cells, and even individuals, evolution, and disease. Progress achieved in recent years is summarized, including the detection of chromosome-chromosome-interactions which, if damaged, lead to malfunction and disease. However, chromosomics in the Human Genetics field is not progressing presently, as research interest has shifted from single cell to high throughput, genomic approaches.

CONCLUSION

Chromosomics and its impact were predicted correctly in 2005 by Prof. Claussen. Although some progress was achieved, present reconsiderations of the role of the chromosome and the single cell in Human Genetic research are urgently necessary.

Evolution of large extrachromosomal elements in HL-60 cells during culture and the associated phenotype alterations

In the HL-60 sublines that were isolated after a long-term continuous culture, abnormally stained or abnormally banded regions on chromosomes replaced extrachromosomal double minutes. The c-MYC gene is amplified in these structures. We followed the c-MYC gene loci during a consecutive passage by using FISH, and have found a large extrachromosomal element (LEE) that preexisted at the earliest passage in a very small fraction of cells. No chromosomal integration of c-MYC sequences was observed in up to 225 passages. The LEEs persistently evolved during culture and were not excluded from the nucleus. In the LEE-positive cells, the spontaneous differentiation was blocked and the granulocytic differentiation that was induced by treatment with dimethyl sulfoxide was reversed by withdrawal of the drug. The c-MYC gene integration into LEEs is unlikely to lead to these phenotypes. The reversibility might be related to the reversible c-MYC down-regulation during the early phase of the drug treatment of HL-60 cells at early cell passages.

Chromosome breakpoints near CpG islands in double minutes

Double minute chromosomes (DMs) are the principal genetic vehicles for amplifying oncogenes in human tumors and drug resistance genes in cultured mouse cells. Mouse EMT-6 cells resistant to methotrexate (MTX) generally contain circular DMs, approximately 1 megabase (Mb) in size, that amplify the dihydrofolate reductase (DHFR) gene. The 1 Mb DMs generally have CpG islands located 500 kb upstream of the DHFR gene. The purpose of this study was to determine the relationship between CpG islands and chromosomal breakpoints giving rise to the DM. We show that EMT-6 cells growing in very low levels of MTX that do not yet contain the 1 Mb DHFR-amplifying DM, develop a NotI/EagI site 500 kb upstream of the DHFR gene. This NotI site is close to, if not identical with, one of the chromosomal breakpoints giving rise to the DM. We show that 500 kb of DM DNA from upstream of the DHFR gene is derived from 500 kb of chromosomal DNA upstream of the chromosomal DHFR gene. The downstream breakpoint maps to a region approximately 200 kb downstream of the DHFR gene near a chromosomal SstII/EagI site. Therefore, approximately 700 kb of DM DNA was derived from the genomic region surrounding the DHFR gene. To confirm the organization of the DM DNA, we isolated DNA probes from the 1 Mb DM. Using pulsed field gel electrophoresis and Southern hybridization, we determined the approximate location of each probe with respect to the CpG island in both the DM and the chromosome. Approximately 300 kb of chimeric DNA from a region unrelated to the DHFR gene was incorporated during DM formation. Implications for the mechanism of DM formation are discussed.

CpG islands and double-minute chromosomes

Double-minute chromosomes (DMs) amplify oncogenes in human tumors. The organization of genomic DNA in four independently isolated DMs amplifying the DHFR (dihydrofolate reductase) gene has been compared by mapping locations of CpG islands. When cleaved with methylation-sensitive rare-cutting restriction endonucleases, three hypomethylated GC-rich DNA sequences were frequently found in specific regions in these DMs. One such zone was in the CpG island containing the divergently transcribed promoter separating the DHFR and the Rep-3 genes. The other two sites were approximately 500 kb upstream and 300 kb downstream of the DHFR gene. An approximately 800-kb amplified core genomic region containing the DHFR gene using DM-specific probes has been identified in this study. All the DMs consisted of the core amplified region combined with additional DNA fragments. These additional fragments are different for each DM. Therefore, while the DNAs in each of the DMs are different, they have common hypomethylated regions in similar locations. These results suggest a role for the location of hypomethylated GC-rich sites such as the CpG islands in genesis of DMs.

Role of heterochromatin variation in the instability of a marker chromosome during tumor progression

Karyotypic evolution of the poorly metastasizing tumorigenic RSV-transformed B77-3T3 fibroblast line was investigated both in highly metastasizing clones (selected by growth in hard agar) and in spontaneous metastases. Analysis of structural chromosome aberrations associated with the transition from the nonmetastatic to the metastatic phenotype was focused on a readily identifiable marker chromosome (A), displaying an extracentromeric heterochromatic region as a main feature promoting genetic instability. Well-defined changes in the structure of this marker were observed, both in vitro and in vivo, and invariably involved C-heterochromatic variation. In the metastatic clones, a specific rearrangement of the A chromosome was selected. This structural variant (B) showed two extracentromeric C-positive regions and probably originated from duplication of the segment of A included between the centromere and the internal C-band. On the other hand, selection of a modified form of chromosome A, not displaying the interpolated C-heterochromatin, had occurred in the extremely rare B77-3T3 spontaneous metastases. The connection among heterochromatin variants, genetic instability, and chromosome aberrations is discussed.

Karyotype analysis of carcinogen-treated Chinese hamster cells in vitro evolving from a normal to a malignant phenotype

The relationship of cytogenetic changes with the acquisition of an indefinite life span in vitro, the ability of cells to grow in soft agar and their tumourigenicity in syngeneic animals has been studied in control, trans-7,8-dihydrodiolbenzo(a)pyrene and 7 beta,8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-tetrahydrobenzo(a)-pyrene-treated secondary cultures derived from Chinese hamster embryonic lung. Karyotype analysis revealed a sequence of chromosome changes as the cells progressed through culture. Aneuploidy, namely trisomy of chromosome 4, the long arm in particular, was an early dominant change. The possible association of this trisomy with the acquisition of immortality in vitro is implicated, although the involvement of other nonrandom chromosome changes cannot be eliminated, implying that there may be several genomic sites in the Chinese hamster which may potentially be involved with the acquisition of unlimited growth potential. Neither the ability of cells to grow in soft agar nor as tumours could be associated with any specific chromosome(s). Double minutes were observed in metaphases from the cell lines, agar colonies and tumours; their possible relationship with growth advantage is discussed.

Somatic cell fusion as a source of genetic rearrangement leading to metastatic variants

Tumor cell populations displaying metastatic properties often have higher gene dosage than their less malignant progenitor tumors, as shown by increased ploidy levels, chromosome duplication and gene amplification. The acquisition by tumor cells of high chromosome numbers may be due to endoreduplication or somatic hybridization either between tumor cells or between tumor and host cells. All such mechanisms increase genetic variability and instability in tumor cells since they trigger a polyploidization-segregation cycle. Among the wide variety of segregants which may emerge from high-ploidy cells, variants with increased malignancy can be positively selected in vivo. Evidence for in vivo fusion of tumor and normal host cells has been reported in different tumor systems. However the attainment by tumor-host hybrids of a higher degree of malignancy has only been observed following substantial chromosome segregation. The involvement of a cell of bone marrow origin as preferential host partner in the fusion process has been proved both by studies on tumor-host hybrids in bone marrow radiation chimeras and in vitro hybridization experiments between non-metastatic tumors and normal lymphoreticular cells which have led to the establishment of metastatic variants. Several different segregational mechanisms may bring about homozygosity or hemizygosity of recessive alleles in tumor-host hybrids, leading to their expression. The marked chromosome dynamics of tumor-host hybrids are also responsible for extensive chromosome rearrangements. At the molecular level these may represent mechanisms causing altered oncogene activity. The activation of new oncogenes by transposition or amplification as well as the amplification of previously activated oncogenes are the mechanisms most likely to be responsible for transition from low to high malignancy, occurring through ploidy changes, such as those produced by somatic mating.

Characterization of exogenous proviral sequences in hamster tumor cell lines transformed by Rous sarcoma virus rescued from XC cells

Alterations in viral structural genes have been studied in five cell lines derived from Syrian hamster tumors which had been induced by the virus rescued from XC cells by transfection. Two cell lines, H-18 and H-20, have all the viral structural genes expressed, but a new EcoRI recognition site appeared in the region of the pol gene sequence. Provirus present in H-12 lacks the 3' part of the gag gene sequences as well as the pol gene, therefore, it gives rise to an anomalous 1.8 Md EcoRI fragment. This line also does not synthesize viral RNA of genomic size, and none of the subgenomic RNAs found hybridized with the DNApol probe. The H-19 cell line harbors only the src gene and LTR sequences, the U3 part of which seems incomplete or different from that of PR-RSV. The cryptic proviral structure in H-19 is transcribed into src mRNA. The degree of transcription of the src gene is about 25 viral RNA equivalents per cell. The H-9 cells harbor the complete provirus and, in addition, proviral structures having the deletion in gag-pol genes. The possible ways of development of provirus alterations and the role of cryptic proviral sequences in oncogenesis are discussed.

Double minutes in mouse neuroblastoma cells and their hybrids

Cytogenetic studies were carried out on three clones of mouse neuroblastoma cells and six interspecific hybrid cells derived from the mouse neuroblastoma cells with either rat glioma cells and liver cells or Chinese hamster brain cells. The hybrid cells possessed characteristic karyotypes with marker chromosomes originating from the neuroblastoma cells. The parental chromosome constitution in the hybrid cells was clone-specific, even in the clones derived from the same parental cells. Double minutes (DMs) were demonstrated in the neuroblastoma cells and in all the hybrid cells studied. In addition other chromosome aberrations, such as microchromosomes and chromosome pulverization, were also observed in these cells. DMs varied in number and morphology among the cells. The number of DMs per cell correlated positively with the level of ploidy and with the karyological constitution contributed by the parental neuroblastoma cells. The results indicate that DMs have a chromosome nature and that the DMs of neuroblastoma chromosomes were transferred into the hybrid cells.

Marked karyotype abnormalities in two cases of acute myelogenous leukemia

Two patients with acute myelogenous leukemia with severe chromosome abnormalities are described. The cytogenetic analysis shows the following karyotype: patient No. 1: 41,XY,-1,-2,-4,-5,-13,-15,-17,-18,-22,+5 markers; patient No. 2: 46,XY,-2,-5,-7,-13,+16,-21,-21,+5 markers. In each patient one set of double minute chromosomes was observed.

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.

Ultrastructure of double minutes from a human tumor cell line

Double minutes (dm) have been isolated from human tumor cells by zonal centrifugation and by differential pelleting of chromosome suspsension. These methods allowed collection of dm in sufficient quantity and purity for visualization with electron microscopy. Ultrastructurally, the chromatin fibers in dm resemble thrance fragments was found. When the two isolation protocols were compared, differential pelleting was shown to increase purity twofold to 85% dm by mass. The differential pelleting procedure enables easy collection of dm in sufficient quantity and purity for chemical analysis.

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.

Incomplete viral genome in a non-virogenic mouse tumour cell line (RVP3) transformed by Prague strain of avian sarcoma virus

Two cell lines, RVP3 and RVA4, derived originally from mouse tumors induced by the Prague and Schmidt-Ruppin strain of RSV, respectively, were studied. tall attempts failed to induce infectious virus production in RVP3 cells by fusion with chicken fibroblasts even if the cells were infected with avian leukosis viruses. Also, attempts to rescue the viral genome by transfection were unsuccessful. RVP3 cells harboured 31-45% of the viral genome sequences, as was shown by molecular hybridization, and therefore they were designated cryptovirogenic. The tumour cell line RVA4 did not contain any detectable viral sequences. The significance of the detection of the incomplete Rous virus genome sequences in mammalian cells is discussed.

Detailed cytogenetic study of a metastatic bronchial carcinoma

Karyotyping and marker analysis of G- and C-banded metaphases from a metastatic bronchial carcinoma revealed a dominant stemline with five markers and four sidelines with additional markers. One to three minute bodies were noted in the majority of cells and these were classified as markers. On the basis of this analysis it was possible to postulate an evolutionary pathway within the tumour whereby the stemline was derived from existing sidelines.