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Toledo F. Mechanisms Generating Cancer Genome Complexity: Back to the Future. Cancers (Basel) 2020; 12:E3783. [PMID: 33334014 PMCID: PMC7765419 DOI: 10.3390/cancers12123783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022] Open
Abstract
Understanding the mechanisms underlying cancer genome evolution has been a major goal for decades. A recent study combining live cell imaging and single-cell genome sequencing suggested that interwoven chromosome breakage-fusion-bridge cycles, micronucleation events and chromothripsis episodes drive cancer genome evolution. Here, I discuss the "interphase breakage model," suggested from prior fluorescent in situ hybridization data that led to a similar conclusion. In this model, the rapid genome evolution observed at early stages of gene amplification was proposed to result from the interweaving of an amplification mechanism (breakage-fusion-bridge cycles) and of a deletion mechanism (micronucleation and stitching of DNA fragments retained in the nucleus).
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Affiliation(s)
- Franck Toledo
- Genetics of Tumor Suppression, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR3244 Dynamics of Genetic Information, 26 rue d'Ulm, CEDEX 05, 75248 Paris, France
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Twa DDW, Steidl C. Structural genomic alterations in primary mediastinal large B-cell lymphoma. Leuk Lymphoma 2015; 56:2239-50. [DOI: 10.3109/10428194.2014.985673] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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3
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Meng X, Qi X, Guo H, Cai M, Li C, Zhu J, Chen F, Guo H, Li J, Zhao Y, Liu P, Jia X, Yu J, Zhang C, Sun W, Yu Y, Jin Y, Bai J, Wang M, Rosales J, Lee KY, Fu S. Novel role for non-homologous end joining in the formation of double minutes in methotrexate-resistant colon cancer cells. J Med Genet 2014; 52:135-44. [PMID: 25537274 PMCID: PMC4316941 DOI: 10.1136/jmedgenet-2014-102703] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Gene amplification is a frequent manifestation of genomic instability that plays a role in tumour progression and development of drug resistance. It is manifested cytogenetically as extrachromosomal double minutes (DMs) or intrachromosomal homogeneously staining regions (HSRs). To better understand the molecular mechanism by which HSRs and DMs are formed and how they relate to the development of methotrexate (MTX) resistance, we used two model systems of MTX-resistant HT-29 colon cancer cell lines harbouring amplified DHFR primarily in (i) HSRs and (ii) DMs. Results In DM-containing cells, we found increased expression of non-homologous end joining (NHEJ) proteins. Depletion or inhibition of DNA-PKcs, a key NHEJ protein, caused decreased DHFR amplification, disappearance of DMs, increased formation of micronuclei or nuclear buds, which correlated with the elimination of DHFR, and increased sensitivity to MTX. These findings indicate for the first time that NHEJ plays a specific role in DM formation, and that increased MTX sensitivity of DM-containing cells depleted of DNA-PKcs results from DHFR elimination. Conversely, in HSR-containing cells, we found no significant change in the expression of NHEJ proteins. Depletion of DNA-PKcs had no effect on DHFR amplification and resulted in only a modest increase in sensitivity to MTX. Interestingly, both DM-containing and HSR-containing cells exhibited decreased proliferation upon DNA-PKcs depletion. Conclusions We demonstrate a novel specific role for NHEJ in the formation of DMs, but not HSRs, in MTX-resistant cells, and that NHEJ may be targeted for the treatment of MTX-resistant colon cancer.
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Affiliation(s)
- Xiangning Meng
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Xiuying Qi
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Huanhuan Guo
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Mengdi Cai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Chunxiang Li
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jing Zhu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Feng Chen
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Huan Guo
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jie Li
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Yuzhen Zhao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Peng Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jingcui Yu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Chunyu Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Yang Yu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Yan Jin
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, China
| | - Jing Bai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Mingrong Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jesusa Rosales
- Departments of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Ki-Young Lee
- Cell Biology & Anatomy, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, China
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Reshmi SC, Roychoudhury S, Yu Z, Feingold E, Potter D, Saunders WS, Gollin SM. Inverted duplication pattern in anaphase bridges confirms the breakage-fusion-bridge (BFB) cycle model for 11q13 amplification. Cytogenet Genome Res 2007; 116:46-52. [PMID: 17268177 DOI: 10.1159/000097425] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 07/03/2006] [Indexed: 11/19/2022] Open
Abstract
The homogeneously staining region (hsr) involving chromosome band 11q13 includes amplified genes from this chromosome segment and carries a relatively poor prognosis in oral squamous cell carcinomas (OSCC), with shorter time to recurrence and reduced overall survival. We previously identified an inverted duplication pattern of genes within the 11q13 hsr in OSCC cells, supporting a breakage-fusion-bridge (BFB) cycle model for gene amplification. To validate our hypothesis that 11q13 gene amplification in OSCC occurs via BFB cycles, we carried out fluorescence in situ hybridization (FISH) using probes for band 11q13 on 29 OSCC cell lines. We demonstrate that all OSCC cell lines with 11q13 amplification express a significantly higher frequency of anaphase bridges containing 11q13 sequences compared to cell lines without amplification, providing further experimental evidence that 11q13 gene amplification in OSCC cells occurs via BFB cycles. Elucidation of mechanisms responsible for initiating and promoting gene amplification provides opportunities to identify new biomarkers to aid in the diagnosis and prognosis of oral cancer, and may be useful for developing novel therapeutic strategies for patients with OSCC.
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Affiliation(s)
- S C Reshmi
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
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5
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Abstract
Chromosomal instability is a common feature of human tumors, including oral cancer. Although a tumor karyotype may remain quite stable over time, chromosomal instability can lead to 'variations on a theme' of a clonal cell population, often with each cell within a tumor possessing a different karyotype. Thus, chromosomal instability appears to be an important acquired feature of tumor cells, since propagation of such a diverse cell population may facilitate evasion of standard therapies. There are several sources of chromosomal instability, although the primary causes appear to be defects in chromosomal segregation, telomere stability, cell-cycle checkpoint regulation, and the repair of DNA damage. Our understanding of the biological basis of chromosomal instability in cancer cells is increasing rapidly, and we are finding that the seemingly unrelated origins of this phenomenon may actually be related through the complex network of cellular signaling pathways. Here, we review the general causes of chromosomal instability in human tumors. Specifically, we address the state of our knowledge regarding chromosomal instability in oral cancer, and discuss various mechanisms that enhance the ability of cancer cells within a tumor to express heterogeneous karyotypes. In addition, we discuss the clinical relevance of factors associated with chromosomal instability as they relate to tumor prognosis and therapy.
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Affiliation(s)
- S C Reshmi
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, 130 DeSoto Street, Room A300, Pittsburgh, PA 15261, USA
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6
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Toledo F, Buttin G, Debatisse M. The origin of chromosome rearrangements at early stages of AMPD2 gene amplification in Chinese hamster cells. Curr Biol 2005; 3:255-64. [PMID: 15335745 DOI: 10.1016/0960-9822(93)90175-n] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/1993] [Revised: 03/31/1993] [Accepted: 04/01/1993] [Indexed: 01/03/2023]
Abstract
BACKGROUND Gene amplification and chromosomal rearrangements are frequent properties of cancer cells, provoking considerable interest in the mechanism of gene amplification and its consequences - particularly its relationship to chromosomal rearrangements. We recently studied the amplification of the gene for adenylate deaminase 2 (AMPD2) in Chinese hamster cells. Using fluorescent in situ hybridization (FISH), we found that early amplification of the AMPD2 gene is based on unequal gene segregation at mitosis, rather than local over-replication. We observed large inverted repeats of the amplified sequences, consistent with an amplification mechanism involving cycles of chromatid breakage, followed by fusion after replication and, in mitosis, the formation of bridges between the fused sister chromatids that leads to further breaks - a process we refer to as chromatid breakage-fusion-bridge (BFB) cycles. Our previous work left open the question of how this mechanism of gene amplification is related, if at all, to the chromosomal rearrangements that generate the dicentric, ring and double-minute (DM) chromosomes observed in some AMPD2-amplified metaphase cells, which are not predicted intermediates of chromatid BFB cycles, although they could be generated by related chromosome BFB cycles. RESULTS We have addressed this question using FISH with probes for the AMPD2 gene and other markers on the same chromosome. Our results are not consistent with the chromosome BFB cycle mechanism, in which two chromatids break simultaneously and fuse to generate, after replication, a dicentric chromosome. Rather, they suggest that dicentric chromosomes are generated by secondary events that occur during chromatid BFB cycles. Our results also suggest that DM chromosomes are generated by the 'looping-out' of a chromosomal region, generating a circular DNA molecule lacking a centromere; in this case, gene amplification would result from the unequal segregation of DM chromosomes at mitosis. CONCLUSION We conclude that, at early stages of AMPD2 gene amplification, chromatid BFB cycles are a major source of both 'intrachromosomal' gene amplification and genomic rearrangement, which are first limited to a single chromosome but which can then potentially spread to any additional chromosome. It also seems that, occasionally, a DNA sequence including the AMPD2 gene can be excised, generating a DM chromosome and thus initiating an independent process of 'extrachromosomal' amplification.
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Affiliation(s)
- F Toledo
- Unité de Génétique Somatique (URA CNRS 361), Institut Pasteur 25, rue du Dr. Roux, 75724 Paris Cedex 15, France
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Debatisse M, Malfoy B. Gene amplification mechanisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2005; 570:343-361. [PMID: 18727507 DOI: 10.1007/1-4020-3764-3_12] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Michelle Debatisse
- UMR 7147, Institut Curie, CNRS, Université Pierre et Marie Curie, Paris, France
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8
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Anglana M, Debatisse M. Dual control of replication timing. Stochastic onset but programmed completion of mammalian chromosome duplication. J Biol Chem 2001; 276:36639-46. [PMID: 11454865 DOI: 10.1074/jbc.m104501200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In mammalian cells, DNA replication proceeds according to a precise temporal order during the S phase, but how this program is controlled remains poorly understood. We analyzed the replication-dependent bromodeoxyuridine banding of chromosomes in Chinese hamster cells treated with the spindle poison nocodazole. In these cells, nocodazole induces a transient mitotic arrest, followed by DNA re-replication without intervening cell division. Nuclear fragmentation is often observed in tetraploid derivatives, and previous studies suggest that replication timing of chromosomes could be affected when they are segregated into different micronuclei. Here we show that the onset of replication is frequently asynchronous on individual chromosomes during the re-replication process. Moreover, fluorescence in situ hybridization analysis revealed that replication synchrony is equally altered in fragmented and non-fragmented nuclei, indicating that asynchronous onset of replication is not dependent on physical separation of the chromosomes into isolated compartments. We also show that the ordered program of replication is always preserved along individual chromosomes. Our results demonstrate that the onset of replication of individual chromosomes in the same nuclear compartment can be uncoupled from the time of S-phase entry and from the programmed replication of chromosome sub-domains, revealing that multi-level controls contribute to establish replication timing in mammalian cells.
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Affiliation(s)
- M Anglana
- UMR147, Batiment Trouillet-Rossignol, Institut Curie/CNRS, 26 Rue d'Ulm, 75248 Paris, France
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9
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Toledo F, Coquelle A, Svetlova E, Debatisse M. Enhanced flexibility and aphidicolin-induced DNA breaks near mammalian replication origins: implications for replicon mapping and chromosome fragility. Nucleic Acids Res 2000; 28:4805-13. [PMID: 11095694 PMCID: PMC115181 DOI: 10.1093/nar/28.23.4805] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Common fragile sites are chromosomal loci prone to breakage and rearrangement that can be induced by aphidicolin, an inhibitor of DNA polymerases. Within these loci, sites of preferential DNA breaks were proposed to correlate with peaks of enhanced DNA flexibility, the function of which remains elusive. Here we show that mammalian DNA replication origins are enriched in peaks of enhanced flexibility. This finding suggests that the search for these features may help in the mapping of replication origins, and we present evidence supporting this hypothesis. The association of peaks of flexibility with replication origins also suggests that some origins may associate with minor levels of fragility. As shown here, an increased sensitivity to aphidicolin was found near two mammalian DNA replication origins.
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Affiliation(s)
- F Toledo
- Unité de Génétique Somatique (URA CNRS 1960), Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France.
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10
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Patterson TE, Albrecht EB, Nurse P, Sazer S, Stark GR. Effects of genome position and the DNA damage checkpoint on the structure and frequency of sod2 gene amplification in fission yeast. Mol Biol Cell 1999; 10:2199-208. [PMID: 10397759 PMCID: PMC25435 DOI: 10.1091/mbc.10.7.2199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Schizosaccharomyces pombe sod2 gene, located near the telomere on the long arm of chromosome I, encodes a Na+ (or Li+)/H+ antiporter. Amplification of sod2 has previously been shown to confer resistance to LiCl. We analyzed 20 independent LiCl-resistant strains and found that the only observed mechanism of resistance is amplification of sod2. The amplicons are linear, extrachromosomal elements either 225 or 180 kb long, containing both sod2 and telomere sequences. To determine whether proximity to a telomere is necessary for sod2 amplification, a strain was constructed in which the gene was moved to the middle of the same chromosomal arm. Selection of LiCl-resistant strains in this genetic background also yielded amplifications of sod2, but in this case the amplified DNA was exclusively chromosomal. Thus, proximity to a telomere is not a prerequisite for gene amplification in S. pombe but does affect the mechanism. Relative to wild-type cells, mutants with defects in the DNA damage aspect of the rad checkpoint control pathway had an increased frequency of sod2 amplification, whereas mutants defective in the S-phase completion checkpoint did not. Two models for generating the amplified DNA are presented.
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Affiliation(s)
- T E Patterson
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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11
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Debatisse M, Coquelle A, Toledo F, Buttin G. Gene amplification mechanisms: the role of fragile sites. Recent Results Cancer Res 1999; 154:216-26. [PMID: 10027002 DOI: 10.1007/978-3-642-46870-4_13] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We studied the early stages of gene amplification in a Chinese hamster cell line and identified two distinct amplification mechanisms, both relying on an unequal segregation of gene copies at mitosis. In some cases, a sequence containing the selected gene is looped out, generating an acentric circular molecule, and amplification proceeds through unequal segregation of such extrachromosomal elements in successive cell cycles. In other cases, the accumulation of intrachromosomally amplified copies is driven by cycles of chromatid breakage, followed by fusion of sister chromatids devoid of a telomere, which leads to bridge formation and further break in mitosis (BFB cycles). We showed that some clastogenic drugs specifically trigger the intrachromosomal amplification pathway and strictly correlated this induction of BFB cycles to the ability of these drugs to activate fragile sites. In three model systems, we also established, that the location of centromeric and telomeric fragile sites relative to the selected genes determines the size and sequence content of the early amplicons.
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Affiliation(s)
- M Debatisse
- Unité de Génétique Somatique (URA CNRS 1960), Institut Pasteur, Paris, France
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12
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Kuo MT, Sen S, Hittelman WN, Hsu TC. Chromosomal fragile sites and DNA amplification in drug-resistant cells. Biochem Pharmacol 1998; 56:7-13. [PMID: 9698083 DOI: 10.1016/s0006-2952(98)00040-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
It has been well established that DNA amplification is one of the important mechanisms by which cultured cells acquire resistance to many cytotoxic compounds. Amplification of important genes including those encoding oncoproteins, growth factors, their receptors and cell-cycle regulators has been reported in human neoplasms. Yet, despite intensive research since the first description of DNA amplification in cultured cells about 20 years ago, the mechanisms of DNA amplification remain largely unknown. Many models have been proposed to account for the diverse manifestations of amplified DNA in many different cell sources. It is not the intention of this commentary to review these many different models. Rather, we wil focus on the recent advances in this area of research, made mainly via the fluorescence in situ hybridization technique, that have revealed a fairly common chromosomal manifestation of amplified DNA in the drug-resistant hamster cell lines and have demonstrated the association of chromosomal fragile site breakage with early events in DNA amplification. These new developments underscore the importance of future research toward understanding the molecular bases of chromosomal fragile sites, including mechanisms involved in DNA strand breakage and repair, chromosomal translocations, and deletions, which may, in turn, provide important new insights into genomic plasticity and neoplastic transformation.
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Affiliation(s)
- M T Kuo
- Department of Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, Houston 77030, USA.
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Dixkens C, Posseckert G, Keller T, Hameister H. Structural analysis of the amplified IFN-beta and DHFR genes in a Chinese hamster ovary cell line using multicolour FISH analysis. Chromosome Res 1998; 6:329-32. [PMID: 9688524 DOI: 10.1023/a:1009231110030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Multicolour FISH was used to get insight into the structural arrangement of a homogeneously staining region which bears the co-transfected and subsequently co-amplified IFN-beta and DHFR genes in a CHO cell line. On metaphase chromosomes an arrangement of multiple bands with regular spacing is revealed. On extended chromatin fibres a cluster of directly repeated and interspersed IFN-beta and DHFR genes is visible. Up to three clusters were found arranged in tandem. The different chromosomal mechanisms leading to gene amplification are discussed.
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Affiliation(s)
- C Dixkens
- Abteilung Medizinische Genetik, Universität Ulm
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14
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Toledo F, Baron B, Fernandez MA, Lachagès AM, Mayau V, Buttin G, Debatisse M. oriGNAI3: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques. Nucleic Acids Res 1998; 26:2313-21. [PMID: 9580680 PMCID: PMC147574 DOI: 10.1093/nar/26.10.2313] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The nature of mammalian origins of DNA replication remains controversial and this is primarily because two-dimensional gel replicon mapping techniques have identified broad zones of replication initiation whereas several other techniques, such as quantitative PCR, have disclosed more discrete sites of initiation at the same chromosomal loci. In this report we analyze the replication of an amplified genomic region encompassing the 3'-end of the GNAI3 gene, the entire GNAT2 gene and the intergenic region between them in exponentially growing Chinese hamster fibroblasts. These cells express GNAI3 but not GNAT2 . The replication pattern was first analyzed by two-dimensional neutral-alkaline gel electrophoresis. Surprisingly, the results revealed a small preferential zone of replication initiation, of at most 1.7 kb, located in a limited part of the GNAI3 - GNAT2 intergenic region. Mapping of this initiation zone was then confirmed by quantitative PCR. The agreement between the two techniques exploited here strengthens the hypothesis that preferred sites of replication initiation do exist in mammalian genomes.
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Affiliation(s)
- F Toledo
- Unité de Génétique Somatique (URA CNRS 1960), Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France.
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15
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Coquelle A, Pipiras E, Toledo F, Buttin G, Debatisse M. Expression of fragile sites triggers intrachromosomal mammalian gene amplification and sets boundaries to early amplicons. Cell 1997; 89:215-25. [PMID: 9108477 DOI: 10.1016/s0092-8674(00)80201-9] [Citation(s) in RCA: 284] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Drug-selected intrachromosomal gene amplification by breakage-fusion-bridge (BFB) cycles is well documented in mammalian cells, but factors governing this mechanism are not clear. Here, we show that only some clastogenic drugs induce drug resistance through intrachromosomal amplification. We strictly correlate triggering of BFB cycles to induction of fragile site expression. We demonstrate a dual role for fragile sites in intrachromosomal amplification: a site telomeric to the selected gene is involved in initiation, while a centromeric site defines the size and organization of early amplified units. The positions of fragile sites relative to boundaries of amplicons found in human cancers support the hypothesis that fragile sites play a key role in the amplification of at least some oncogenes during tumor progression.
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Affiliation(s)
- A Coquelle
- Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
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16
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Baron B, Fernandez MA, Carignon S, Toledo F, Buttin G, Debatisse M. GNAI3, GNAT2, AMPD2, GSTM are clustered in 120 kb of Chinese hamster chromosome 1q. Mamm Genome 1996; 7:429-32. [PMID: 8662225 DOI: 10.1007/s003359900127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We studied a polygenic region located on Chromosome (Chr) 1q in Chinese hamster cells that is coamplified along with the AMPD2 gene. Previous sequence analysis identified both members of the GSTM family and the GNAI3 gene within a cloned 120-kb region surrounding the AMPD2 locus. We show here that the GNAT2 gene, which is inactive in the fibroblastic cells, lies within the 20 kb separating the transcriptionally active GNAI3 and AMPD2 genes. We map most gene ends by sequence comparison with human homologs; one is inferred from the presence of an unmethylated CpG island. This Chinese hamster locus corresponds to a region of conserved linkage between human Chr 1 (locus 1p13) and mouse Chr 3 (position 52.5 cM), where Gnai-3 and Gnat-2 have been mapped. The AMPD2 gene is presently unlocalized in human genome; its proposed position on mouse Chr 3 is at 53.4 cM. Our results, obtained by physical mapping, strongly suggest that the order and possibly the tight linkage of these genes are conserved on all three genomes.
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Affiliation(s)
- B Baron
- Unité de Génétique Somatique, Départment d'Immunologie de l'Institut Pasteur (LA CNRS No. 1960), Paris France
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17
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Lunel-Orsini C, Buttin G, de Saint Vincent BR. Reversion in Chinese hamster lines amplified at the AMPD2 locus: spontaneous and benzamide-stimulated gradual loss of amplified alleles of marker genes. Mutat Res 1996; 349:63-75. [PMID: 8569793 DOI: 10.1016/0027-5107(95)00153-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The HC47 and HC474 cell lines of Chinese hamster fibroblasts resist coformycin through the intrachromosomal amplification of the AMP deaminase 2 (AMPD2) gene. Due to the coamplification of a mu glutathione S-transferase (GST) gene, these mutant lines are more sensitive than GMA32 wild-type parental cells to buthionine sulfoximine (BSO), an inhibitor of glutathione biosynthesis. This property was exploited to select revertants of amplification from HC474 cells. Reversion in that line is frequently a gradual process that does not involve extrachromosomal intermediates. The terminal products of this process are commonly cells with a complete deletion of the amplified allele of marker genes and are therefore haploid for these loci on the homologous chromosome. Exposing HC474 cells to benzamide (BA), an inhibitor of polyADP-ribosylation, increased the recovery of revertants to an extent allowing the detection of reverting cells without BSO selection. This effect of BA was used to isolate revertant cells from the HC47 line that is extremely stable and to demonstrate that the mechanism of gradual reversion also occurs in this line. The gradual deletion of amplified copies within the chromosomes suggests that breakage-fusion-bridge (BFB) cycles drive this process.
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Affiliation(s)
- C Lunel-Orsini
- Unité de Génétique Somatique, (URA CNRS 361), Institut Pasteur, Paris, France
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18
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Role of induced genetic instability in the mutagenic effects of chemicals and radiation. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0165-1218(96)90017-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Eijdems EW, De Haas M, Coco-Martin JM, Ottenheim CP, Zaman GJ, Dauwerse HG, Breuning MH, Twentyman PR, Borst P, Baas F. Mechanisms of MRP over-expression in four human lung-cancer cell lines and analysis of the MRP amplicon. Int J Cancer 1995; 60:676-84. [PMID: 7860142 DOI: 10.1002/ijc.2910600518] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Some multidrug resistant cell lines over-express the gene encoding the multidrug-resistance-associated protein (MRP). In all cell lines reported thus far, over-expression is associated with gene amplification. We have studied the predominant mechanisms of MRP over-expression in 4 human lung-cancer cell lines that cover a range of drug-resistance levels, and we have analyzed the MRP amplicon. In the SW-1573-derived, weakly resistant cell line 30.3M, MRP mRNA is elevated 3-fold in the absence of gene amplification. Run-on analysis shows that the increased MRP gene expression in this cell line is due to transcriptional activation. In the highly resistant GLC4/ADR and COR-L23/R cells, MRP gene amplification predominates, whereas in the moderately resistant MOR/R cells, gene amplification is combined with a mechanism resulting in an additional increase in the level of MRP mRNA. Fluorescence in situ hybridization shows that, in the GLC4/ADR cells, amplified MRP sequences are present both in double minute chromosomes (DM) and in homogeneously staining regions (HSR). By pulsed-field gel electrophoresis we show that the MRP-containing DM are 1 Mb in length. Chromosome-16-specific repetitive sequences adjacent to the MRP gene are also present in the DM and HSR, compatible with the involvement of these sequences in recombination events underlying MRP gene amplification. Our results show that low levels of drug resistance may arise by transcriptional activation of the MRP gene, whereas at high levels of drug resistance amplification of the MRP gene predominates, possibly facilitated by the presence of recombination-prone sequences.
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MESH Headings
- ATP-Binding Cassette Transporters/biosynthesis
- ATP-Binding Cassette Transporters/genetics
- Antineoplastic Agents/pharmacology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Small Cell/genetics
- Carcinoma, Small Cell/metabolism
- Carcinoma, Small Cell/pathology
- Chromosomes, Human, Pair 16
- DNA, Complementary/genetics
- DNA, Neoplasm/genetics
- Drug Resistance, Multiple/genetics
- Gene Amplification
- Gene Expression Regulation, Neoplastic
- Genes
- Humans
- In Situ Hybridization, Fluorescence
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Multidrug Resistance-Associated Proteins
- Myosins/biosynthesis
- Myosins/genetics
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- RNA, Messenger/genetics
- RNA, Neoplasm/genetics
- Recombination, Genetic
- Repetitive Sequences, Nucleic Acid
- Tumor Cells, Cultured/drug effects
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Affiliation(s)
- E W Eijdems
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam
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20
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Chromosome breakage at a major fragile site associated with P-glycoprotein gene amplification in multidrug-resistant CHO cells. Mol Cell Biol 1994. [PMID: 7913517 DOI: 10.1128/mcb.14.8.5202] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Recent studies of several drug-resistant Chinese hamster cell lines suggested that a breakage-fusion-bridge mechanism is frequently involved in the amplification of drug resistance genes. These observations underscore the importance of chromosome breakage in the initiation of DNA amplification in mammalian cells. However, the mechanism of this breakage is unknown. Here, we propose that the site of chromosome breakage consistent with the initial event of P-glycoprotein (P-gp) gene amplification via the breakage-fusion-bridge cycle in three independently established multidrug-resistant CHO cells was located at 1q31. This site is a major chromosome fragile site that can be induced by methotrexate and aphidicolin treatments. Pretreatments of CHO cells with methotrexate or aphidicolin enhanced the frequencies of resistance to vinca alkaloid and amplification of the P-gp gene. These observations suggest that chromosome fragile sites play a pivotal role in DNA amplification in mammalian cells. Our data are also consistent with the hypothesis that gene amplification can be initiated by stress-induced chromosome breakage that is independent of modes of action of cytotoxic agents. Drug-resistant variants may arise by their growth advantage due to overproduction of cellular target molecules via gene amplification.
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21
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Kuo MT, Vyas RC, Jiang LX, Hittelman WN. Chromosome breakage at a major fragile site associated with P-glycoprotein gene amplification in multidrug-resistant CHO cells. Mol Cell Biol 1994; 14:5202-11. [PMID: 7913517 PMCID: PMC359039 DOI: 10.1128/mcb.14.8.5202-5211.1994] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Recent studies of several drug-resistant Chinese hamster cell lines suggested that a breakage-fusion-bridge mechanism is frequently involved in the amplification of drug resistance genes. These observations underscore the importance of chromosome breakage in the initiation of DNA amplification in mammalian cells. However, the mechanism of this breakage is unknown. Here, we propose that the site of chromosome breakage consistent with the initial event of P-glycoprotein (P-gp) gene amplification via the breakage-fusion-bridge cycle in three independently established multidrug-resistant CHO cells was located at 1q31. This site is a major chromosome fragile site that can be induced by methotrexate and aphidicolin treatments. Pretreatments of CHO cells with methotrexate or aphidicolin enhanced the frequencies of resistance to vinca alkaloid and amplification of the P-gp gene. These observations suggest that chromosome fragile sites play a pivotal role in DNA amplification in mammalian cells. Our data are also consistent with the hypothesis that gene amplification can be initiated by stress-induced chromosome breakage that is independent of modes of action of cytotoxic agents. Drug-resistant variants may arise by their growth advantage due to overproduction of cellular target molecules via gene amplification.
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Affiliation(s)
- M T Kuo
- Department of Molecular Pathology, University of Texas M. D. Anderson Cancer Center, Houston 77030
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22
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Corvi R, Amler LC, Savelyeva L, Gehring M, Schwab M. MYCN is retained in single copy at chromosome 2 band p23-24 during amplification in human neuroblastoma cells. Proc Natl Acad Sci U S A 1994; 91:5523-7. [PMID: 8202521 PMCID: PMC44028 DOI: 10.1073/pnas.91.12.5523] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Amplification of the human N-myc protooncogene, MYCN, is frequently seen either in extrachromosomal double minutes or in homogeneously staining regions of aggressively growing neuroblastomas. MYCN maps to chromosome 2 band p23-24, but homogeneously staining regions have never been observed at this band, suggesting transposition of MYCN during amplification. We have employed fluorescence in situ hybridization to determine the status of MYCN at 2p23-24 in five human neuroblastoma cell lines. All five lines carried, in addition to amplified MYCN in homogeneously staining regions or double minutes, single-copy MYCN at the normal position. In one line there was coamplification of MYCN together with DNA of the host chromosome 12, to which MYCN had been transposed. Our results suggest a model of amplification where MYCN is retained at its original location. They further sustain the view that either the initial events of MYCN amplification or the further evolution of amplified MYCN copies follow mechanisms different from those leading to amplification of drug-resistance genes.
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Affiliation(s)
- R Corvi
- Department of Cytogenetics, German Cancer Research Center, Heidelberg
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23
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Abstract
The determination of mutation rates is an important experimental procedure for characterizing mutation processes. The accepted method of determining mutation rates, the fluctuation test, was introduced by Luria and Delbrück in 1943. Since then it has been applied to various microorganisms and cells. The Luria-Delbrück test is based on a restrictive hypothesis of mutations being due to single irreversible events. However, some inherited changes in phenotype, like gene amplification, may be due to two or more genetic changes, some of which may be reversible. The Luria-Delbrück model of mutation was compared to other models which included reversibility and more than one mutation stage. The Luria-Delbrück model has been confirmed to be consistent with the original bacteriophage resistance data. However, for gene amplification this model gives incompatible estimates of mutation rates by the P0 and r methods. Relaxing the hypotheses of the single-stage models did not improve the fit. In contrast, a two-stage reversible model provided a fit. Analysis of gene amplification data by the two-stage reversible model provides new information, including estimates of rates for each of the two forward stages and of the reverse step.
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Affiliation(s)
- M Kimmel
- Department of Statistics, Rice University, Houston, TX 77251
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24
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Roelofs H, Schuuring E, Wiegant J, Michalides R, Giphart-Gassler M. Amplification of the 11q13 region in human carcinoma cell lines: a mechanistic view. Genes Chromosomes Cancer 1993; 7:74-84. [PMID: 7687456 DOI: 10.1002/gcc.2870070203] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We previously proposed that a local duplication, not the loss of the subsequently amplified marker from its original site, might be the first step in gene amplification in human cells. It is important to investigate this issue in naturally occurring amplification and when copy numbers are relatively low. We have examined the location of single-copy and amplified 11q13 sequences in cell lines from human breast cancers and squamous cell carcinomas using fluorescence in situ hybridization both with a probe specific for the 11q13 amplifying region and with a chromosome 11-specific library. We show that in most cell lines the 11q13 amplicons are physically linked to chromosome 11 or to a chromosome derived from chromosome 11 by various rearrangements near the 11q13 region. In none of the cell lines were interstitial deletions of 11q13 detected. These results indicate that 11q13 amplification in human tumor cells generally does not involve deletion as the initial step. One cell line with chromosomally located amplified 11q13 sequences contained double minutes that harbored the MYC gene but no 11q13 sequences. This suggests that the genetic outcome and the mechanism of gene amplification are probably dependent on specific DNA sequences rather than on the origin of the cells.
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Affiliation(s)
- H Roelofs
- Department of Molecular Genetics, Gorlaeus Laboratories, University of Leiden, The Netherlands
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25
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Affiliation(s)
- G R Stark
- Research Institute, Cleveland Clinic Foundation, Ohio 44195
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26
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Vagnarelli P, Giulotto E, Fattorini P, Mucciolo E, Bensi M, Tessera L, De Carli L. Variation of minisatellites in chemically induced mutagenesis and in gene amplification. EXS 1993; 67:71-7. [PMID: 8400716 DOI: 10.1007/978-3-0348-8583-6_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A mutation assay in cultured mammalian cells was developed based on direct analysis of minisatellite DNA. Chinese hamster cells (V79) were mutagenized with nitrosoguanidine and independent colonies were isolated and expanded. DNA fingerprints were then obtained after digestion with HinfI or HaeIII and hybridization with 33.15 and 33.6 probes (Jeffreys et al., 1985). 12 colonies from untreated cells were also analyzed. Digestion with HaeIII and hybridization with 33.15 probe detected the highest frequency of induced variants. The results suggest that minisatellite sequences are hypermutable sites that can be used to monitor the mutagenic effect of chemical agents. We have also analyzed the DNA fingerprints of 17 independent Chinese hamster (CHO) cell lines carrying amplification of the CAD gene. The DNA fingerprint analysis showed a variation in minisatellite regions in 3 lines while no variation was observed in independent colonies from the CHO parental cell line. The results suggest that these sequences may be hot spots for recombination during gene amplification.
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Affiliation(s)
- P Vagnarelli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy
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27
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Gray JW, Kallioniemi A, Kallioniemi O, Pallavicini M, Waldman F, Pinkel D. Molecular cytogenetics: Diagnosis and prognostic assessment. Curr Opin Biotechnol 1992; 3:623-31. [PMID: 1369118 DOI: 10.1016/0958-1669(92)90006-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This review describes molecular cytogenetic techniques for detection and characterization of genetic aberrations associated with human disease. The techniques of fluorescence in situ hybridization, primed in situ labeling and comparative genome hybridization are described, as are probes for repeated sequences, whole chromosomes and specific loci. Also reviewed are applications of these technologies to pre- and neonatal diagnosis and to the characterization of human malignancies.
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Affiliation(s)
- J W Gray
- Department of Laboratory Medicine, University of California, San Francisco 94143-0808
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28
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Hartwell L. Defects in a cell cycle checkpoint may be responsible for the genomic instability of cancer cells. Cell 1992; 71:543-6. [PMID: 1423612 DOI: 10.1016/0092-8674(92)90586-2] [Citation(s) in RCA: 614] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- L Hartwell
- Department of Genetics, University of Washington, Seattle 98195
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