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Grasser F, Neusser M, Fiegler H, Thormeyer T, Cremer M, Carter NP, Cremer T, Müller S. Replication-timing-correlated spatial chromatin arrangements in cancer and in primate interphase nuclei. J Cell Sci 2008; 121:1876-86. [PMID: 18477608 DOI: 10.1242/jcs.026989] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Using published high-resolution data on S-phase replication timing, we determined the three-dimensional (3D) nuclear arrangement of 33 very-early-replicating and 31 very-late-replicating loci. We analyzed diploid human, non-human primate and rearranged tumor cells by 3D fluorescence in situ hybridization with the aim of investigating the impact of chromosomal structural changes on the nuclear organization of these loci. Overall, their topology was found to be largely conserved between cell types, species and in tumor cells. Early-replicating loci were localized in the nuclear interior, whereas late-replicating loci showed a broader distribution with a higher preference for the periphery than for late-BrdU-incorporation foci. However, differences in the spatial arrangement of early and late loci of chromosome 2, as compared with those from chromosome 5, 7 and 17, argue against replication timing as a major driving force for the 3D radial genome organization in human lymphoblastoid cell nuclei. Instead, genomic properties, and local gene density in particular, were identified as the decisive parameters. Further detailed comparisons of chromosome 7 loci in primate and tumor cells suggest that the inversions analyzed influence nuclear topology to a greater extent than the translocations, thus pointing to geometrical constraints in the 3D conformation of a chromosome territory.
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Affiliation(s)
- Florian Grasser
- Department of Biology II, Human Genetics, Ludwig-Maximilians University Munich, Planegg-Martinsreid, Germany
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Nardone RM. Eradication of cross-contaminated cell lines: A call for action. Cell Biol Toxicol 2007; 23:367-72. [PMID: 17522957 DOI: 10.1007/s10565-007-9019-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 05/11/2007] [Indexed: 10/23/2022]
Abstract
This "white paper" was prepared and widely disseminated in an attempt to sound an alarm about the long-term existence of a grave, unresolved and growing problem that affects a significant portion of biomedical research, namely, the use of misidentified and cross-contaminated cell cultures. The "white paper" shows how bold action could bring about a profession-wide change in practice that would prevent further erosion. Misidentification and inter- and intra-specific cross-contamination of mammalian cell cultures used in research continues as a widespread problem despite an awareness that dates back more than 45 years. Awareness of the problem has led to a good understanding of the causes of cross-contamination and appropriate preventive measures. It has also led to the application of robust methods for the authentication of cell lines. Yet the problem continues unabated. Estimates of the incidence of research papers flawed by the use of misidentified and cross-contaminated cell cultures approximate 15-20%. The gravity of the situation calls for a strategy that would deliver a remedial message of authentication to virtually all cell culture researchers and also ensure compliance with the message. At the core of the strategy proposed herein is having cell line authentication as a condition for the award of research grants and for the publication of research findings.
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Affiliation(s)
- Roland M Nardone
- Biology Department, Catholic University of America, McCort Ward Hall, Washington, DC 20064, USA.
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Multipoint interphase FISH in childhood T-acute lymphoblastic leukemia detects subpopulations that carry different chromosome 3 aberrations. ACTA ACUST UNITED AC 2007; 172:54-60. [DOI: 10.1016/j.cancergencyto.2006.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 08/07/2006] [Accepted: 08/09/2006] [Indexed: 11/17/2022]
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Müller S, Wienberg J. Multicolor chromosome bar codes. Cytogenet Genome Res 2006; 114:245-9. [PMID: 16954661 DOI: 10.1159/000094208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Accepted: 04/03/2006] [Indexed: 01/02/2023] Open
Abstract
Chromosome bar codes are multicolor banding patterns produced by fluorescence in situ hybridization (FISH) with differentially labeled and pooled sub-regional DNA probes. These molecular cytogenetic tools facilitate chromosome identification and the delineation of both inter- and intra-chromosomal rearrangements. We present an overview of the various conceptual approaches which can be largely divided into two classes: Simple bar codes designed for chromosome identification and complex bar codes for high resolution aberration screening of entire karyotypes. We address the issue of color redundancy and how to overcome this limitation by complementation of bar codes with whole chromosome painting probes.
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Affiliation(s)
- S Müller
- Institute for Anthropology and Human Genetics, Department of Biology II, Ludwig-Maximilians-University, Munich, Germany.
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Hande MP, Azizova TV, Burak LE, Khokhryakov VF, Geard CR, Brenner DJ. Complex chromosome aberrations persist in individuals many years after occupational exposure to densely ionizing radiation: an mFISH study. Genes Chromosomes Cancer 2005; 44:1-9. [PMID: 15912529 DOI: 10.1002/gcc.20217] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Long-lived, sensitive, and specific biomarkers of particular mutagenic agents are much sought after and potentially have broad applications in the fields of cancer biology, epidemiology, and prevention. Many clastogens induce a spectrum of chromosome aberrations, and some of them can be exploited as biomarkers of exposure. Densely ionizing radiation, for example, alpha particle radiation (from radon or plutonium) and neutron radiation, preferentially induces complex chromosome aberrations, which can be detected by the 24-color multifluor fluorescence in situ hybridization (mFISH) technique. We report the detection and quantification of stable complex chromosome aberrations in lymphocytes of healthy former nuclear-weapons workers, who were exposed many years ago to plutonium, gamma rays, or both, at the Mayak weapons complex in Russia. We analyzed peripheral-blood lymphocytes from these individuals for the presence of persistent complex chromosome aberrations. A significantly elevated frequency of complex chromosome translocations was detected in the highly exposed plutonium workers but not in the group exposed only to high doses of gamma radiation. No such differences were found for simple chromosomal aberrations. The results suggest that stable complex chromosomal translocations represent a long-lived, quantitative, low-background biomarker of densely ionizing radiation for human populations exposed many years ago.
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Affiliation(s)
- M Prakash Hande
- Center for Radiological Research, Columbia University Medical Center, New York, USA
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Letessier A, Mozziconacci MJ, Murati A, Juriens J, Adélaïde J, Birnbaum D, Chaffanet M. Multicolour-banding fluorescence in situ hybridisation (mbanding-FISH) to identify recurrent chromosomal alterations in breast tumour cell lines. Br J Cancer 2005; 92:382-8. [PMID: 15655561 PMCID: PMC2361837 DOI: 10.1038/sj.bjc.6602228] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recurrent chromosome breakpoints in tumour cells may point to cancer genes, but not many have been molecularly characterised. We have used multicolour-banding fluorescence in situ hybridisation (mbanding-FISH) on breast tumour cell lines to identify regions of chromosome break created by inversions, duplications, insertions and translocations on chromosomes 1, 5, 8, 12 and 17. We delineate a total of 136 regions of break, some of them occurring with high frequency. We further describe two examples of dual-colour FISH characterisation of breakpoints, which target the 1p36 and 5p11–12 regions. Both breaks involve genes whose function is unknown to date. The mbanding-FISH strategy constitutes an efficient first step in the search for potential cancer genes.
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Affiliation(s)
- A Letessier
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
| | - M-J Mozziconacci
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
- Department of Biopathology, Paoli-Calmettes Institute, Marseille, France
| | - A Murati
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
- Department of Biopathology, Paoli-Calmettes Institute, Marseille, France
| | - J Juriens
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
| | - J Adélaïde
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
| | - D Birnbaum
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
| | - M Chaffanet
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
- Institut Paoli-Calmettes, 232, Bd Sainte Marguerite BP156, 13273 Marseille Cedex 9, France. E-mail:
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Parson W, Kirchebner R, Mühlmann R, Renner K, Kofler A, Schmidt S, Kofler R. Cancer cell line identification by short tandem repeat profiling: power and limitations. FASEB J 2005; 19:434-6. [PMID: 15637111 DOI: 10.1096/fj.04-3062fje] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cancer cell lines are used worldwide in biological research, and data interpretation depends on unambiguous attribution of the respective cell line to its original source. Short-tandem-repeat (STR) profiling (DNA fingerprinting) is the method of choice for this purpose; however, the genetic stability of cell lines under various experimental conditions is not well defined. We tested the effect of long-term culture, subcloning, and generation of drug-resistant subclones on fingerprinting profiles in four widely used leukemia cell lines. The DNA fingerprinting profile remained unaltered in two of them (U937 and K562) throughout 12 months in culture, and the vast majority of subclones derived therefrom by limiting dilution after long-term culture revealed the same profile, indicating a high degree of stability and clonotypic homogeneity. In contrast, two other cell lines (CCRF-CEM and Jurkat) showed marked alterations in DNA fingerprinting profiles during long-term culture. Limiting dilution subcloning revealed extensive clonotypic heterogeneity with subclones differing in up to eight STR loci from the parental culture. Similar heterogeneity was observed in subclones generated by selection culture for drug resistance where DNA fingerprinting proved useful in identifying possible resistance mechanisms. Thus, common tissue culture procedures may dramatically affect the fingerprinting profile of certain cell lines and thus render definition of their origin difficult.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Department Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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