Abstract
Cancer genes are often deregulated by genomic rearrangements. Accordingly, analysis of the participant chromosomes responsible now occupies a key role in characterizing and identifying cancer cell lines. Cytogenetics may also be used to study the nature and extent of chromosome breakage induced by radiation or chemicals (“clastogenesis”), to distinguish individual cells or clones within a tumor cell population and to monitor the stability of chromosome rearrangements. This chapter describes cytogenetic procedures for characterizing cancer cells in culture. Cell lines allow the use of a wider range of harvesting and hypotonic treatments to optimize metaphase chromosome preparations than that possible with primary cultures. This assists improved banding, fluorescence in situ hybridization (FISH), and Spectral Karyotyping (SKY) analysis for research, rendering cell lines ideal tools for oncogenomics, ideally in parallel with transcriptomic analysis of the same cells. The experience of the writers with more than 800 cell lines has shown that no single hypotonic harvesting protocol is adequate consistently to deliver satisfactory chromosome preparations. Thus, evidence-based protocols are described for hypotonic harvesting, rapid G-banding, and FISH and SKY analysis of cell cultures to allow troubleshooting and fine-tuning to suit the requirements of individual cell lines.
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References
MacLeod, R.A.F., Nagel, S., Scherr, M., Schneider, B., Dirks, W. G., Uphoff, C. C., et al. (2008) Human leukemia and lymphoma cell lines as models and resources. Current Medicinal Chemistry 15, 339–359.
Mitelman, F., Johansson, B., and Mertens, F. (2007) The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7, 233–45.
Deininger, M., Buchdunger, E., Druker, B. J. (2005) The development of imatinib as a therapeutic agent for chronic myeloid leukemia. Blood 105, 2640–53.
Drexler, H. G, MacLeod, R. A. F., and Uphoff, C. C. (1999) Leukemia cell lines: in vitro models for the study of Philadelphia chromosome-positive leukemia. Leukemia Res 23, 207–15.
Drexler, H. G., MacLeod, R. A. F., Borkhardt, A., and Janssen, J. W. G. (1995) Recurrent chromosomal translocations and fusion genes in leukemia–lymphoma cell lines. Leukemia 9, 480–500.
Marini, P., MacLeod, R. A. F., Treuner, C., Bruchelt, G., Böhm, W., Wolburg, H., et al. (1999) SiMa, a new neuroblastoma cell line combining poor prognostic cytogenetic markers with high adrenergic differentiation. Cancer Genet Cytogenet 112, 161–4.
Drexler, H. G., Matsuo, Y., and MacLeod, R. A.F. (2000) Continuous hematopoietic cell lines as model systems for leukemia–lymphoma research. Leukemia Res 24, 881–911.
Tosi, S., Giudici, G., Rambaldi, A., Scherer, S.W., Bray-Ward, P., Dirscherl, L., et al. (1999) Characterization of the human myeloid leukemia-derived cell line GF-D8 by multiplex fluorescence in situ hybridization, subtelomeric probes, and comparative genomic hybridization. Genes Chromosomes Cancer 24, 213–21.
Schneider, B., Nagel, S., Kaufmann, M., Winkelmann, S., Drexler, H. G., and MacLeod, R. A. F. (2008) t(3;7)(q27;q32) fuses BCL6 to a non-coding region at FRA7H near miR-29. Leukemia 22, 1262–6.
Vanasse, G. J., Concannon, P., and Willerford, D. M. (1999) Regulated genomic instability and neoplasia in the lymphoid lineage. Blood 94, 3997–4010.
Küppers, R. and Dalla-Favera, R. (2001) Mechanisms of chromosomal translocations in B cell lymphomas. Oncogene 20, 5580–94.
MacLeod, R. A. F., Dirks, W. G., Matsuo, Y., Kaufmann, M., Milch, H., and Drexler, H. G. (1999) Widespread intraspecies cross-contamination of human tumor cell lines arising at source. Int J Cancer 83, 555–63.
Drexler, H. G., Dirks, W. G., and MacLeod, R. A.F. (1999) False human hematopoietic cell lines: cross-contaminations and misinterpretations. Leukemia 13, 1601–7.
Nelson-Rees, W. A., Daniels, D. W., and Flandermeyer, R. R. (1981) Cross-contamination of cells in culture. Science 212, 446–52.
Markovic, O. and Markovic, N. (1998) Cell cross-contamination in cell cultures: the silent and neglected danger. In Vitro Cell Dev Biol Anim 34, 1–8.
MacLeod, R. A. F., Dirks, W. G., and Drexler, H. G. (2002) Persistent use of misidentified cell lines and its prevention. Genes Chromosomes Cancer 33, 103–5.
Stacey, G.N., Masters, J. R., Hay, R.J., Drexler, H. G., MacLeod, R. A. F., and Frechney, R. I. (2000) Cell contamination leads to inaccurate data: We must take action now. Nature 403, 356.
Caspersson, T., Zech, L., and Johansson, C. (1970) Differential binding of alkylating fluorochromes in human chromosomes. Exp Cell Res 60, 315–19.
Sumner, A. T., Evans, H. J., and Buckland, R. A. (1971) New technique for distinguishing between human chromosomes. Nature New Biol 232, 31–2.
Seabright, M. (1973) Improvement of trypsin method for banding chromosomes. Lancet 1, 1249–50.
Rowley, J. D. (1973) A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 243, 290–3.
Nowell, P. C. and Hungerford, D. A. (1960) A minute chromosome in human granulocytic leukemia. Science 132, 1497.
Cremer, T., Lichter, P., Borden, J., Ward, D. C., and Manuelidis, L. (1988) Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes. Hum Genet 80, 235–46.
Lichter, P., Cremer, T., Borden, J., Manuelidis, L., and Ward, D. C. (1988) Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet 80, 224–234.
Lichter, P. (1997) Multicolor FISHing: what’s the catch? Trends Genet 12, 475–79.
MacLeod, R. A. F., Kaufmann, M., and Drexler, H.G. (2007) Cytogenetic harvesting of commonly used tumor cell lines. Nature Protocols 2, 372–82.
Kubonishi, I., Niiya, K., and Miyoshi, I. (1985) Establishment of a new human lymphoma line that secretes plasminogen activator. Jpn J Cancer Res 76, 12–5.
Kubonishi, I., Niiya, K., Yamashita, M., Yano, S., Abe, T., Ohtsuki, Y., and Miyoshi, I. (1986) Characterization of a new human lymphoma cell line (RC-K8) with t(11;14) chromosome abnormality. Cancer 58, 1453–60.
ISCN 1985: An International System for Human Cytogenetic Nomenclature: report of the Standing Committee on Human Cytogenetic Nomenclature. Karger, Basel.
ISCN 1991: Guidelines for Cancer Cytogenetics: Supplement to an International System for Human Cytogenetic Nomenclature. Karger, Basel.
ISCN 2009: An International System for Human Cytogenetic Nomenclature: Recommendations of the International Standing Committee on Human Cytogenetic Nomenclature. Published in collaboration with “Cytogenetic and Genome Research”, Karger, Basel, in press, 2009.
Drexler, H. G. (2001) The Leukemia-Lymphoma Cell Line FactsBook, Academic Press, San Diego.
Drexler, H. G. (2009) Guide to Leukemia-Lymphoma Cell Lines, eBook (available from the author), DSMZ, Braunschweig, Germany.
Acknowledgment
We wish to thank Maren Kaufmann for her expert technical input and suggestions, many of which are silently incorporated into the text.
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MacLeod, R.A.F., Kaufmann, M., Drexler, H.G. (2011). Cytogenetic Analysis of Cancer Cell Lines. In: Cree, I. (eds) Cancer Cell Culture. Methods in Molecular Biology, vol 731. Humana Press. https://doi.org/10.1007/978-1-61779-080-5_6
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DOI: https://doi.org/10.1007/978-1-61779-080-5_6
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