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DNA Profiling and Characterization of Animal Cell Lines

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Animal Cell Biotechnology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1104))

Abstract

The history of the culture of animal cell lines is littered with published and much unpublished experience with cell lines that have become switched, mislabelled, or cross-contaminated during laboratory handling. To deliver valid and good quality research and to avoid waste of time and resources on such rogue lines, it is vital to perform some kind of qualification for the provenance of cell lines used in research and particularly in the development of biomedical products. DNA profiling provides a valuable tool to compare different sources of the same cells and, where original material or tissue is available, to confirm the correct identity of a cell line. This chapter provides a review of some of the most useful techniques to test the identity of cells in the cell culture laboratory and gives methods which have been used in the authentication of cell lines.

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References

  1. Nelson-Rees WA, Daniels DW, Flandermeyer RR (1989) Cross-contamination of cells in culture. Science 212:446–452

    Article  Google Scholar 

  2. Stacey G, Masters JRW, Hay RJ, Drexler HG, MacLeod RAF, Freshney IR (2000) Cell contamination leads to inaccurate data: we must take action now. Nature 403:356

    Article  CAS  Google Scholar 

  3. Stacey GN (2002) Standardisation of cell lines. Dev Biol 111:259–272

    CAS  Google Scholar 

  4. Nardone RN, Masters JRW, Bradlaw JA, Jacobsen LB, Nims RW, Price PJ, Lewis D, Stacey G, McCormick JJ, Gartler SM, Pathak S, Butler JM, Buchring GC, Massaro EJ, Steuer AF, Gold M, Freshney IR, Krause D, O’Brien SJ (2007) An open letter regarding the misidentification and cross contamination of cell lines: significance and recommendations for correction. US Department of Health and Human, Washington, DC, July 11th 2007 to MO.Leavit

    Google Scholar 

  5. Coecke S, Balls M, Bowe G et al (2005) Guidance on good cell culture practice. A report of the second ECVAM task force on good cell culture practice. Altern Lab Anim 33:1–27

    Google Scholar 

  6. ISCBI (2009) Consensus guidance for banking and supply of human embryonic stem cell lines for research purposes. Stem Cell Rev 5:301–314

    Article  Google Scholar 

  7. Hsu TC (1952) Mammalian chromosomes in vitro the karyotype of man. J Hered 43:167–172

    Google Scholar 

  8. Tjio JH, Leven A (1956) The chromosome number of men. Hereditas 42:1–6

    Article  Google Scholar 

  9. Simpson WF, Stulberg CS, Petersen WD (1978) Monitoring species of cells in culture by immunofluorescence. Tissue Culture Association Manual 4:771–774 (Available from the American Type Culture Collection, USA)

    Article  Google Scholar 

  10. O’Brien SJ, Kleiner G, Olson R et al (1977) Enzyme polymorphisms as genetic signatures in human cell cultures. Science 195:1345–1348

    Article  Google Scholar 

  11. Ferrone S, Pellegrino MA, Reisfeld RAA (1971) A rapid method for direct HLA typing of cultured lymphoid cells. J Immunol 107:613–615

    CAS  Google Scholar 

  12. Christensen B, Hansen C, Debiek-Rychter M et al (1993) Identity of tumorigenic urothelial cell lines and “spontaneously” transformed sublines. Br J Cancer 68:879–884

    Article  CAS  Google Scholar 

  13. Jeffreys AJ, Wilson V, Thein S-L (1985) Hypervariable minisatellite regions in human DNA. Nature 314:67–73

    Article  CAS  Google Scholar 

  14. Jeffreys AJ, Wilson V, Thein S-L (1985) Individual specific fingerprints of human DNA. Nature 316:76–79

    Article  CAS  Google Scholar 

  15. Folmer O, Black M, Hoeh W et al (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–299

    CAS  Google Scholar 

  16. Hebert PD, Cywinska A, Ball SL et al (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270:313–321

    Article  CAS  Google Scholar 

  17. Vassart G, Georges M, Monsieur R, Brocas H, Lequarre AS, Christophe D (1987) A sequence in M13 phage detects hypervariable minisatellites in human and animal DNA. Science 235:683–684

    Article  CAS  Google Scholar 

  18. Burke T, Dolf G, Jeffreys AJ et al (eds) (1990) DNA fingerprinting: approaches and applications. Birkhauser, Basel

    Google Scholar 

  19. Thacker J, Webb MBT, Debenham PG (1988) Fingerprinting cell lines: use of human hypervariable DNA probes to characterise mammalian cell cultures. Somat Cell Mol Genet 14:519–525

    Article  CAS  Google Scholar 

  20. Van Helden PD, Wiid IJF, Albrecht CF et al (1988) Cross-contamination of human oesophageal squamous carcinoma cell lines detected by DNA fingerprint analysis. Cancer Res 48:5660–5662

    Google Scholar 

  21. Stacey GN, Bolton BJ, Doyle A et al (1992) DNA fingerprinting: a valuable new technique for the characterisation of animal cell lines. Cytotechnology 9:211–216

    Article  CAS  Google Scholar 

  22. Gilbert DA, Reid YA, Gail MH et al (1990) Application of DNA fingerprints for cell line individualisation. Am J Hum Genet 47:499–517

    CAS  Google Scholar 

  23. Doherty I, Smith KT, Lees GM (1994) DNA fingerprinting as a quality control marker for the genetic stability of production cells. In: Spier RJ, Griffiths JB, Berthold W (eds) Animal cell technology: products for today prospects for tomorrow. Butterworth-Heinemann Ltd., Oxford, pp 76–79

    Google Scholar 

  24. Stacey GN, Bolton BJ, Morgan et al (1992) Multi-locus DNA fingerprint analysis of cell banks: stability studies and culture identification in human B-lymphoblastoid and mammalian cell stocks. Cytotechnology 8:13–20

    Article  CAS  Google Scholar 

  25. Racher AJ, Stacey GN, Bolton BJ et al (1994) Genetic and biochemical analysis of a murine hybridoma in long term continuous culture. In: Spier RJ, Griffiths JB, Berthold W (eds) Animal cell technology: products for today prospects for tomorrow. Butterworth-Heinemann Ltd., Oxford, pp PP69–PP75

    Google Scholar 

  26. Slade RW, Moritz C, Heideman A et al (1993) Rapid assessment of single-copy nuclear DNA variation in diverse species. Mol Ecol 2:359–373

    Article  CAS  Google Scholar 

  27. Stacey GN, Hoelzl H, Stephenson JR et al (1997) Authentication of animal cell cultures by direct visualization of DNA, Aldolase gene PCR and isoenzyme analysis. Biologicals 25:75–83

    Article  CAS  Google Scholar 

  28. Liu M, Liu H, Tang X et al (2008) Rapid identification and authentication of closely related animal cell culture by polymerase chain reaction. In Vitro Cell Dev Biol Anim 44:224–227

    Article  Google Scholar 

  29. Loman NJ, Misra RV, Dallman TJ et al (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30:434–439

    Article  CAS  Google Scholar 

  30. Wong Z, Wilson V, Patel I et al (1987) Characterization of a panel of highly variable minisatellites cloned from human DNA. Ann Hum Genet 51:269–288

    Article  CAS  Google Scholar 

  31. Tautz D (1989) Hypervariability of simple sequences as a general source of polymorphic DNA markers. Nucleic Acids Res 17:6463–6471

    Article  CAS  Google Scholar 

  32. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in-vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Genet 44:397–401

    CAS  Google Scholar 

  33. Masters JR, Thomson JA, Daly-Burns B et al (2001) Short tandem repeat profiling provides an international reference standard for human cell lines. Proc Natl Acad Sci U S A 98:8012–8017

    Article  CAS  Google Scholar 

  34. Dirks WG, Faehnrichm S, Estella IA et al (1995) Short tandem repeat DNA typing provides an international reference standard for authentication of human cell lines. ALTEX 22:103–109

    Google Scholar 

  35. MacLeod RA, Dirks WG, Matsuo Y et al (1999) Widespread intra-species cross-contamination of human tumor cell lines arising at source. Int J Cancer 12:555–563

    Article  Google Scholar 

  36. Thompson EW, Waltham M, Ramus SJ et al (2004) LCC15-MB cells are MDA-MB-435: a review of misidentified breast and prostate cell lines. Clin Exp Metastasis 21:535–541

    Article  CAS  Google Scholar 

  37. Milanesi E, Ajmone-Marsan P, Bignotti E et al (2003) Molecular detection of cell line cross-contaminations using amplified fragment length polymorphism DNA fingerprinting technology. In Vitro Cell Dev Biol Anim 39:124–130

    CAS  Google Scholar 

  38. Hussein MR, Haemel AK, Sudilovsky O et al (2005) Genomic instability in radial growth phase melanoma cell lines after ultraviolet irradiation. J Clin Pathol 58:389–396

    Article  CAS  Google Scholar 

  39. Schröck E, Veldman T, Padilla-Nash H et al (1997) Spectral karyotyping refines cytogenetic diagnostics of constitutional chromosomal abnormalities. Hum Genet 101:255–262

    Article  Google Scholar 

  40. Pollack JR, Perou CM, Alizadeh AA (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23:41–46

    Article  CAS  Google Scholar 

  41. Murray JI, Whitfield ML, Trinklein ND et al (2004) Diverse and specific gene expression responses to stresses in cultured human cells. Mol Biol Cell 15:2361–2374

    Article  CAS  Google Scholar 

  42. Närvä E, Autio R, Rahkonen N et al (2010) High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol 28:371–377

    Article  Google Scholar 

  43. Ishkanian AS, Malloff CA, Watson SK et al (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36:299–303

    Article  CAS  Google Scholar 

  44. Speicher MR, Carter N (2005) The New cytogenetics: blurring the boundaries with molecular biology. Nat Rev 6:782–792

    Article  CAS  Google Scholar 

  45. Lichtenbelt KD, Knoers NV, Schuring-Blom GH (2011) From karyotyping to array-CGH in prenatal diagnosis. Cytogenet Genome Res 135:241–250

    Article  CAS  Google Scholar 

  46. World Health Organisation expert committee on biological standardisation and executive board (2010) Recommendations for the evaluation of animal cell cultures as substrates for the manufacture of biological medicinal products and for the characterization of cell banks (Proposed replacement of TRS 878, Annex 1). World Health Organisation, Geneva, (http://www.who.int/biologicals/expert_committee/en/)

    Google Scholar 

  47. Pörtner R (2007) Animal cell biotechnology: methods and protocols, 2nd edn. Springer, New York

    Book  Google Scholar 

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Stacey, G.N., Byrne, E., Hawkins, J.R. (2014). DNA Profiling and Characterization of Animal Cell Lines. In: Pörtner, R. (eds) Animal Cell Biotechnology. Methods in Molecular Biology, vol 1104. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-733-4_5

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  • DOI: https://doi.org/10.1007/978-1-62703-733-4_5

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-732-7

  • Online ISBN: 978-1-62703-733-4

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