Cancer cell line identification by short tandem repeat profiling: Power and limitations

Institute of Legal Medicine, Department Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
The FASEB Journal (Impact Factor: 5.04). 04/2005; 19(3):434-6. DOI: 10.1096/fj.04-3062fje
Source: PubMed


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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Available from: Anita Kofler, Oct 09, 2015
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    • "Supra-physiologic levels of O 2 might have deleterious effects, as they have been reported to increase the generation of oxygen radicals that may, in turn, increase the rate of cellular oxidative damage, DNA strand breaks, and mutations [3]. Many available leukemia cell lines demonstrate DNA microsatellite instability, indicating loss of DNA mismatch repair activity [4] [5]. Such cell lines, and especially those that have been extensively expanded over decades, are likely to have accumulated significant genetic and epigenetic changes under nonphysiologic selection pressures since their isolation from the patient. "
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    ABSTRACT: Cancer cells typically exhibit increased glycolysis and decreased mitochondrial oxidative phosphorylation, and they continue to exhibit some elevation in glycolysis even under aerobic conditions. However, it is unclear whether cancer cell lines employ a high level of glycolysis comparable to that of the original cancers from which they were derived, even if their culture conditions are changed to physiologically relevant oxygen concentrations. From three childhood acute lymphoblastic leukemia (ALL) patients we established three new pairs of cell lines in both atmospheric (20%) and physiologic (bone marrow level, 5%) oxygen concentrations. Cell lines established in 20% oxygen exhibited lower proliferation, survival, expression of glycolysis genes, glucose consumption, and lactate production. Interestingly, the effects of oxygen concentration used during cell line initiation were only partially reversible when established cell cultures were switched from one oxygen concentration to another for eight weeks. These observations indicate that ALL cell lines established at atmospheric oxygen concentration can exhibit relatively low levels of glycolysis and these levels are semi-permanent, suggesting that physiologic oxygen concentrations may be needed from the time of cell line initiation to preserve the high level of glycolysis commonly exhibited by leukemias in vivo. Copyright © 2015. Published by Elsevier Inc.
    Experimental Cell Research 04/2015; 334(1). DOI:10.1016/j.yexcr.2015.03.024 · 3.25 Impact Factor
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    • "To allow typing of these two TIC lines a breakpoint for AMC700T and B and a breakpoint unique for AMC700B were included. Short tandem repeat profiling of cells has previously been described as a method permitting the unambiguous identification of cell lines [19] [20] [21]. This method was used to obtain the DNA fingerprints of the eight neuroblastoma TICs using probes for 16 short tandem repeat markers (Supplementary Table 2). "
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    ABSTRACT: Recently protocols have been devised for the culturing of cell lines from fresh tumours under serum-free conditions in defined neural stem cell medium. These cells, frequently called tumour initiating cells (TICs) closely retained characteristics of the tumours of origin. We report the isolation of eight newly-derived neuroblastoma TICs from six primary neuroblastoma tumours and two bone marrow metastases. The primary tumours from which these TICs were generated have previously been fully typed by whole genome sequencing (WGS). Array comparative genomic hybridisation (aCGH) analysis showed that TIC lines retained essential characteristics of the primary tumours and exhibited typical neuroblastoma chromosomal aberrations such as MYCN amplification, gain of chromosome 17q and deletion of 1p36. Protein analysis showed expression for neuroblastoma markers MYCN, NCAM, CHGA, DBH and TH while haematopoietic markers CD19 and CD11b were absent. We analysed the growth characteristics and confirmed tumour-forming potential using sphere-forming assays, subcutaneous and orthotopic injection of these cells into immune-compromised mice. Affymetrix mRNA expression profiling of TIC line xenografts showed an expression pattern more closely mimicking primary tumours compared to xenografts from classical cell lines. This establishes that these neuroblastoma TICs cultured under serum-free conditions are relevant and useful neuroblastoma tumour models.
    European journal of cancer (Oxford, England: 1990) 12/2013; 50(3). DOI:10.1016/j.ejca.2013.11.015 · 5.42 Impact Factor
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    • "However, due to the lack of standard references, the application of such techniques for authentication purposes maybe limited. In addition, alteration of the DNA fingerprinting profiles for cancer cell lines over a period of time has been reported, restricting its use as stable identifiers for a particular cell line [43]. The fact that the standard references are available for STR analysis, the technique has acquired considerable popularity worldwide as a means for authentication of the newly established cell lines [40]. "
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    ABSTRACT: Transitional cell carcinoma of the urinary bladder is one of the common diseases that causes morbidity and mortality worldwide. In Malaysia, bladder cancer is in the 10 most frequent cancer occurred among males. Since most of the current urinary bladder cancer cell lines were established from populations in western countries while significant genotypic variations have been reported among various populations, this project aimed at establishing the first continuous cell line for providing an ideal cancer cell model for Malaysian population and nearby countries acquires significance. The urinary bladder cancer cells were isolated from bladder cancer tissues obtained from a Malay patient. The obtained cells were cultured continuously over 30 passages. This cell line was characterized by observing its morphology, growth characteristics, presence of cytokeratin 7 and desmin markers, expression of Ki-67, VEGF as well as p21 proteins. The authenticity of the obtained cells was investigated using Short Tandem Repeat (STR) analysis and contamination by Mycoplasma was ascertained. Results revealed that this newly established cell line (USM-BC-1) has been well characterized as an ideal cancer cell model which may prove useful in cancer research towards developing future diagnostic and therapeutic targets, taking into consideration the genotypic variations among Asian population.
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