Assessing Cell Line Integrity: Cell Line Authentication versus Cell Line Characterization
Presently, there is a compelling call in the scientific community to authenticate cell lines used in research, especially before publication and cell banking. A frequently recommended inexpensive test for authentication is the DNA Short Tandem Repeat Assay. At KaryoLogic, we believe this recommendation is not enough.
When it comes to assessing cell line integrity, it is important to first make a distinction between cell line authentication and cell line characterization. One identifies, the other describes. What many fail to realize is that DNA profiling tests (such as the Short Tandem Repeat Assay and similar assays that detect DNA sequences unique to a particular cell line) will merely determine whether or not one has the correct cell line, yet tell little about the integrity of that cell line. Once one has confirmed that they do indeed have the correct cell line, further testing to characterize isozymes, specific gene expression, and karyotypes is necessary to reveal any changes that may have accrued in culture over time.
Karyotyping is typically thought of as a characterization assay, though it can be used for authentication in some cases, such as when a cell line has enough uncommon identifying characteristics. For example, say a human cell line used to study a particular disease state is known to have a near diploid count, a sex chromosome complement of XY, a specific Chromosome 8 to Chromosome 14 balanced translocation, a particular small deletion of the Chromosome 17 p arm, and Chromosome 18 trisomy. These are enough unique identifiers that detection of these characteristics alone would be enough to authenticate the cell line. Here, karyotyping effectively serves to authenticate as well as to characterize.
Karyotyping would not suffice for authentication, however, when karyotypes are expected to be normal, as in stem cells. Then, DNA profiling is needed. Yet why stop there? Why skip the characterization assays that provide even more information about the cell line? Here at KaryoLogic, we have unfortunately too often uncovered chromosomal aberrations in “stem cells”. Some investigators sent cells to us because they suspected that something was not right, while some were completely caught off guard by the karyotype results. The Short Tandem Repeat Assay will not detect tetraploidy, some trisomies, balanced translocations, minor deletions, minor additions, nor inversions, to name a few, yet tetraploidy, trisomies, and balanced translocations are the some of the most common aberrations acquired in cultured mammalian cells! Furthermore, it is unlikely that DNA profiling assays will detect abnormalities present in less than 20% of the cells. The strength of karyotyping is that it analyzes cell by cell, chromosome by chromosome, thus providing very detailed specific information. In contrast, DNA profiling protocols pool large populations of cells, dissolve the cells, cut up the chromosomes to release the DNA, and then analyze these composite DNA samples. The result is an overview of the genetic status, thus much information is lost.
Therefore, we believe that it is not enough to merely authenticate cell lines, but that one must also characterize, through karyotyping and other assays, to ensure scientific data is valid and reproducible.
Posted December 24, 2015 by Elizabeth Livanos