It is time for all involved to tackle the chronic scandal of cell-line contamination. Funders first.
Some 40 years after it was first recognized, the use of contaminated and misidentified cell lines in biological research remains a growing problem. But it is a problem that has a simple solution: routine, cheap, DNA profiling of laboratory cultures. It is now time to implement that solution. To do so, scientists need the funding and motivation to verify the cell lines in their possession, as well as a curated electronic database of authenticated DNA profiles against which they can compare their results.
Thousands of biology labs use cell lines, yet many do not know that between a fifth and a third of the lines in common use may not be what they seem. In the past 25 years, numerous studies, as well as the experience of cell-culture repositories in the United States, Britain, Germany and Japan, have found that 18–36% of cultures contain a misidentified species or cell type. The effect of using such cells varies depending on the project involved. When the lines are used as a source of biochemicals, for example, the misidentified lines are innocuous. Deployed in the study of a general cellular process, they can have minor drawbacks. But on the rare occasions that the cell lines are thought to reflect the properties of a particular tissue, cancer or disease state, the outcome can be severely damaging as funding and research get driven into work based on false premises.
Repositories need to authenticate all of their cell lines, and the major funders must direct support accordingly.
To make matters worse, papers are still published that contain unwarranted conclusions derived from misidentified lines. It is ironic that many researchers who are obsessed with using only the highest-quality chemicals and biologics from the most trusted suppliers don't think twice about using cell lines known to be misidentified.
Cell repositories do carry out quality-control assays on deposited lines, although the tests performed vary. Even a venerated panel of 60 tumour lines at the US National Cancer Institute was found to have some that were either HeLa (the first human cancer cell line) or subcultures of one another.
This crisis of identification can be solved by analysing repository cell lines using DNA fingerprinting — short tandem repeat (STR) assays — and making the 'authenticated' profiles available in a database. Some of the cell-line profiles in the American Type Culture Collection, for example, already have their STR profiles listed. The German DSMZ cell repository performs DNA profiles for every line, but has also reported that 29% of its human tumour line deposits are cross-contaminated. It costs between $20 and $400 to fingerprint a cell sample (depending on country and circumstance), and some predict that the $2 STR analysis is not far away. At that price, what lab could not afford to regularly recheck its cultures?
In an open letter in 2007, Roland Nardone of the Discovery Center for Cell and Molecular Biology in Washington DC, and his colleagues brought the issue of misidentification to the attention of Michael Leavitt, until recently director of the US Department of Health and Human Services. This moved the issue forward: by the end of the year the National Institutes of Health (NIH) formally recognized in a public notice that “misidentification of cell cultures is a serious problem”. However, the notice went on to state that “it would be impractical for the NIH to require application of particular methods in all grant applications”, and put the onus on peer reviewers to quality-control their colleagues' research proposals and manuscripts.
This merely capitulates to the status quo. Four decades after the problem came to light, it is time for this cavalier attitude to be jettisoned. Repositories need to authenticate all of their lines, and the NIH and other major funders must direct support accordingly. The STR profiles should be lodged in a global database that provides tools for readily comparing a culture's fingerprint with authenticated profiles. The funders should motivate investigators by encouraging the inclusion in grant proposals of expense estimates for cell-line verification, in recognition that this quality assurance will increase the costs of research. The community, in turn, should accept that it makes sense to verify cell lines routinely.
Once this research framework is sufficiently established, major funders will be able to require the validation of all immortal cell lines in order for investigators to retain funding, and journals should (and Nature will) require that all lines used in a paper were verified before publication.
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Identity crisis. Nature 457, 935–936 (2009). https://doi.org/10.1038/457935b
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