You think you’ve found what you need – a cell model for a specific type of cancer you’re studying. But the label on those cells may have you fooled. In labs around the world, many cell lines are mistaken for characters they are not. Dr. Amanda Capes-Davis has seen it happen, time and again. She received her medical training and PhD in cancer genetics from the University of Sydney. After six years as a research officer at the Children’s Medical Research Institute (CMRI), she helped establish CellBank Australia, a non-profit cell line repository. Now working as a cell culture consultant and chair of the International Cell Line Authentication Committee (ICLAC), Capes-Davis is on a mission to bring the long-standing problem of cell line misidentification to light – and she’s using PubMed Commons as a tool in this fight.
Cell culture is a part of everyday life for many life science and biomedical researchers. To address biological questions, scientists often work with populations of cells grown in incubators. Typically, cells isolated from a human or other animal will only survive and multiply for a few days or weeks, even under optimal conditions. “Immortalized cell lines,” on the other hand, can be grown in flasks or dishes for months, even years. Often these lines are derived from cancers that allow cells to bypass checkpoints that would normally stop them from dividing.
The advent of immortalized cell culture 60 years ago opened doors for new studies, but there are also persistent problems. Many cell lines bear mistaken identities. So far, ICLAC has identified 472 cross-contaminated or misidentified cell lines, based on 89 publications. The cell type or tissue origin of cells grown is sometimes mislabeled at the outset. Other times, a cell line cross-contaminates another, overtaking the original line. “Perhaps 10-15% of all cell lines are cross-contaminated,” Capes-Davis reports.
HeLa cells exemplify the potential and the pitfalls of cell culture. Henrietta Lacks was a woman who unknowingly pushed biomedical science forward. While she was under treatment for aggressive cervical cancer, a sample of her tumor was taken. Shortly before her death in 1951, those cells were used to establish the first reported immortalized human cell line. Within a few years, the cells were widely used, including in development of the polio vaccine. However, HeLa cells grow so robustly that, if a few cells mistakenly get mixed in with another cell type, HeLa can quickly overtake the others. In their survey of the literature, ICLAC has noticed an abundance of HeLa contamination. Capes-Davis notes, “There are 135 different cell line contaminants, but HeLa is by far the commonest. We list 113 misidentified cell lines where HeLa is the contaminant.”
HeLa cross-contamination of cell lines was first reported in 1967. Yet many new publications continue to misidentify cross-contaminated cell lines. “It’s very understandable, I think, for a scientist,” Capes-Davis says. “You’re doing research in that field. You’re seeing everyone else using this cell line. You think this must be appropriate because all of your colleagues use it.” Reports of cross-contamination disappear under the mountain of other publications using the cell line. In doing as they were trained – building on work published by others – many scientists are actually perpetuating errors. Capes-Davis notes, “They say, research is meant to be self-correcting, but with these cell lines, that doesn’t appear to be the case.”
It’s impossible to fully assess the impact that cell line contamination has had – and continues to have – on research and development. “You only really get hints here or there,” Capes-Davis says. “I first learned about cell line contamination as a PhD student… The lab I was working in started to require testing as I was writing up my PhD. That was quite a stressful experience for me – my PhD was entirely cell culture-based, and it was frightening to think that all my hard work might be wasted if those cell lines were contaminated.” In some cases, experimental results from misidentified cell lines supported patenting and testing of compounds in people. “These days, I think, with the level of regulation that comes in, problems with cross-contaminated cell lines will be picked up before an agent is trialed, but you have to wonder about the waste of time and waste of money required to get to that point.
For Capes-Davis, though, solving cell line misidentification is about more than scientists’ time and research funding. “I am also a medical doctor and would go in to operating theatres to collect tissue samples from individuals who consented to their tissue being used in research. Many cell lines represent a legacy from donors who have died as a result of that disease. To me, testing of cell lines is part of our responsibility to the donor, and makes sure that we put the donor’s gift to the best use we can in finding future treatments.”
Correcting the record and the future course
In 2009, Capes-Davis joined two initiatives to address cell line misidentification. The American Type Culture Collection (ATCC) Standards Development Organization established a workgroup (ASN-0002) to develop standards for human cell line authentication. Capes-Davis recalls, “Some members wanted to have an ongoing group on cross-contamination.” During this time, she also collaborated with Ian Freshney to develop a database of cross-contaminated cell lines. “We could really see the value of having involvement of a larger group of people, the advantages of people being able to contribute data or having additional expert opinions on whether a cell line was cross-contaminated, whether or not it’s possible to find authentic stocks.” In 2012, she and other scientists with a shared interest in the problem of cell line misidentification founded ICLAC.
“I think publicity and awareness is always a challenge. It’s always a bit of a surprise to people, even people who’ve been in the field a number of years,” Capes-Davis notes. “A lot of what we’re involved with is making people aware of the need for quality, even when they’re doing preclinical research. It’s not a series of steps that are going to be difficult to do, but it’s something that should be part of good lab practice. It’s part of good research.” ICLAC is also seeking to establish infrastructure for researchers, such as maintaining the database she and Freshney created, developing guidelines for best practices, and making resources available online.
Capes-Davis has taken to PubMed Commons to annotate publications that misreport identities of known cross-contaminated cell lines. “Ideally we want these things picked up as part of peer review, but it’s not as easy sometimes as you might think,” she notes. “Correcting the scientific record is a really important thing because even if you take the assumption that a signaling pathway isn’t going to be affected, that’s not necessarily going to be the case for another paper that cites that work. The assumption is that if you describe a cell line as oral carcinoma, that’s what it is. It might not matter for one person’s work, but it could well matter for the person who reads that paper.”
“I use PubMed pretty much everyday… it’s an area where a lot of people come to look at abstracts and hunt down papers,” Capes-Davis notes. “So [PubMed Commons] seemed like a great opportunity to raise awareness of our database… We’re hoping that if we do the best we can to bring all the known publications that relate to cross-contaminated cell lines into our database, that will be a useful resource for people. It’s not enough…but it’s certainly a step in the right direction.”