Retraction Watch

Tracking retractions as a window into the scientific process

Hundreds of researchers are using the wrong cells. That’s a major problem.

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Amanda Capes-Davis

Amanda Capes-Davis

What if we told you that approximately 1 in 6 researchers working with human cells are using the wrong cell line? In other words, they believe they are studying the effects of a drug on breast cancer cells, for instance, but what they really have are cells from the bladder. That is the unfortunate reality in life science research today, affecting hundreds of labs. It’s a major source of problematic papers which cannot be replicated, wasting scientists’ time and funding.

We’re pleased to present a guest post from Amanda Capes-Davis, chair of the International Cell Line Authentication Committee (ICLAC), a voluntary scientific committee created to improve awareness of misidentified cell lines. She also collects news about cell line and culture contamination. This is the first in a series of two posts from guest authors about how problematic cell lines are contaminating the scientific literature, and how we can clean it up.  

In 2010, I worked alongside Ian Freshney of Glasgow University and other colleagues to publish a list of cross-contaminated or otherwise misidentified cell lines in the International Journal of Cancer. This database of false cell lines is now curated by the International Cell Line Authentication Committee (ICLAC).

All of us who have contributed to the database are aware that cross-contamination is an important ongoing problem.  But I think the number of cell lines affected was a surprise, even to many of us in the field who see these problems on a daily basis.

The latest version of the database, updated in October 2014 (v7.2), lists 438 false cell lines where we do not have any evidence for authentic stock. We know of 37 other cell lines where instances of cross-contamination have been published but where evidence does exist for authentic stock, usually from the originator or a cell line repository.

These figures fit with previous work showing that many cell lines are cross-contaminated at source, most likely during establishment.

It’s astonishingly easy for cell lines to become contaminated. When cells are first placed into culture, they usually pass through a period of time when there is little or no growth, before a cell line emerges.  A single cell introduced from elsewhere during that time can outgrow the original culture without anyone being aware of the change in identity.

One of the most commonly used cell lines is HeLa, made up of immortal cells derived from a patient who died of cancer in the 1950s. Cross-contamination of human cell lines by HeLa was first reported by Stanley Gartler in 1966 and brought to the attention of the scientific community by Walter Nelson-Rees in the 1970s. This is still an important issue — HeLa cells are the most common contaminant in our database, responsible for 24% of its false cell lines.  But HeLa is not the only culprit.

At last update, the database of misidentified cell lines listed 138 different contaminating cell lines.  Widely used cell lines such as T-24 (bladder cancer), HT-29 (colon cancer) and K-562 (chronic myeloid leukemia) are common contaminants, silently taking over the identity of cultures that researchers believe to be prostate, thyroid or other types of cancer.

Fifty cell lines in the database are cross-contaminated by another species.  Examples include CHB (“human astrocytoma” but actually rat); AMDURII (“human skin” but actually pig); and ACCNS (“human salivary gland carcinoma” but actually mouse).

It has been estimated that 15% or more of human cell lines are not derived from the claimed source.

All these numbers add up – to scientific mayhem.  Decisions are being made about new anticancer drugs and other treatments based on work in misidentified cell lines.  Hundreds of articles are published using these cell lines under their false identities, and read by other scientists who will use those cell lines for their own work.

Journals have started to take notice: This year, Nature and Nature journals began requiring that authors check that their cell lines have not been flagged as misidentified or contaminated, and report their testing status.

Can we reduce the impact of these false cell lines?

How can we tell whether published work using cell lines can be trusted?

As a first step, use ICLAC’s database of misidentified cell lines to look for known problems.  Misidentified cell lines are listed in alphabetical order, along with the contaminant and the reference where the problem was documented.

But while that first step helps, it is not enough.  Your cell line may have been cross-contaminated just before you started using it, or you might be working with a false cell line that no-one else knows about.

There is only one real solution: Scientists must also authenticate their cell lines.

Note: We will be publishing a guest post tomorrow about ways scientists can authenticate their cell lines.

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Written by Alison McCook

December 8th, 2015 at 2:00 pm

Comments
  • dr db Karron December 8, 2015 at 2:31 pm

    How do you positively identify cell cultures and they are truly clones?

  • Anonymous December 8, 2015 at 3:19 pm

    A query was raised in February, 2015 about the accuracy of cancer cell lines in treatments using Thai medicinal plants:
    http://retractionwatch.com/2014/01/25/weekend-reads-trying-unsuccessfully-to-correct-the-scientific-record-drug-company-funding-and-research/#comment-355853

  • A Capes-Davis December 8, 2015 at 6:06 pm

    dr db Karron that’s a very good question. The biggest problem with cell lines comes from cross-contamination by a classic tumor cell line, like HeLa. HeLa and other commonly used tumor cell lines tend to grow quickly, so they easily overgrow other cultures. To pick up that problem we typically use STR profiling, which will be covered in the post tomorrow. Contamination of clones from the same individual is harder to pick up and takes in-depth analysis using techniques like whole genome sequencing.

  • J Pippin December 9, 2015 at 8:54 am

    Most alarmingly, most researchers continue to use contaminated cell lines despite common knowledge of the problem. What does this tell us about scientific integrity and the basic science process? Publications more important than honesty, I think. Seems to me that the only solution is for ALL journals to require proof of cell line verification before reviewing manuscripts.

    • Vira August 1, 2016 at 5:11 pm

      Keep in mind the pressure for scientists to publish. It’s not always fair to paint people as villains when they have good intentions and enormous pressures from businesses, government and management.

      • JPippin August 1, 2016 at 10:21 pm

        No, this has nothing to do with good intentions. Researchers know that cell lines are notoriously unreliable, and that validation is necessary. Those who ignore this are cheating to get published, even though their results may be flawed.

  • murali April 25, 2016 at 7:15 am

    very useful information, thank you Amanda Capes

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