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Cells In Disguise

This is a good read for anyone who’s depending on cell assays to tell them something useful. Longtime cell biologists will know that there have been several upheavals over the years about misidentified or contaminated cell lines. HeLa cells have been involved in several of these, as well as mycoplasma and other unwanted guests.
In fact, you can look back to a comment made back here in the summer. An anonymous commenter noted that:

Unrelated, I’ve always felt a big issue with cancer research has been the cell lines. Decreased funding has labs skimping on the science without them realizing it. I invite you to talk with an academic lab (the postdocs and grad students, not the PI) about where they got their cell lines. Most are “borrowed” from neighboring labs, with contamination along the weigh (cell type and mycoplasm). Very few people are culturing them from mice, the clinic, or buying them from ATCC.

And that’s exactly what Janet Stemwedel’s getting at in that piece linked above, an issue that’s even shown up on NPR. People are cutting too many corners in cell culture – whether by trying to rush results out the door, through unwillingness to spend the money, or just sheer inertia (or unwillingness to face the potential repercussions). What if, as she suggests, the NIH made it part of a grant award to get the all the relevant cell lines in the lab tested?

16 comments on “Cells In Disguise”

  1. ESIMS says:

    PI’s are cheap, its the good old “just send an @ all message” or “we have them somewhere in the liquid nitrogen”. And if you ask for the passage number you get the “I don’t know, but they are still growing”
    If you start your Phd or Postdoc, buy them from the ATCC/DSMZ/… and freeze them down!

  2. RKN says:

    Shouldn’t these 1000+ papers be retracted then?
    To the extent some or all of these papers concluded this or that protein or this or that pathway is critically dys-regulated in breast cancer metastasis, the result is likely bogus. If the results in these papers were obtained fraudulently I bet people would call for retraction, no matter how practically difficult that might be.
    And what of all the papers that cited these papers? What a mess.

  3. Eric says:

    It takes time and costs money to fully characterize a cell line. Furthermore, you need to be vigilant and periodically re-examine the cells because contamination and cell line drift occur in the best of labs. It’s not at all surprising that scientists cut corners.
    I’ve always been of the belief that if you can’t demonstrate that a pathway is important in multiple cell lines, then it’s probably not important in an animal. Reproduce your work in various cell culture systems and have other labs reproduce your findings – then I start to believe it.

  4. Guest says:

    @1
    Something that I discovered as a student was that there indeed was expression-drift (is this a coined phrase yet?) over time with regard to protein expression. I had a human cell line with shRNA that would loose knockdown, which was intuitive…However, I also had mouse cell line with stable E6/E7 and Ras that for some reason would alter the expression of my protein of interest as I passaged the cells. My PI was [surprisingly] interested in this at first. However, both of our interests waned as he was looking to re-up his R01, I was looking to graduate, and my data didn’t involve an E6/E7/Ras pathway. My solution was just to keep my passage number under 5. (is this how we kill our curious minds?)
    Another interesting item that us students picked up on is that confluence can also alter your protein expression. This is also intuitive (I’m looking at you, cell-cell interactions and signaling pathways!), however it isn’t something that is taught, it is just something you tend to notice. For cells that have lots of arms (as opposed to cells that are rounded or block shaped) this is pretty much a judgement call.
    Now, I ask your overworked, gradstudent self that wants to get home for Christmas next week. Do you lyse those cells now and hope you have enough to get a good signal? Or do you let them grow another day to make sure you have enough lysate for those pull-down assays?

  5. Anonymous says:

    Why are people with Phd’s anywhere near a freaking cell incubator? How much time is being wasted messing about with cells, coming in on weekends to do cells, splitting cells, forgetting to split cells etc.
    Hire 20 folk for the University and let them deal with it. Mycoplasma testing, passage monitoring all that boring stuff that absolutely has to be done.

  6. KeithD says:

    Some journals like AACR have been requesting additional info for a while now…not perfect but a work in progress, at least helps to address the genetic drift issues.
    1. From where and when the cells were obtained
    2. Whether the cell lines have been tested and authenticated
    3. The method by which the cells were tested
    4. How and when the cells were last tested
    The race for grants to simply survive is killing ‘the lab work behind the lab work’….whether it’s a research assistant or PhD doing the prep work it all costs money and not well acknowledged in budgets with applicants trying to get more band for their buck. Complex issue but can be fixed.

  7. Nick K says:

    The pressure on PI’s to publish and bring in grant money is at the root of this phenomenon, and it’s destroying the integrity and trustworthiness of the scientific literature. Same thing in Org Chem.

  8. anonmous says:

    Where I work, we always run into this problem. I am a chemist by training and all my efforts go to waste because of this issue. Specifically, I am working on the Bombesin and NYP receptor expressed on breast cancer cell lines. It took a while to realize that some of the cancer lines (grown here in our labs) do not express these receptors, though it was reported (erroneously?) that they do in the literature. Since biology is the driver, the chemists are always at the receiving end. Arghhh!

  9. NMH says:

    Also consider the fact that cells in culture in an incubator are replete with oxygen, but the environment in a tumor is often hypoxic. Cell lines are of limited value.

  10. a. nonymaus says:

    Re: 9
    Aren’t most incubators designed for a controlled atmosphere? Even normal tissue is far from saturation relative to the atmospheric oxygen partial pressure unless you’re studying lung cells.

  11. Hap says:

    I think the NIH person cited in the article has forgotten what the point of NIH funding is – it’s not to keep professors or grad students or administrators in milk and cookies, it’s to create work that improves the state of knowledge (of human health) and that may (as a consequence) be used to make useful things, and eventually money and jobs. If results aren’t accurate or of questionable truth because the people doing the research don’t care enough to understand what they’re doing, then NIH can’t achieve any of the missions given it. Eventually, people are going to get tired of spending money on creating cheap labor for wealthy people and money for universities and getting nothing in return, and when it does, all those people being funded now won’t be.
    There’s also the point that the unwillingness to mandate knowing what your cell lines are sends a clear message to PIs – “Just publish, baby.” If quality doesn’t matter, then I’m sure professors will get the point, and conduct research accordingly. That system will also favor professors who don’t care about the quality of their work over those who do. If you’re funding an arms race of crap, with no other values necessary to winning, then all we’ll be left with at the end of the race is crap. Very expensive crap.

  12. Emjeff says:

    #6, your comments are, frankly, offensive. Do you honestly believe that competition for funds is an excuse to cut corners? That is an egocentric mindset, pal, you need a wake-up call, because if you think competition is a valid reason to cut corners, then you haven’t been thinking.

  13. Derek Lowe says:

    #12 EmJeff – I think you’ve misunderstood KeithD in comment #6. He’s not, from what I can tell, justifying cutting corners at all. In fact, he’s bemoaning the fact that competition is causing this vital work to be neglected.

  14. Anonymous says:

    Of course you will get genetic drift. It’s virtually impossible to maintain a consistent cell culture (passage at the same exact confluence after the same number of hours etc etc) because life simply gets in the way. Cell density alone is enough to vastly alter the global expression of miRNAs:
    http://www.cell.com/abstract/S0092-8674(14)00019-1

  15. KeithD says:

    #12…..and thanks to Derek. My point is that there are ways to facilitate adequate funding for the underlying work required to keep the ‘cogs’ of a lab moving and healthy. For example, fixed proportion of budgets/grants to be spent on ‘central’ rather than ‘project-based activities might help. I’m just trying to offer a suggestion. I work in industry now but spent a decade in academia in three different countries so am drawing on personal experiences….. Comments not intended to offend PI’s….actually if I’m critical of anyone it is the system and unintended consequences that we as researchers (past or present) created……it’s a bothemeth so not easy to change…and in our urgency culture it’s difficult to stop and try to get back to basics sometimes….teaching isn’t what it used to be because it’s not revered or rewarded in the same way…I sure had a supervisor for my PhD to actually spent months teaching me techniques, stats etc… I doubt that happens anymore.

  16. newnickname says:

    I’m a little late but will repost what I often post on the cell based assay problem: Gerald B Dermer made the case against cancer screening in cell culture in “The Immortal Cell” (Avery Press, 1995). Dermer is a pathologist who has been looking at cells from cultures and from real tumors his whole life. He said that cultured cancer cells are really screwed up and almost irrelevant to finding a cancer treatment in vitro.

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