Mutations in pluripotent stem cells: No, the sky is not falling

Figure 3 Merkle et al.
Figure 3 Merkle et al. Nature 2017

By Jeanne Loring

“Mutation” and “cancer” are eye-catching words for a headline; add “stem cells” and there is a good chance that a lot of people will hear about it. These words have been liberally used in the press to describe the results of a recent publication: “Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations.”

Every time a scientific report suggests that human stem cells are dangerous, I feel the need to reassure both scientists and non-scientists that we should not panic.  The sky is NOT falling (contrary to Henny Penny), and pluripotent stem cells remain valuable for cell replacement therapies.

Human embryonic stem cells (hESCs) have been around for 20 years, and the NIH has registered 384 different hESC lines that meet ethical guidelines and are eligible for use with NIH grant funding.  The cell lines are held by their owners, and Kevin Eggan, the senior author on the mutation publication, spent years convincing the owners to give him samples of 140 of them for genomic analysis.

His research group sequenced all of the protein coding regions of the genomes of these cells, looking for errors that might affect their suitability for both clinical and research use.  They found many differences among the cells, but focused on one particular gene, TP53, because of its association with many kinds of cancers.  The protein, called p53, is a tumor suppressor. This means that having two healthy copies of the TP53 gene protects cells from becoming cancerous.  The publication reported that about 5% of the cell lines tested had only one good copy of TP53. This means that they are less protected and more likely to form tumors.

Problems with TP53 in hESCs have been reported before by two papers from my research group:  and  But the current study went to the heart of the potential problem:  scientists who provided the cells to Eggan DID NOT KNOW that they carried TP53 mutations.  This is definitely something to be concerned about.

Why didn’t the scientists know?

Allow me to have a small rant…I have been on this soapbox since 2000, when I received my first NIH grant for genomic analysis of human stem cells  (NIH). I’ve been telling anyone who will listen that they need to use genomic and epigenetic methods to ensure the safety of stem cell derivatives used for transplantation.  Our cell replacement project to treat Parkinson’s disease with autologous dopamine neurons has numerous quality control steps, including whole genome sequencing (WGS), epigenetic profiling, and gene expression analysis. These measures go far beyond what is required by the FDA, but we want to use all of the tools we can to make sure that the transplanted cells won’t harm the patients.

But stem cell scientists without a background in DNA sequencing can often find the huge datasets to be daunting and some researchers are concerned that they won’t be able to understand the results. I’ve been lucky that I have a background in genomics and close colleagues who specialize in bioinformatics.  And I’ve had my own genome sequenced (three times, but that’s another story), which makes me more comfortable about the normal variations among different people and the significance of disease-causing mutations.  Luckier still, CIRM has funded my lab for 9 years to perform extensive genetic analysis of human pluripotent stem cells and their derivatives.

What can a stem cell scientist do now (instead of panicking)?  I can’t invite everyone to collaborate with me, but I can recommend that researchers look around them to find scientists down the street or across campus who can analyze WGS datasets.  WGS costs about $2,000, a tiny fraction of the cost of developing a bank of stem cell-derived cells for cell replacement therapy or of potentially stopping an actual trial that inadvertently used insufficiently validated cells later found to contain functionally important mutations.

Last year my lab reported ways to identify dangerous mutations that might occur in induced pluripotent stem cells, using WGS.  Once a bioinformaticist agrees to work on stem cell sequences, this would be a good place to start.

Don’t panic!  Check your cells instead.

About the author. Jeanne Loring is a professor in the Department of Molecular Medicine at The Scripps Research Institute in La Jolla, CA.  Her lab focuses on stem cell applications for Parkinson’s disease, multiple sclerosis, Fragile X Syndrome, and rescue of endangered species.

12 thoughts on “Mutations in pluripotent stem cells: No, the sky is not falling”

  1. The biggest issue of all has been only obliquely touched on. It’s nothing but a matter of time before Andy Harris becomes the next director of NIH,and just guess what his stance is… if you guess that “Some expressed worry that his policy positions — including staunch opposition to research with human embryonic stem cells — would be at odds with the NIH’s culture”, (per the January 19th article in Nature) then I’m afraid you won’t be winning any prizes, because it was a little too obvious. VP Mike Pence has spent his political career fighting against effective stem cell research.The religious right is gaining more and more political power, and they have a very definite attitude about stem cell research. What it all adds up to is that we’re headed in a very unpleasant direction. Serious stem cell research in the U.S. doesn’t look like it’s going to be decided by science, but by religion and politics. We have to start speaking plainly about this. Maybe we can’t have scientists writing about this issue so directly (it doesn’t really look good,) but I’m going to keep pointing out the truth.

  2. Mark Kotsatos

    very interesting and enlightening. Now what can we do to combat subarachnoid hemorrhagic brain stem bleeds?

  3. Dear Admin:

    You have to admit. This is one of Admin’s most biased, self conflict of interest rants to date. Look! Artificially derived pluripotent stem cells (hESCs and unfortunately iPSCs, too) often have both genetic and epigenetic mutations. This is now a well-established and well-documented feature of their biology. The evidence is so sound that now those in the field who favor these cells for cell therapy development, Admin included, have been looking for ways to minimize the problems their mutagenesis presents for the past decade now.

    Some individual mutations maybe detrimental and others may not. But as a general biological characteristic, the high frequency of mutation in pluripotent stem cells precludes their use for cell therapy (of course, this isn’t their only shortcoming for cell therapy applications!). Scientists who favor the use of pluripotent stem cells for cell therapy have moved on to unsound Rube Goldberg-like approaches for picking out mutation free cells (Admin’s suggestion here) or hoping that mutations will not affect the function of differentiated cells derived from pluripotent cells or pose similar cancer risk. Their position is either politically obtuse or biologically naive, but it is not scientifically tenable.

    Remember natural tissue stem cells? The field can return to more effort with them now, or it can return to them later after billions of cell therapy research funding is wasted, but the biology of the thing guarantees that if there will be the desired successes in stem cell therapy, it with be with appropriately evolved tissue stem cells.

    James at Asymmetrex

    1. @James,
      First of all, I did not write the piece you are commenting on so how exactly is this my rant?
      Second, how is this piece a rant? That seems way off base. Your comment, on the other hand, strikes me as more like a rant.
      The best thing for patients and the stem cell field is to pursue a wide variety of types of stem cells as each one has strengths and weaknesses. Pluripotent stem cells just cannot be matched by adult ones in terms of potency and IPS cells in particular have potential for personalized medicine plus great potency, while adult ones have lower risk of causing cancer, which admittedly is a real advantage. But all of them can acquire mutations in culture even including adult stem cells so how one treats the cells and validates them is a big deal across the board. “Natural” cells is probably almost always going to be a misnomer as once they are removed from the body they are no longer natural and the more they are manipulated the greater the risk.

      1. Dear Paul:

        My error and my apology. I overlooked that the post was the original author’s article and not an Admin commentary on it.

        My choice of characterization as a rant was taken with the lead from the article: “Allow me to have a small rant…I have been on this soapbox since 2000, when I received my first NIH grant for genomic analysis of human stem cells (NIH). I’ve been telling anyone who will listen that they need to use genomic and epigenetic methods to ensure the safety of stem cell derivatives used for transplantation.” Combined with my initial error, perhaps you can see how that got me to my characterization.

        Now your statement, this time for sure, that “The best thing for patients and the stem cell field is to pursue a wide variety of types of stem cells as each one has strengths and weaknesses,” is a cliche aphorism that abounds to promote large amounts of limited research funds into pluripotent cells for an application, for which they are ill-suited. I’m not saying that we shouldn’t investigate iPSCs. I am saying that we should be more upfront about their limitations for cell therapy and what they predict for applications for stem cell therapy based on them.

        That’s right. You don’t have to culture adult tissue stem cells to use them effectively, though methods to produce them in larger number would certainly be beneficial for treating more patients. Whether their mutation rate, when cultured, matches the high starting mutant fraction of pluripotent stem cells remains to be seen, when it is possible to measure adult tissue stem cell-specific mutant fractions.

        When it comes to cancer risk, empirically, a significant risk has not emerged in decades of HSC transplant and not yet in recent years with other adult stem cell transplants. In contrast, the pluripotent stem cell cancer risk is a part of their characterization. Need more be said? You would think not; but as it turns out, many scientists are not talking or thinking about this significant shortcoming nearly enough. And like you, they don’t even mention the preemptive biological deficit of pluripotent stem cells. They don’t possess the asymmetric self-renewal kinetics that are obligatory for long-term renewal of vertebrate organs and tissues.

        Still James at Asymmetrex

      2. Jeanne F Loring

        Paul: There is no reported danger of cancers from differentiated cells, so we should take that into consideration when evaluating risk. The concern comes from the fact that transplants of cells differentiated from hPSCs engraft. If adult stem cells engrafted, they might well may more prone to cancers. Since they just sail through the body (unless they are trapped in the lungs or liver), such cells are “safe”.

        1. Jeanne,
          Do you mean cells like MSCs by “differentiated cells” or fully differentiated cells? As to the former, I believe there isn’t zero risk from them on the tumor level and they do accumulate mutations in culture as well.

    2. Jeanne F Loring

      It’s my piece. Every time a cell replicates its DNA, there is a chance for a mutation to arise. Since all stem cells divide, all stem cells accumulate mutations. You should check your cells – have you sequenced them? Here’s an interesting article on this subject:

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