A new paper from Shoukhrat Mitalipov’s lab on stem cell mitochondria points to a pattern whereby induced pluripotent stem (IPS) cells tend to have more problems if they are from older patients.
New Mitalipov paper
What does this paper mean for the stem cell field and could it impact more specifically the clinical applications of IPS cells?
The new paper Kang, et al is entitled “Age-Related Accumulation of Somatic Mitochondrial DNA Mutations in Adult-Derived Human iPSCs”.
This paper reminds us of the very important realities that mitochondria are key players in stem cell function and that mitochondria have their own genomes that impact that function. A lot of us don’t think about mitochondria and their genome as often as we should.
The paper came to three major scientific conclusions (this from the Highlights section of the paper and also see the graphical abstract for a visual sense of the results overall):
- Human iPSC clones derived from elderly adults show accumulation of mtDNA mutations
- Fewer mtDNA mutations are present in ESCs and iPSCs derived from younger adults
- Accumulated mtDNA mutations can impact metabolic function in iPSCs
Importantly the team looked at IPS cells derived from both blood and skin cells and found that the former were less likely to have mitochondrial mutations.
Stem cell mitochondria and mutations
This study suggests that those teams producing or working with human IPS cells (hIPSCs) should be screening the different lines for mitochondrial mutations. This excellent piece from Sara Reardon on the Mitalipov paper quotes IPS cell expert Jeanne Loring on this very point:
“It’s one of those things most of us don’t think about,” says Jeanne Loring, a stem-cell biologist at the Scripps Research Institute in La Jolla, California. Her lab is working towards using iPS cells to treat Parkinson’s disease, and Loring now plans to go back and examine the mitochondria in her cell lines. She suspects that it will be fairly easy for researchers to screen cells for use in therapies.”
Mitalipov goes further and suggests that his team’s new findings could support the use of human embryonic stem cells (hESC) derived by somatic cell nuclear transfer (SCNT) which would be expected to have mitochondria with fewer mutations. However, as Loring points out in the Reardon article, SCNT is really difficult to successfully perform and only a few labs in the world can do it at present. In that context, working with hIPSC and adding on the additional layer of mitochondrial DNA mutation screening could be more practical.
New York stem cell researcher Dieter Egli, however, is quoted that hIPSC have other differences with hESC as well such as epigenetic differences and he’s quoted in the Reardon piece, “It’s going to be very hard to find a cell line that’s perfect.”
One might reasonably ask both Egli and oneself, “What is a perfect cell line?”
In the end the best approach for use of human pluripotent stem cells of any kind is going to involve a balance between practicality of production and the potentially positive or negative traits of those cells as determined by rigorous validation screening.
With this new paper we’ve just learned more about another layer of screening that is needed. An interesting question is whether adult stem cells such as mesenchymal stromal/stem cells (MSC) also should be screened for mitochondrial mutations. They are often produced from patients who are getting up there in years. I hope that someone will publish on that too.
As to pluripotent cells, I expect that sometimes the best lines, meaning those most perfect for a given clinical application, will be hIPSC (autologous or allogeneic in some instances) and in other cases they may be hESC made from leftover IVF embryos. If SCNT-derived hESC can be more widely produced in an affordable manner and they pass validation as well then those (sometimes called NT-hESC) may also come into play clinically. So far that hasn’t happened for the SCNT cells, but it may over time.
The more types of pluripotent cells and indeed stem cells more generally including adult stem cells that we have in our clinical arsenal to help patients the better as long as the cells and any derivatives made from them have gone through vigorous validation in each case and there’s hard data to support their use in patients with a reasonable expectation of both safety and efficacy going into any particular clinical study.
Hi Everybody,
I may be missing something in the Mitalipov team article, but I could not find any reference to the characterization of the hiPSC generated from older or younger donors.
I find it a bit odd, usually an hiPSC can be qualified as pluripotent only when it has at least proven to be able to efficiently generate derivatives of the 3 germ layers through EBs or teratoma (or directed differentiation). Mitochondrial mutations can significantly impair the ability of iPSC to differentiate in EBs or teratoma (see Wahlestedt et al., 2014, Stem Cells using miPSC). One could then argue that if the hiPSC from the Mitalipov study had been stringently assayed for differentiation potential, those with the most mitochondrial anomalies may not have passed QC. Therefore in the finally selected hiPSC, there would likely have been less differences between hiPSC from old donor, or young donor, or even with hESC?
@Julien,
I need to go back and look at the paper again.
You raise some interesting points.
Depending on the validation studies done or not done on the IPSC for this paper, it is possible that the older IPSC are not even real IPSC in some cases. If so, I’m not sure it is a fair comparison. On the other hand, if the old patient IPSC fully passed QC and are actually full-fledged IPSC, then one wonders if perhaps such cells might in fact be fine functionally despite what the paper argues about some functional differences. What a lot of this points to more broadly is the need both in this kind of study as well as in the clinical pipeline for rigorous validation of one’s stem cells. If mitochondrially mutant IPSC would nearly always fail the more basic pluripotency testing anyway, then perhaps it is not necessary to go to the trouble of sequencing the mitochondrial genome.
Paul
If Yamanaka had performed some key experiments as I proposed to him and agreed by him as important nine years ago then the iPS sky might have fallen down long time ago. See one of my earlier publication at:
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.552.5144&rep=rep1&type=pdf
The sky is not falling but a crack has been shown in the sky. Once mainstream recognizes my perspective on iPS reprogramming and my view on iPSCs the sky – iPSCs are ethical and safe replacements for ESCs – will fall down for sure.
Cells for potential clinical use will be the endogenous, pluripotent stem cells which exist in all adult organs – not iPS/ES/SCNT-ES cells grown in Petri dish. Regeneration has to be endogenous – not replacement of diseased cells with healthy cells grown and differentiated in a dish. These endogenous stem cells remain quiescent throughout life, have very few mitochondria and thus do not accumulate mutations.
See this recent research by the Genome Institute of Singapore on how oocyte-based reprogramming rejuvenates mitochondria via the Tcl1 gene acting via the mitochondrial enzyme, PnPase. It seems that this does not presently take place during iPSC reprogramming.
Paper summary:
http://www.gis.a-star.edu.sg/internet/site/article_data/sufian_3/aug-2015/GIS_media_release-Cell_rejuvenation-FINAL.pdf
Full free paper in Cell:
http://www.cell.com/cell-reports/fulltext/S2211-1247(15)00792-5
Gary-
the phenotypes you’re talking about are caused by genomic mutations, so aren’t instructive about mitochondria.
If you read the paper, you’ll see that there aren’t nearly enough data to support the age-related mitochondrial defect idea – there should have been hundreds in order to present an unbiased conclusion. See that there are almost no cases of mitochondrial mutations actually being manifest- they are mostly heterokaryons- just a few mitochondria affected- not enough to have a physiological effect.
The sky is still not falling.
Jeanne
@Jeanne,
Yes, no sky falling here.
Just another thing to keep in mind for validation and probably should be on our radar screens for all stem cell types in the pipeline for potential clinical use. Of course, Shoukhrat also is a fan of SCNT so it’s not surprising that he’d see things in a certain way in terms of the context.
Paul
Gary, the so-called Reverting to an ’embryonic” state by iPS reprogramming is a illusion. iPSCs are essentially adult (stem) cells that are locked (at least temporarily) into an “non-differentiation” and also highly reproductive state. But this may also means the iPSCs are man-made cancer cells.
Mitalipov group’s study (Cell Stem Cells 18:1-12, 2016) provides some evidence for supporting my earlier published views on iPS reprogramming and iPSCs. These views include that iPSCs should be distinguishable from ESCs because they are originated from adult cells which should thus contain more aging-related changes than the embryonic cells have. I also pointed out that iPSCs are incorrectly programmed stem cells because iPS reprogramming provides a very potent oncogenesis program. The observation that iPSCs demonstrate reduced oxygen consumption rates (OCR) correlates with my speculations that iPS reprogramming switches cells into neoplastic metabolism and thus makes otherwise normal cells into cancer cells.
Thanks for the heads-up Paul. Really fascinating and may answer a curious observation. Why do neurons generated from iPS cells made from Parkinson’s patient fibroblasts so quickly recapitulate the Parkinson phenotype in cell culture (synuclein aggregation, axonal transport defects)?
These iPS cells have been reversed to an “embryonic” state but nevertheless become Parkinsonian after a short time in cell culture. Are we seeing the carrier of “age” in the mitochondrion?