4 areas of debate on 1st human embryo genetic modification paper

Last week was a big one for the life sciences in that we saw the milestone of the first ever published paper reporting genetic modification of human embryos (see here and here).

It was one of those situations where we knew it was coming, but it was still a jolt.

Not surprisingly this event sparked intense discussion and even some arguments.human genetic modification

Below are 4 areas of contention at this moment and some additional thoughts on them. I value diverse views so please weight in with comments.

A big deal or a mountain out of a molehill?

My own view is that this paper is on the one hand a very big deal because it crossed the line and reported the production of GM human embryos. This certainly paves the way for more such research and papers.

On the other hand, the actual research methods and data reported were not especially surprising, groundbreaking, or enabling of other new research. So perhaps it was not such a big deal in that latter sense?

Did use of non-viable embryos largely negate ethical concerns?

The non-viability of the embryos is notable and that does make a difference, but I’m not sure how much that changed the line that was crossed in the long run. My sense is that reports of editing of near-normal human embryos (e.g. normal except containing a single mutation to be targeted) will just be a matter of time.

I support the idea of gene editing research in vitro on human embryos, but only in certain cases with specific oversight and bioethics training. I also feel that there should be some compelling rationale for doing the work in embryos versus just say a human cell line.

Disrespect to oversight in China?

Not really.

Yes, some of us pointed out that there are different ethical and regulatory paradigms at work in China compared to say the US or the European Union, but that’s just a fact. I don’t see why that should be some kind of taboo topic.

For instance, Mitalipov’s Mitogenomics, which is operating in the cutting edge and controversial area of 3-person IVF and mitochondrial transfer, is now set to do that work in China specifically because of the liberal oversight there related to this work. You can’t do that work in the US, but you can in China. That’s a fact and one that concerns me. Notably you can also do this 3-person IVF research in the UK too and that worries me as well. I have certainly voiced concerns about the 3-person IVF regulatory oversight situation in the UK as well.

It is worth noting that the day after the embryo editing paper came out, a Cell paper came out from a team at the Salk that was very pro-human embryo editing and I raised concerns about that level of enthusiasm for clinic use of human genetic modification technology as well.

You can expect that if a human embryo editing paper comes out of my own home country of the US or other places that I will provide a rigorous critique of it too.

Human embryo editing a non-starter clinically?

This is the most important and contentious area of discussion today.

There certainly are advocates for using germline genetic modification of human embryos to try to prevent any number of genetic diseases and the aforementioned Salk group is just one.

At the same time others think to put it mildly that this is a really bad idea. Edward Lanphier, et al. presented just one example of a case articulated against heritable human genetic modification and they are opposed even to in vitro research in this area. They view this kind of work as dangerous.

A nice NY Times piece by Gina Kolata includes comments from scientists raising additional concerns including stem cell and genetic modification pioneer, Dr. Rudy Jaenisch:

“A pressing question, said Rudolf Jaenisch, an M.I.T. biology professor, is why anyone would want to edit the genes of human embryos to prevent disease. Even in the most severe cases, involving diseases like Huntington’s in which a single copy of a mutated gene inherited from either parent is enough to cause the disease with 100 percent certainty, editing poses ethical problems. Because of the way genes are distributed in embryos, when one parent has the gene, only half of the parent’s embryos will inherit it. With gene editing, the cutting and pasting has to start immediately, in a fertilized egg, before it is possible to know if an embryo has the Huntington’s gene. That means half the embryos that were edited would have been normal — their DNA would have been forever altered for no reason. “It is unacceptable to mutate normal embryos,” Dr. Jaenisch said. “For me, that means there is no application.”

The bottom line at this point in a new week since the embryo editing paper came out is that there is a whole range of opinions on germline human genetic modification as well as about how it has been discussed. I view the fact that these discussions and even arguments are ongoing as a very positive thing even if disagreements can be uncomfortable.

Just a few months ago there was essentially complete silence on germline human genetic modification. Things have changed greatly for the better in terms of the level of dialogue and this will aid in charting a positive course to deal with this new area of biomedical research.

Review of Mitalipov group Nature paper: cloned ES cells versus iPS cells

Just how good are human embryonic stem (ES) cells made by therapeutic cloning via nuclear transfer?

How do they compare to induced pluripotent stem (iPS) cells or traditional ES cells made from IVF embryos?

A new paper in Nature directly tackles these key questions, but first a bit of context.

Three separate groups have now successfully made ES cells using somatic cell nuclear transfer (SCNT), with the successful technique first reported by the lab of Shoukhrat Mitalipov at OHSU last year.

I have reviewed those three therapeutic cloning papers (see here, here and here).

It’s worth noting that I felt that therapeutic human cloning was the top stem cell story of 2013. For an illustration of how therapeutic cloning differs from reproductive cloning see a handy illustration here.

It is pretty clear then that transferring a somatic cell nucleus into an oocyte in place of its own nucleus is a new, now established method of making human ES cells and this new kind of pluripotent stem cells (termed NT ES cells) is yet another potential tool for stem cell-based regenerative medicine.

However, let’s return to the big question: given the power, flexibility, and relative ease of making iPS cells, is there good reason to go to all that trouble to make NT ES cells?

Or to put it more bluntly, are NT ES cells any better than iPS cells in some important way to justify how much more of a pain they are to make?

Mitalipov’s lab has a new Nature paper (Ma, et al.) that argues strongly “yes” to that question. The paper is entitled “Abnormalities in human pluripotent cells due to reprogramming mechanisms”.

In this new paper published today, Mitalipov’s group teamed up with several others has done a comprehensive genomic, epigenetic, and transcriptomic analysis of NT ES cells. They compared them to iPS cells and IVF ES cells with each also compared to parental human dermal fibroblasts (HDFs).

The paper argues that in pretty much every way, NT ES cells are significantly more similar to IVF ES cells than iPS cells were. In other words, the authors argue that if IVF ES cells are the gold standard, NT ES cells are closer to that gold standard than iPS cells are.

NT ESC gene expression

This team also reports that iPS cells have more genomic abnormalities and DNA methylation differences.

They also assert that transcription factor-based reprogramming is inherently just not as good as SCNT at reprogramming. For example, in terms of global gene expression, NT ESCs clustered with IVF ES cells (see Figure 6A above; green and red columns of names across the top, respectively), while iPS cells (orange names) were further way and hence less similar. It’s notable that iPS cells uniquely had abnormal expression of Zinc finger protein coding genes (yellowish region of bars constituting “Cluster 10” in the bottom right of the heat map).

Overall, the paper is very convincing, but there are a few issues and limitations here that are notable.

First, the paper does not provide mechanistic insight into reprogramming. It is basically saying that the inherent physical nature of NT ES cells is better than that of iPS cells. I would have loved some specific insight into why NT is better than transcription-based reprogramming, but I understand that that is a tough nut to crack.

Second, the paper did not address important cellular functions like differentiation or tumorigenicity. In other words, do the reported differences between NT ES cells and iPS cells actually have any functional consequence? Are they meaningful? The paper does not address the function of the cells. I was left wondering, “How do these cells behave? Are there meaningful functional differences in differentiation or tumorigenicity?”

By analogy you might say you are comparing two boxers who are going to be in a fight soon. You examine and compare their heights, weights, ages, BMIs, and such physical traits, but until you see how they actually box, can you really predict who will do better? Function over form.

To extend this analogy a step further, one boxer (iPS cells) has already boxed in a number of matches over the years and has a proven track record of doing well, while the other (NT ES cells) has never boxed before. I’m sure we’ll learn more from this and other groups about NT ES cell function in the coming months/years.

Third (and related to above), the NT ESC paper does not address the endogenous retroviral elements that Yamanaka has linked to differentiation-defective phenotypes of reprogrammed cells. In their Koyanagi-Aoi, et al. paper (reviewed here), Yamanaka’s team made a strong case that specific retroviral elements should be examined as indicators of defective reprogrammed cells. Why not check out those elements in the NT ESCs?

I am also puzzled at the title of the paper. Why focus on the negative?

A more minor point is that I would have liked to have seen how iPS cells made with episomal vectors compared.

Overall, despite a few issues, I would say this is a very important, thorough, compelling paper.

I still am concerned from a broader perspective about unintentional enabling of human reproductive cloning as well and hope that more dialogue will emerge on that important element.

While from a big picture standpoint I’m still not entirely convinced that NT ES cells (given the egg donation, expense, and complications of making them) will give iPS cells a practical run for the money when it comes to regenerative medicine, at the same time this paper made the case for NT ESCs relatively much stronger.

Adult human therapeutic cloning of embryonic stem cells by SCNT

An international team of stem cell scientists has replicated human therapeutic cloning to make embryonic stem cells via somatic cell nuclear transfer (SCNT).

The team was led by Drs. Dong Ryul Lee of CHA Stem Cell Institute in Korea and Robert Lanza of Advanced Cell Technology (ACT) and reported the advance in the Chung, et al. paper today in the journal Cell Stem Cell entitled “Human Somatic Cell Nuclear Transfer Using Adult Cells”. The cells expressed pluripotency markers (see Figure 1A at left) and had normal karyotypes.

Human SCNT

The research has replicated the human therapeutic cloning work reported last year by Mitalipov’s group and has advanced the field’s knowledge further in some ways.

One major important element of the new paper is the successful use of adult and elderly somatic cell nuclear donors (ages 35 and 75). Therefore, this new work indicates that SCNT may become a viable option for production of ES cells from in principle almost any person. Further, the new paper suggests that a slightly longer period of incubation prior to activation following SCNT may yield better results.

Some questions and challenges remain, which is not surprising for such a new technology. For example, why is it still relatively speaking so difficult to make SCNT work to make NT-ESCs in humans compared to other animals? An additional hurdle is that efficiency remains a challenge. In the current paper, 2 lines were made from a total of 77 human oocytes.

Again, it is early days for human SCNT and we can be almost certain that further refinements to the technology will boost efficiency.

For perspective, production of iPS cells is also an inefficient process, but the key difference here is that to make human iPS cells one can easily start with an almost unlimited numbers (easily in the 10s of millions) of say skin cells. In contrast, the low efficiency of human SCNT is much more of a challenge because every attempt involves a unique, difficult to obtain human oocyte. In specific countries and states in the US, oocyte procurement faces complicated regulatory and legal hurdles. In this regard, it is worth noting that Mitalipov’s group has just recently reported in Nature successfully conducted mouse SCNT to make ES cell lines using 2-cell embryo cells generated from fertilized eggs rather than naive oocytes. If this works in the human context, egg procurement may become less of a challenging issue.

As with the Mitalipov group paper, this team also did not mention the broader context whereby human SCNT technology could be misused by rogue scientists to pursue human reproductive cloning. As with many powerful technological advances, dual use ethical issues can arise and that is certainly the case here with therapeutic human cloning.

Some interesting questions that remain open include why this SCNT process is relatively inefficient in humans versus other species and also why certain human donors produce eggs that have the “right stuff” for successful SCNT.

Overall, I think this paper is an exciting, important, and technically convincing. SCNT ES cells may give us another potential tool to help patients via stem cells. Mouse studies hint that SCNT ES cells may have some advantages over iPS cells, but the jury is still out on that.


Human cloning Cell paper under investigation: some perspectives

Is it really deja vu all over again with allegations of potential wrongdoing in a paper on human cloning?3 day cloning

“Say it isn’t so!”, is basically the universal reaction I’m getting from people in the stem cell field.

Well, sadly it seems to be so folks.

What’s going on?

Allegations have emerged on a website called PubPeer (a post-publication review kind of website) about the recent Cell paper by the Mitalipov lab on human therapeutic cloning.

A person called “Peer 1” has pointed out alleged instances of image duplication and cropping in the paper. The story was also picked up by Retraction Watch. Science is on the story too. Just to be clear, I am not “Peer 1” as some people have suggested.

A quick look at the paper would suggest there are indeed 3 separate instances of image duplication and images are cropped in various ways that make them look kinda different on first glance.

It makes one feel a bit queasy.

A fourth allegation of inaccurate representation of microarray data related to two panels in Figure S6 in the paper remains more difficult to confirm or deny to this scientist.

The other thing I’m hearing from readers of this blog and others is that they are astonished over the microscopic 3-day period (see image above from the paper) between when the journal Cell received the Mitalipov paper and when it was accepted. A leading stem cell scientist said to me, “Are you f’ing kidding me? 3 days for a human cloning paper?”

Given the 2004/2005 cloning papers by Hwang Woo-suk that proved to be bogus and the highly sensitive nature of human therapeutic cloning, an intense review of the paper before publication would indeed seem like it should have been a no-brainer, eh?

Another leader in the stem cell field told me that Cell should have had 5 independent reviewers look the paper over and have a highly detailed, methodical examination of the paper figure-by-figure, line-by-line, by at least two editors.

Now I’m hearing that we’ll see an announcement by OHSU and Cell as early as tomorrow about this, in all likelihood saying it was all a big innocent mistake.

Maybe it was. I’m betting that to some people though, there will always be doubts after this though.