The Niche top posts of 2016

stem cell fireworksWhat were the top posts here on The Niche for the past year? I’ve listed some of them below along with some posts from 2015 that remain highly read.

Some top 2016 posts

2015 and older posts that remain highly read every day

Public stem cell skirmish erupts between Hanna & Jaenisch

Professor Rudolf Jaenisch of MIT and his former postdoc/now assistant professor at The Weizmann Jacob Hanna have gotten into a very public, stem cell skirmish over conflicting papers. Hanna raised concerns over a Jaenisch lab paper and things have escalated from there.

Jaenisch & Hanna

This mess is playing out before our eyes on PubMed (there was a comment from Hanna on the Jaenisch lab paper, but now removed), PubPeer (scroll down near the bottom of the comments on that page for several items), on the website of the journal Cell Stem Cell where Hanna also left a comment, and on Twitter, where Hanna posted an edgy series of tweets (see latest below).

Note that the now deleted PubMed comment was nearly the same as the one from Hanna still on PubPeer. Hanna also posted a comment on a Jaenisch PNAS paper from this year and that comment has now been removed as well from PubMed.

It’s not every day that you see biologists duking it out in the wide open like this. Well, maybe a stem cell skirmish happens every month or two, but not every day. This one has quickly gotten pretty ugly.

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New Nature papers debunk STAP cells

Today marks nearing the completion of a full circle for one of science’s biggest controversies: the STAP cell fiasco. Today STAP cells are completely refuted with the publication of two new papers in Nature and we know much more–with some notable gaps still–about what went wrong.

In January of last year, an international team of collaborators from RIKEN in Japan and Harvard/Brigham & Women’s Hospital (including the lab of Charles Vacanti where the STAP idea reportedly originated) here in the US published two Nature papers making the extraordinary claim that ordinary cells could be reprogrammed into embryonic stem cell (ESC)-like cells.

And it could be done simply, cheaply, and quickly using various forms of cellular stress including low pH. I was highly skeptical when I read the papers, but tried to keep an open mind. This sounded cool, even if also too good to be true.

I published a review of the papers here on this blog on the day they were published and I included six key open questions that would be required to assess the real impact of these papers. Over the next few weeks I posted an increasingly skeptical series of posts questioning STAP.

Others in the larger community including anonymous scientific sleuth JuuichiJigen and some on PubPeer were skeptical as well. In fact, they started noticing issues with the data and text of the papers.

RIKEN and Nature began investigations. Ultimately the papers were retracted in relatively quick fashion. While a lot of harm was done even so and tragedy would strike later, the rapid refutation of STAP attenuated the overall damage.

For more background on the key STAP events check out this comprehensive STAP history timeline. Ken Lee’s lab took the lead in scientific refutation of STAP and published their work in F1000 here after Nature rejected it under unclear circumstances.

I also started a novel, but admittedly somewhat basic attempt at crowdsourcing global efforts at STAP replication. Very quickly we came to a consensus that autofluorescence was likely a key stumbling point for the STAP papers as the authors probably misinterpreted it as real signal from a GFP pluripotency reporter.

Suspicions grew elsewhere that STAP cells might really be ESCs or some other pluripotent stem cells, possibly mixed with trophoblastic stem cells (TSC). Ultimately, STAP first author Haruko Obokata was found by RIKEN to have committed misconduct and she is no longer working at the institution. RIKEN underwent a big shakeup as a result of STAP as well. STAP co-author and highly respected biologist Yoshiki Sasai committed suicide, which was one of the most tragic and sobering events I’ve seen in science during my career. In Japan there had been a media frenzy on the STAP problems. In the US things on the STAP front were and continue to be quieter. As recently as about a year ago, Vacanti and co-author Koji Kojima publicly expressed complete confidence in STAP and put up a refined protocol on the web.

So what was the real deal with STAP?

Today Nature published two articles thoroughly refuting STAP cells and providing some further insights.

In one of the papers, STAP cells are derived from ES cells, the authors used whole genome sequencing (WGS) to examine archived STAP cell-related samples and other cells present in the laboratories where the STAP work was conducted. Using essentially a form of genomic fingerprinting, the team reports conclusive evidence that STAP cells were in actuality ESCs:

In summary, our investigations based on WGS of STAP-cell related materials reveal that all of these materials are derived from previously established ES cell lines and refute the evidence shown in the two Nature papers that cellular stress can reprogram differentiated cells into pluripotent cells.

You can see Figure 1b from this study showing the WGS comparison that the genomic characteristics of various cell lines.

STAP refutationThe matching patterns between two STAP-derived lines FLS3 and CTS1 and the supposedly unrelated FES1 ESC line are particularly striking. It now seems almost certain that a number of STAP cells are in reality FES1-related ESC lines and that the STAP cells were not created by cellular stress.

The other new paper from another team, Failure to replicate the STAP cell phenomenon, comes to similar conclusions and further clarity arises:

“In summary, our replication attempts and genetic analysis indicate that existing STAP protocols are neither robust nor reproducible. To substantiate future claims of reprogramming and alternative states of potency, we urge a rigorous application of several independent means for validating functional pluripotency and genomic profiling to confirm cell line provenance. Ultimately, the essential standard of robustness and reproducibility must be met for new claims to exert a positive and lasting influence on the research community.”

This second team led by George Daley at Brigham and Women’s spans the globe, but importantly they did some of the work actually in Vacanti’s lab, still finding no evidence that STAP is real. They wrote, “Working within the Vacanti laboratory where the concept of STAP cells originated, and assisted by a co-author of the STAP papers…”

Seven laboratories were involved in this second STAP replication effort: Daley, Deng, Hanna, Hochedlinger, Jaenisch, Pei and Wernig. This is an all-star team of stem cell research labs.

One bottom line from the paper is that this team collectively worked very hard to try to get STAP to work, but it didn’t:

“In summary, 133 replicate attempts failed to document generation of ES-cell-like cells, corroborating and extending a recent report.”

Like the other team, these scientists analyzed the STAP cells including their genomes. They found inconsistencies between their new findings and the claims in the original STAP papers:

“In the original STAP reports, the authors stated that they mixed CD451 cells from male and female mice owing to the small number of CD451 cells retrieved from individual neonatal spleens. However, our analysis indicates that CD451 cells were female, whereas the derived cells (STAP cells, STAP stem cells and FI-SCs) were all male, a clear inconsistency.”

These authors also found indications of trophoblastic stem cells (TSC) being mixed into the STAP samples. TSC may explain the reported totipotency of some derivations of supposed STAP cells.

Nature itself explained why it published these new papers (in the Brief Communications Arising or BCA format):

“Why is Nature publishing these pieces? The main reason is to update the scientific record. The wording of the STAP retraction notices left open the possibility that the phenomenon was genuine. It said: “Multiple errors impair the credibility of the study as a whole and we are unable to say without doubt whether the STAP-SC phenomenon is real.” The two BCAs clearly establish that it is not.”

We are just about, but not quite at the end of the STAP story it seems. In my opinion there is still more to be learned about what went so wrong. How did the ESCs and in some cases TSCs end up in the cell culture mix? Accidental contamination? Intentional attempt to bolster the seductive hypothesis?

We may never know, but today there is a great deal more clarity overall at least.

The publication of these two new papers is a very positive step, but it is important to stress that absent post-publication review, rapid and open team science, and social media efforts, the STAP cell myth may have continued to have been believed by many in the research world until this day when these debunking papers were published. That delay would likely have caused immeasurable damage. Thus, there were important roles both for traditional scientific correction via journals and new, transformative types of rapid post-publication review.

Michael Cea’s conversation with Jeanne Loring: frank views on all things stem cell

By Michael Cea

Jeanne Loring of the Scripps Research Institute in La Jolla, California kindly sat down with me at the ISSCR annual meeting for a broad discussion of her history, views on the field and developments in the science.

I found Jeanne a refreshing character, as I did a number of others I was fortunate to meet in Sweden. Her style I can only best describe as natural. It must be the Southern California air or something but there is a definite quality of relaxed confidence about her. I liked her a lot and hope to have the opportunity to meet her again sometime – perhaps at the birth of her “to be” Northern White Rhino! If she invites me 🙂 that would be something.

The format of the interview was free flowing and what was clear to me from her long standing scientific focus and deep knowledge of the sector was it takes determination and a varied set of skills to maintain one’s position in today’s fast paced world of cutting edge science and more so even to successfully translate that to the clinic.Jeanne Loring

Kudos to Jeanne for her efforts to continue the fight to bring forward a therapy for Parkinson’s after near on 30 years and for her passion to help our planet’s most endangered.

Hope you find the interview interesting, as much as I enjoyed it.

Cheers

Interview:

M: Tell me a little about your background

JL:  I was trained in embryology and neurobiology, I studied neural crest cells, which are actually stem cells and I was fascinated by them. Then when I finished graduate school I got a job as an assistant professor at the University of California Davis and I then realized I could either teach or do research but not both. There were not enough hours in my day, so I took the opportunity to join a biotech company in California called Hana Biologics. There were lots of companies around in 1987. I joined specifically because they were planning a stem cell therapy for Parkinson’s disease. I was getting a little bit tired of generating just knowledge. I wanted to generate practical knowledge, which made me a little bit different from most biologists at the time.

Lewy_Body_alphaSynuclein

Lewy Body characteristic of Parkinson’s

M: Was that motivated by personal experience?

JL: No, I didn’t know anybody who was sick at all; it was just I wanted to have more impact than just writing papers. I wanted to do something more important. When you go into biotech there’s a high probability that you’ll not be at the same job for more than 5 years. I didn’t know that at the time but I’ve learned it now- it’s good for learning how to survive. The first company I went to work for (in the late 1980’s) was developing a cell therapy for Parkinson’s disease, but there were no pluripotent stem cells yet so we were using fetal cells -trying to expand them. That was the heyday of the fetal transplants for Parkinson’s disease and it was clear they were working for some people, so why couldn’t we take fetal cells and expand them and treat more patients?

M: I attended the pre-meeting symposium @ Karolinska on the aging brain. The eye and brain are related of course but the brain is less accessible.

Lewy Body characteristic of Parkinson’s. Image from Wikipedia.

JL:  The eye is accessible; therefore it is a good testing ground for therapies. Once you put things in the brain you pretty much don’t know what’s happened until the person dies.

M:  Why did the fetal work not continue?

JL: There were two main efforts – Andreas Bjorklund of Karolinska/Lund and two groups in the US who were funded by the NIH to do clinical trials. I think the people in Sweden will always argue that they had a better success rate. The researchers In the US were required to, or decided to, do a double blind clinical trial to assess placebo effects.

M: And surgery?

JL: Yes, they did sham surgeries for the double blind trial.

M: Isn’t that unethical?

JL:  I would never do it but it was the expectation of the NIH-funded trial. The patients did have the promise of treatment if they were part of the control group.

M: You mean opening them up again?

JL:  Yes, but the people who routinely do brain surgery don’t take this issue as seriously as I do, and they know what they’re doing.

To continue, the problem was that maybe 25%-30% of the patients, depending on the study, had an adverse effect that was quite dramatic, called dyskinesia. When they got the cells they had Parkinson’s disease, which was treatable with L-Dopa, but then after they had the cells they started having uncontrollable events, like the opposite of that sort of frozen kind of characteristic of people with Parkinson’s disease. They had to be treated separately and it had obviously been caused by the transplant. The question was…

M: Why?

JL: Exactly. The fetal cell therapies stopped in about 2003. I remember I was at the Society of Neuroscience meeting when the results were discussed and everyone in the room was saying… we can’t do this anymore.

M: But 75% of the patients were…

JL: Were either not helped or they were helped for the rest of their lives and went off drugs. So it was clearly a spectacular therapy.

M: This was so early, late 80s early 90s, wouldn’t you think that with more push in the science?

JL: Everything sort of dropped off the map at that stage and people just didn’t pursue it anymore.

M: Was it ethically charged?

JL: The question was: do you want to do something to people that has a clear probability of an adverse effect? Parkinson’s disease is not a life threatening disease.

M: It is a debilitating disease.

JL: Yes, it is a debilitating disease.

M: I have a relative that has Parkinson’s, in my wife’s family, and it’s not just the disease it’s what it does to you aside from that. Your whole spinal column changes and that makes everything more painful and difficult.

JL: Everything is more challenging and you can never predict whether you’re going to have a good time or bad time today or this morning or afternoon. I have a friend in Texas who has Parkinson’s disease – I talk to him on the phone every once in a while and it has to be at a particular time of day. Otherwise I can’t understand him at all.

M: Devastating disease, all the neuronal diseases are devastating.

JL: That was the whole basis for my Parkinson’s disease focus, after there was a resurgence in interest when human pluripotent stem cells were made. We can turn these cells into real dopamine neurons and do just what we want with quality control.

M: This was the question I had at the brain symposium, why wouldn’t you test the neural stem cells themselves as a method of action and let them stimulate the environment.

JL: People have tried that. There was a whole interval where people were trying to treat Parkinson’s with cells that were not dopamine neurons. Actually it damaged the field because it didn’t work and turned organizations like the Michael J. Fox foundation, an organization that had supported it, against cell therapy entirely. They’re not funding cell therapy now.

M: Were those stem cell originated?

JL: No, this was all before pluripotent stem cells were available. They were either adult cells or fetal derived stem cells, and they didn’t become dopaminergic neurons.

M: Isn’t there a big difference in terms of your understanding of the pluripotent sources in terms of that?

JL: Of course. There’s a huge difference. The cells you get from an adult or fetus have not been successfully turned into the same neuronal cell type that dies in Parkinson’s. They don’t seem to be able to.

M: So what about the pluripotent neural stem cells?

JL: Neural stem cells from brain aren’t pluripotent- they can’t develop into all cell types. We use pluripotent stem cells to make neural stem cells, which we then turn into dopamine neurons.

M: Ok

JL: So my next job, because fetal dopamine neuron precursor cells couldn’t be expanded, was to work at a company called GenPharm. This was in the early 90s and we were doing gene knockouts and deriving mouse embryonic stem cells so I got to be at the beginning of one field and the beginning of another field. That company lasted about five years. https://www.gsb.stanford.edu/faculty-research/case-studies/genpharm-international.

M: What technology did you use?

JL: Using homologous recombination, which was a brand new idea at the. Mario Capecchi, who was a scientific advisor to the company, won a Nobel Prize for it in 2007. I like being in the situation where the technology I’m using wins Nobel prizes for people. I kind of think that validates it. We could just about do anything. We could knock-out genes and we could change genes. This was all pre Crispr-Cas, which is the way people are doing it now. So that was early days for that as well.

I made a lot of mouse embryonic stem cell lines. This was the same time as Austin Smith and Rudolf Jaenisch were using, making and knocking-out genes in mouse embryonic stem cells. That’s where our histories all overlapped; we were all doing this in the early 90s, although I was at a company, and they were academics. It was a spectacular five years and we did a lot of amazing work. The work I did then is still some of the most highly cited work that I have ever done. It was really pioneering and it was fun. Then after that company failed (most of them do), I moved on to a company called Incyte Genomics. This was at the peak of the human genome sequencing era, which started around the mid-90s. I worked at Incyte for around 5 years learning how sequencing worked.

M: Uncovering the map

JL: Yes, and the technology was evolving very fast at that time. So I now had three things I knew well – the Parkinson’s neural cell transplant idea, embryonic stem cells and now genomics/DNA.

M: This all was at the same time as the other groups but your work went unheralded?

JL:  It was not a big deal- if you’re going to be heralded you have to stick in one field for a long time. My approach has been to learn something then learn something else and try to put the two things together.

M: and it’s all coming together now?

JL: It is, everything I’ve done is coming together now.

M: Tell me about that, because that’s why you’re back.

JL:  That’s why I’m back. Regarding Parkinson’s disease – we now have human pluripotent stem cells that can be turned into dopamine neurons, so all the things that were wrong with the early work I was doing in the late 80s I can now fix.

M: You’re independent in an academic setting now.

JL: Yes, I’m an academic with my own lab. I have the Parkinson’s history and I have the mouse embryonic stem cell history, which Austin and Rudolf share. You know it’s interesting people who come from a mouse embryonic background and then started working on human ES or iPS cells have been really annoyed that the human cells don’t act like the mouse cells. They’re much harder to grow. So both Rudolf and Austin have been trying to turn human pluripotent stem cells into cells like the mouse.

M: Is this kind of an internal debate?

JL: Yes, this is what they’re focused on now & intensely competing with each other over whether you can make human cells with the qualities of mouse cells. I’m not involved- I just went straight to human pluripotent stem cells and realized they were not going to be like mouse and lived with it.

M: Is that because of the quality and body of evidence in the mouse?

JL: Yes, the history is with mouse ES cells and the kind of things you can do with them. They’re much more robust than human pluripotent stem cells. Human embryonic stem cells have to be babied, but mouse ES cells you can pretty much leave in an incubator and they’re fine. The researchers have moved in the direction of trying to make hESCs be like that.

M: To perform better?

JL: Yes, so that then can take all those techniques they used in the mouse and now apply them to human. As I said, I’ve just bypassed that. My cells can become what I want them to become and that’s it – I’m done. They don’t need to be like mouse cells.

To continue, while I was still at Incyte I started a company and made a bunch of hESC derivations that were on George Bush’s original list.

M: From IVF donations?

JL: Yes, that’s right. I started a company, so I did it in my own company. There were 3 employees. I was the scientist and I had an assistant.

M: You had a number of lines. What ever happened to those lines?

JL: Well, they got acquired by another company and I have no idea, they’re probably still in the freezer somewhere. They never did anything with them. But it’s not important any more as there are so many lines out here. There are 300 lines or so on the NIH registry of lines that can be used in federal grants.

M: And they’re sufficient to do the science work?

JL: Yes. But my lab doesn’t work much on hESCs anymore. We work with iPSCs because they are equivalent to hESCs and you can get them from individual people. This is where my genome experience comes in because I learned sequencing and genomics when I was at Incyte, so I had an appreciation of the methods used to study the genomes of cells.

M: The translational aspect of what you’re working on is focused on Parkinson’s as a primary program?

JL: Yes. There are a lot of reasons for it. The person who came to me with the idea to do a therapy for Parkinson’s disease is the head of the movement disorders clinic at Scripps Health, which is across the street from me. She thought there ought to be a stem cell therapy for Parkinson’s disease and together we did fundraising to start the project. We want to do a personalized therapy, an iPSC therapy, and genomics is very important as we want to have quality control throughout the process of developing a therapy.

M: This is your approach to it?

JL: Yes. One of the things we’ve learned from studying pluripotent stem cells is that they acquire mutations if they spend a lot of time in culture. You don’t want to put cells with dangerous mutations into people, so that’s where genomics expertise comes in, essentially in assuring the quality control of the cells we want to transplant.

M: Is that the same risk factor in regard to hESCs?

JL: Yes, they will do the same thing. In fact everything we’ve done to date shows that iPS and ES cells are identical. Our approach has been to analyze lots of cell lines, not just one, to learn what to expect from cell lines in general. Almost everything we’ve done was done on 100s of cell lines so we can come up with general principles.

M: I remember you putting out a paper on this recently that was very exhaustive – 2 years of work

JL: Yes, 2 years of cell culturing. The scientist I worked with on that is here at the meeting – I’m going to take him to lunch tomorrow. The whole idea was to try to come up with things that were generalizable to cell lines and different conditions.

M: So if you use 1 cell line that is on the edge of a uniform grouping that will be different than if you select and productize something else within that sequence?

JL: Yes

M: and that’s where we’re at?

JL: Yes, right now. Here’s the challenge. If you have different cell lines we know they’ll have some diversity. They act a little bit differently, a lot due to the personal genomes, of course. The challenge we have is to develop technologies and quality control methods to allow us to know how every one of those cell lines becomes the same thing every single time.

M: Is that a far reaching goal?

JL: I think it’s actually going to work pretty well. A lot of this has been developed already. That’s been a high priority all along. Some people think it’s never going to work but I don’t believe that.

M: Is RNA a part of that process?

JL: Yes, absolutely.

M: So the work presented recently by Yamanaka will factor into this.

JL: Yes. The way we make the cells is important – we’ve investigated that. How you reprogram the cells so that the cells aren’t harmed.

M: Is that Sendai?

JL: Yes, that’s right. We’ve done whole genome sequencing on a lot of cell lines and we’ve discovered that using Sendai vectors for reprogramming is benign. The other methods are also benign, which is important to keep in mind.

M: So looking at this from a cost perspective, autologous patient specific treatments are highly personalized but are highly expensive. Is that part of the process strategically?

JL: Yes, that’s right. It’s part of the process. There’s a lot of discussion on personalized therapy and whether it’s worth the cost.

M: Of course, if it costs $1 million dollars how many people can actually be treated?

JL: Well, more than you think. It turns out for cancer treatments the amount of money that people are paying is similar.

M: Is this about annuities, is that where we’re going?

JL: No. Somebody needs to figure out how to have insurance reimburse for therapies. Right now we’re not worried about that yet. But I can see how it’s going to work because the work that’s being done now with T-Cells, CAR-T therapeutics.

M: I wrote about that 3 years ago.

JL: There you go. That’s about how much it costs for what I’m doing and yet there are multiple companies developing this technology now that it’s been shown to work.

M: There are many now but there were none before.

JL: Well I remember the first time I heard about it I thought I had no idea you could do that. I didn’t know the immune system could do that.

M: The immune system is a powerful force to employ.

JL: Yes it is, and that’s one of the reasons we’re using autologous therapy. We want the cells to be matched and don’t want them to be rejected.

M: Isn’t there a movement towards allogeneic?

JL: It’s hard to say. Yes, probably because of the effort in characterizing cells, but let me put it this way. As soon as we demonstrate we can make the same cells from 8 different patients and they all work, then the story’s over. Autologous therapy and the price point will be worth it. It will be like CAR-T therapy. It will be what you have to do for the best possible therapy.

M: Wouldn’t you want to test an allogeneic source?

JL: I don’t want to as others are doing it. I’m going to let them go ahead and do it.

M: and who are those others?

JL: The Studer Lab in the US. Actually there’s one other autologous therapy which is being done in Japan by Jun Takahashi.

M: Coming out next year.

JL: Yes, his and my projects are very similar. We’re trying to collaborate but I don’t think it’s going to work, as it’s almost impossible to exchange materials between the US and Japan.

M: Really I thought we were friends in many ways.

JL: We are but when it comes to scientific IP, it’s very hard.

M: They do want to license a lot of their underlying technology, Japan Academia, Healios.

JL: and I would be licensing it if I were a company but I don’t have to as an academic and that’s another strategy of mine.

M: Don’t they have underlying patents?

JL: Oh yes, and if I decide to commercialize what I develop I’m going to have to license patents from Japan. But I’m going to worry about that later. I know a bit about patents too.

M: I remember that.

JL:  I think we have a good strategy. The thing is you can never be certain, but the science makes sense, the strategy makes sense.

M: To be clear on this patent issue – you don’t need a license to do clinical trials.

JL: No. I don’t need a license to develop anything, as long as I’m an academic and I’m not commercializing it,

M: The concept is Japan Academia is licensing for research purposes because they deliver a package.

JL: Yes – and I don’t need it yet because I’m a non-profit. They will license their technology for research purposes to companies but they won’t let anybody sell the iPS cells.

M: The process of development can happen independently using Sendai without a license.

JL: Yes that’s correct. I was in biotech and I was affected rather negatively by patents at times. I remember this very clearly: my friends and I wanted to challenge the WARF patents that gave them ownership of all human embryonic stem cells, and we worked on this for many years. The patents expired just before we asked the Supreme Court to hear the case for overturning the patents, and they declined to hear it. When I became an academic, as I liked to say to the WARF attorneys as many times as I could, I had the freedom to operate and not require a patent from them to do embryonic stem cell research. Our patent challenge was very interesting and very educational; as a result of our challenge, WARF narrowed the claims of their patents to limit them specifically to embryonic stem cells. Their original patents claimed all pluripotent stem cells, so if we hadn’t challenged the patents, they could have retroactively claimed iPSCs.

M: There are a few words in there which are specific to embryo derived.

JL:  What happened was, we challenged the patents, the patent office rejected all of them, and in order to get the patent office to reinstate them they had to change the language for their primary patent.

M: It was their intent in the first place.

JL: I think we caught them by surprise. I met some really great people as a result of the patent challenge. The attorney who was with me was the same attorney who brought the challenge to the Myriad patents. He was at the Supreme Court for that case and I went to the Court to watch them argue that case.

M: Interesting isn’t it?

JL: It was fascinating

M: The legal system is a world apart

JL: It’s so bizarre

M: Somewhat like the science world?

JL: No, well in theory yes. What really struck me was the fact that the Supreme Court justices, and I think lay people, need metaphors in order to understand science.

M: They do and communication from science to the world is vital as the boxed view of old school scientists just doing experiments to publish needs to change.

JL: I don’t know why people would do that, to tell you the truth.

M: I think there is a value. My curiosity brought me here. So I think there’s a great value in curiosity and the maintenance of that throughout your life

JL: I agree.

M: I like that analogy the Salk Professor, Rusty Gage, presented. He spoke of a running an experiment where brain cells develop due to vitality, even in disease states. I’m not sure how a Parkinson’s patient can actually get on a treadmill but….

JL: Exercise does help Parkinson’s patients, physically and mentally. Our funding mechanism is patient advocacy based, a partnership with patients.

M: I’m not aware of your funding mechanism.

JL: The funding comes from a private foundation that we started to fund this project

M: I remember this – just recently you did a drive. How did that go?

JL: It’s gotten enough money to get us to the pre-IND stage.

M: Did CIRM ever come in?

JL: CIRM will come through the next round, I believe. We’re certainly going to apply for CIRM money. We’ve been working up to this for a long time. The patients have been going to CIRM meetings so we can educate the panel about the importance of this.

M: How far are you away from the IND

JL: About 2 to 3 years

M: That’s pretty similar to some of the others – Malin Parmer for instance mentioned 2018. Of course the Japanese are coming on fast next year.

JL: They’re on a fast track – there are some positives and negatives about that.

M: Tell me about that. There is I guess a Japanese societal push, an industrial push. They have a tendency to like to do that in industry and it’s been beneficial in the past. Do you see that as a mechanism to dominate?

JL: Yes, absolutely.

M: and will it open up things potentially or will there be a downfall?

JL: The good thing as far as I’m concerned, is if Jun Takahashi gets his therapy through the regulatory agency, he gets to transplant his cells to people and they’ll be doing that before I do. It’s unlikely that our FDA will let me do it sooner. So if nothing bad happens to the patients in Jun’s study, that will help me. However, if somebody else pushes through a therapy because of this fast track, a scientist who are not as careful as Jun Takahashi, there could be issues. Stem cell therapy, just like everything else, if it is strongly promoted, can have setbacks. In Japan we saw what happened with the STAP problem. As soon as there’s a lot of pressure from the Japanese society and Government to move forward there are going to be people that make mistakes. There will be people who are not careful.

M: Masayo Takahashi is trialing iPS cells.

JL: Yes and she has published preclinical work. Essentially she is trying to show equivalency of iPS to ES cells. I think that’s very important, as the FDA is still worried about iPS cells.

M: They are it seems. There was some planning to file an IND for Platelets.

JL: Yes.

M: Do you know that story?

JL: I do, yes.

M: Will you tell it?

JL: I probably can. I can publicly say I was a consultant for them [Ocata/ACT] and that I attended their pre-clinical meeting as a consultant. So I know about the reaction of the FDA about that.

M: This was back 3 years ago?

JL: Yes, I think 2 to 3 years

M: 2013

JL: It turned out that I wasn’t really necessary as an advisor. I didn’t say a word but it was fascinating to see the FDA’s response.

M: The concerns they had were GMP compliance related.

JL: Yes, but they’re getting over that. They’ve approved ES cells that were not made with the intent of using them for therapy. One of the cell lines that they approved was derived in 1998 using bovine serum, which was a concern before the safety trials showed that it wasn’t important.

M: Yes even the Ocata/ACT cell line comes from some time ago on MEF.

JL: Yes, and I’m not concerned about that. There are some issues with using xeno reagents but they are really related to whether you’re making the cells make the wrong kinds of sugars. If you were to put mouse embryonic cells or mouse iPS cells on mouse embryo fibroblasts (MEF), viruses could be transferred into the cells, but this doesn’t happen with human pluripotent stem cells. Nobody has ever shown any kind of viral infection in human cells that comes from the MEFs.

M: That’s why the safety is intact.

JL: Yes, exactly. The process is to imagine bad things that might happen, then prove that they don’t happen.

M: It’s only a transitory process as well.

JL: Yes, you’re not putting mouse cells into people. But you’re also not infecting the cells so there’s no lasting change.

M: There are a lot of other technologies that are far more dangerous – virus delivery for instance.

JL: Yes, of course, and viruses used for early gene therapy have actually been shown to be dangerous in some cases.

M: There have been a lot of adverse events and people have actually died in the CAR-T trials and no one talks about it.

JL: That’s right.

M: My feeling is the xeno movement is a good thing for standardization and some of the work shown here, the BioLamina work and the Thermo Fisher work, these are very good protocols that need to be adopted and the expansion occur.

JL: That’s fine. As long as they are necessary and they work well, I don’t really care what methods are needed. I’m not too worried about the xeno issue because the cells won’t be interspecies transplants.

M: Are they requiring it now, is that the new standard?

JL: Not yet, no. We just had a meeting with our regulatory consultant a couple of weeks ago, but of course you never know.

M: So when the Israelis and BioTime and others in the field are touting the xeno-free, it’s just marketing?

JL: Perhaps, but don’t let’s push that too far; I mean the FDA is never perfectly predictable and they could decide at any time that they think it’s dangerous to have xeno reagents.

M: But the products will be approved without a line switch.

JL: Right, that’s right.

M: What are the programs in the pluripotent space you think will reach the market within the next 5 years?

JL: Obviously there’s a lot of interest in the reagent business and there are a lot of companies that are joining in, especially in Japan. I really didn’t realize how much was involved in Japan in creating reagents for taking the cells to the clinic.

M: ReproCell?

JL: Yeah, ReproCell and others.

M: Takara?

JL: Yes. I’m giving a talk at an innovation showcase tomorrow for another Japanese company. One of my friends asked me to do it for him because he can’t make it here. They’re a very large chemistry company. They’ve been in business a long time and now they want to start to apply what they’ve done to stem cells.

M: Interesting how some of the non-scientific power houses in Japan are involving themselves now. A change in strategy perhaps. Digital is affecting their main lines of business and there’s an opportunity.

JL: Absolutely. They have a lot of bandwidth. Fuji Film just bought Cellular Dynamics. I mean you’re not making film anymore so you might as well make stem cell reagents.

M: I don’t want to press on the point of who’s going to come to market soon but success needs to be translated and your view on early access as being a component of adoption, proof of clinical concept, is that in your view an essential part of regulatory review & language?

JL:  Japan has fast tracked cell therapies, but I think our FDA is not going to fully adopt such regulations. Perhaps this is because the Japanese regulatory authorities have decided to trust their scientists more than the FDA trusts us.

M: In my view Japan also has a symbiotic relationship with the other parts of the system, you know, it works all together – the insurance, the legal, the funding, the university/academic and business community.

JL: I know, it’s really amazing. I’m really envious.

M: Anything else on the program front? I wanted to talk about the Zoo work.

JL: I know that’s what you actually wanted to talk to me about.

M: Yes, it was fascinating that you’re doing that work.

JL: Yes, we decided that we should try to reprogram endangered species cells, so in 2011 we published a paper to say we can – Rhinos, using human technology. We hope to use those cells to help restore the species.

M: The egg/sperm combination?

JL: All that stuff is coming. At that time we just made iPS cells from the animals and the project lay dormant for a while because the zoo we were working with thought it was a bit little creepy, too Jurassic Park. They’ve now decided to embrace it.

M: Weren’t there a number of international groups working on that before?

JL: Yes but not a lot, not in this particular thing. There was a group in Australia that was reprogramming other animals.

M: Interestingly in Spain also.

JL: Yes, that was different though, replacing one animal with another in a habitat.

M: Using an animal to host?

JL: Well they’ve done that too. The essence of our approach with endangered animals is to use the technologies that have been developed for mouse and for humans to make gametes out of the iPS cells. Then use IVF technology, that is also in development for these animals, and have a surrogate host that we’ll be able to put the embryos into and regenerate the species. Just a small thing! I’m doing this with the Northern White Rhino, as there are only 5 of them left. There’s only one male and the females I think, with one exception, are beyond reproductive age and they’re dying. [Note: another Northern White Rhino died in late July, so now there are 4].

M: So how would you approach that?

JL: The Southern White Rhino has a very similar reproductive cycle. The Northern White Rhino are a different species but they’re very similar. No one really knows if you can cross them yet. We want to make the gametes from the Northern White Rhino, inseminate the eggs in a culture dish and transfer the embryos to a Southern White Rhino.

M: The egg would come from the endangered species also?

JL: Yes, from the pluripotent stem cells.

M: Both gametes.

JL: Yes both gametes would be produced from iPS technology.

M: Have you proven that yet?

JL: No, we had no money, so we essentially have been generating more iPS cells and we’re getting better at it. But now there’s going to be an investment, that’s what they tell me. The zoo has decided.

M: Which zoo is that?

JL: The San Diego Zoo.

M: Wonderful.

JL: They’ll be announcing that when they want to, it’s not up to me.

M: Very good, I wish you luck with that.

JL: Thanks, it’s one of those things which seemed obvious at the time.

M: Well worth doing.

JL: Yes, it is worth doing and it was just a matter of timing. I think a lot of this is like that. If you’re too ahead of people’s understanding of what you’re doing then it will just sit there dormant until they understand it.

M: I think in most fields if you’re pioneering something you have a responsibility to educate.

JL: Yes but people also have to accept it. I’ve seen a lot of changes in the stem cell world since we started this in 1998 so it’s been a while.

M: The %s are way higher now.

JL: Yes, they’re higher, that’s right, and it does have to do with education and our patient advocacy approach means we educate patients and the patients educate other people because they’re motivated. They may have not wanted to be scientists but they’re driven to understand it because they want to get cured, they want to get treated.

M: Thank you Jeanne

JL: Ok

###

Ref: Parkinson’s review by EuroStemCells

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.