Harvard STAP cell authors release new protocol, affirm belief in phenomenon

Even as everyone was going through the Science and Nature reviews of the rejected STAP papers this week, something else on the STAP front that happened last week.

What’s up?

Well, the STAP Nature papers are retracted, RIKEN CDB is going to be reorganized, RIKEN CDB has tried at least 22 times to make STAP cells and every time it didn’t work, and senior STAP author Charles Vacanti in theory is now on sabbatical as of September 1st. Even so Vacanti and fellow STAP researcher Koji Kojima, released yet another new STAP protocol on September 3.

The new protocol is intended to have a better chance to work for others.

Their first bullet point is admission of an earlier misstep in saying it was “easy” to make STAP cells. Apparently they concede it’s actually kind of hard to make STAP cells.

One could ask where is the line between hard and impossible?

Their second point is to suggest that people try making STAP cells not just with low pH, but also adding in ATP.

Then they dive into detailing an actual protocol in a step-by-step fashion. They call it the most effective STAP protocol “du jour”.

They close with a paragraph that I think contains a key typo (emphasis mine):

We have developed this most recent protocol to address concerns that to date, to our knowledge, other groups have been able to generate STAP cells using our previously published or posted protocols. While we are confident that the original protocols published, will work if performed with meticulous attention to detail, we have tried to develop a protocol based on new information, that should be much more effective in demonstrating a phenomenon in which we have absolute confidence.

I think they meant in the first sentence to say “other groups have been unable to generate STAP cells…”

In fact as far as I know, nobody has been able to make STAP cells in replication efforts including Obokata herself.

Vacanti and Kojima conclude by saying that they still firmly believe in STAP.

Stem cell landmark: patient receives first ever iPS cell-based transplant

Masayo Takahashi

Today is a historical and very exciting day for the stem cell field.

In a major first for the stem cell and regenerative medicine fields, a patient in Japan today received a pioneering transplant of a retinal pigmented epithelial (RPE) sheet made from induced pluripotent stem (iPS) cells, also known by the acronym IPSC.

This is the first ever iPS cell-based transplant into a human.

The patient is reported to be a 70-something Japanese woman suffering from macular degeneration and the procedure was performed by Dr. Yasuo Kurimoto and other specialists. I highly recommend the article by David Cyranoski, one of my favorite science writers, linked to in the previous sentence for more on the transplant.

The patient is clearly a brave hero. The team transplanted a huge (from a bioengineering perspective) 1.3 x 3.0 mm sheet of RPEs into the retina of the patient, who did not have any clear immediate side effects from the procedure. Keep in mind again that this sheet was made indirectly from the patients own skin cells so it is an autologous (or self) transplant, a notion that 10 years ago would have seemed entirely like sci-fi.

This is not only a huge milestone, but also an astonishingly fast translation of iPS cell technology from the bench to the bedside. Talk about warp speed science.

Nobel laureate Shinya Yamanaka first reported the creation of mouse and human iPS cells just eight and seven years ago, respectively. To get to the clinic so soon thereafter is one of the fastest biomedical translational pathways in history.

How was this possible?

In part this is a story of an extraordinary level of commitment to iPS cell technology by Japan and its scientists including the team led by the amazing Dr. Masayo Takahashi (pictured above) and of course Yamanaka too.

The work was also made possible by Yoshiki Sasai, who did pioneering work in retinal differentiation from pluripotent stem cells. So we are talking about fantastic scientists dedicated to translation and a government willing to fund them generously to make this a reality.

Another important element to this story is that Japan has a clinical translation pipeline that is now faster with recent changes in regulations than that of the US. For example, this and future iPS cell-based transplants were approved as part of a clinical study, a type of clinical research mechanism that doesn’t exist in the US. It is safe to say that the same technology with the same research team and outstanding level of funding would still be at least a few years away from their first patient in the US due to the different regulatory scheme. Another indication of the unusual speed here was indicated in the Cyranoski piece:

Kurimoto performed the procedure a mere four days after a health-ministry committee gave Takahashi clearance for the human trials (see ‘Next-generation stem cells cleared for human trial‘).

With this difference between regulatory frameworks not only comes the potential for speedier clinical innovations, but also the uncertain potential for risks from first in-human studies.

In a sense we have an experiment inside of an experiment here.

We have the actual clinical studies as an experiment and then we have the larger context of a regulatory experiment too. Nobody knows how it will turn out. One can certainly have hope from the fact that the Takahashi team’s preclinical studies were reportedly encouraging from a safety perspective, although that data has not yet been published. Also, on the positive side we have the encouraging results from the ongoing clinical trials from Advanced Cell Technology (ACT) using a similar approach to macular degeneration, but employing human embryonic stem cells to make the RPEs.

For the vision impaired and the broader stem cell field, it is heartening to have two such capable teams working to cure blindness with pluripotent stem cells.

Admittedly, we are now in uncharted territory, which is both exciting and a bit unsettling too. That’s the reality with cutting edge biomedical science and going after huge goals like curing blindness. What an exciting time to be in the stem cell field.

Advanced Cell Technology reinventing itself including new name ‘Ocata Therapeutics’

advanced cell technologyIt’s been a big summer for stem cell biotech Advanced Cell Technology (ACT; stock ACTCD) as it continues what I would call a process of reinventing itself.

What’s been happening?

ACT recently did a notable 100:1 reverse split on its stock, opening it up to a whole new group of investors.

The company has also settled some previously lingering litigation and gotten new some new IP.

The latest development is a move to change the company’s name to Ocata Therapeutics. I asked Bob Lanza about the name changed and he told me that “Ocata is a native American (Huron) word for ‘medicine man’.”

Cool name.

I’m guessing we’ll be saying goodbye to the old logo (above) and I’ll be very curious to see the new one.

Investors following the stock expect some major additional developments in coming days/weeks, which could include a major new paper on the ACT clinical trials for macular degeneration.

It’s an exciting time for the company.

By way of disclosure, I have a relatively recently acquired small amount of stock (in it for the long haul) in the company. This blog is not intended as financial advice.

 

 

“Magical” STAP papers were blistered by Nature’s own reviewers, but then accepted just months later

The reviews of a STAP paper submitted to and rejected by the journal Science in 2012 were posted at Retraction Watch yesterday. They filled in some gaps in the puzzle of the series of events that led to such flawed science being published in Nature in January 2014, but the reviews also raised more questions.

Today, more STAP paper reviews have surfaced.

ScienceInsider posted a piece with additional STAP paper reviews with these coming from Nature reviewers commenting on what would later become accepted and published by Nature only months later in seemingly only moderately revised form.

The Nature reviews (you can read them here on the Science website) are very critical of the STAP papers and raise a host of important, largely still unanswered questions about STAP.

STAP magic

My overall sense is that the three reviewers did a thorough and fair job of reviewing these STAP papers. It sure seems that none of the three reviewers were even remotely close to being comfortable with these papers being published in Nature. In each case it would seem that a major revision would have been necessary prior to even having a remote chance at publication. One of the reviewers summed up a STAP cell article as essentially reporting an unproven, “magical” approach (see screenshot above).

The ball is now firmly in Nature‘s court to facilitate a thorough understanding of the STAP situation. It seems reasonable to expect more from Nature than its one editorial that shrugged off any significant responsibility including this key portion:

“We have concluded that we and the referees could not have detected the problems that fatally undermined the papers. The referees’ rigorous reports quite rightly took on trust what was presented in the papers.”

Nature‘s own reviewers’ comments would seem to directly challenge this statement.

I’m not going to go through all of these criticisms and questions raised in these reviews of the originally submitted Nature STAP papers point-by-point, but the overall consensus was that these papers were seriously flawed. This fits well with the gestalt of the reviewer comments on the rejected STAP/SAC paper at Science.

If you look at the published STAP cell Nature papers and think about the details mentioned in these acidic reviews of the original forms of the same papers, there is a sense that not much fundamentally was improved in the papers during that intervening period of months.

The big question remains then: how did these STAP papers go from being rebuffed based on scathing reviews at Nature on April 4, 2013 to acceptance by the same journal on December 20, 2013 and publication about a month later?

Full Reviews of Rejected STAP Paper Point to Early Signs of Big Trouble

Before the two STAP cell papers were published in Nature in January of 2014, much of the same data was reportedly submitted as single papers to other high-profile journals including Science.

In these cases, the proto-STAP papers as we might call them were rejected.

But why?

Until now we largely could only speculate.

However, the reviews of the 2012 proto-STAP manuscript at Science can now be read at Retraction Watch.

Retraction Watch

As a result of reading the Science reviews, today we know what the reviewers at Science thought in 2012 of this proto-STAP paper and this sheds much light on what went so terribly wrong with STAP overall. There were many big red flags. Keep in mind that the Nature reviewers would not know about the Science reviews unless by chance one or more of the reviewers for Nature had also participated in the review process at Science.

This early generation STAP paper was entitled “Stress altered somatic cells capable of forming an embryo”.

There was no “STAP” acronym at that point. Instead, the stress-produced stem cells were called “SACs”, an acronym presumably standing for “stress-activated somatic cells” or “stress-altered stem cells”. Therefore, let’s call this proto-STAP paper, the SAC paper.

All three Science reviewers had serious doubts about the SAC paper and pointed out numerous specific concerns.

For example, Reviewer 1 right away early in their review pointed out that the SAC phenomenon was probably not real and was instead explainable by two simple experimental problems: stress-associated GFP reporter activation and cell culture cross contamination.

Crucially, this same reviewer noticed the gel splice, later present in the accepted Nature STAP article Figure 1. However, apparently the STAP/SAC team did not take that concern or most of the other reviewer issues to heart.

Reviewer 2 was extremely skeptical of SAC as well, listing twenty-one specific problems/issues to be addressed. Unfortunately, it seems that most of these concerns also remained unaddressed in the later accepted Nature STAP papers. It is fair to say that although 21 issues seems like a lot that these concerns seem reasonable and not overly harsh.

What else did the reviewers say?

Both Reviewers 1 and 2 had the shared concern that pluripotency-related gene expression seemed abnormally high in the SAC cells. Way way too high.

Reviewer 2 wanted much more data before being convinced. For example, they wrote:

Given the novelty of the claims, a thorough characterization of the SACs is warranted, as is some probing of the mechanisms. This would necessitate a more sophisticated genomic analysis of SACs, through microarray or RNA-seq, and genome-wide DNA methylation analysis — analyses that other pluripotent stem cell lines have been routinely subjected to and for which methods for smaller cell numbers have been developed.

Reviewer 3 was not as detailed with their concerns, but more generally identified some areas of concern such as those articulated in this paragraph:

the methods and cell protocols used must be described in far more detail. For example, the section on Oct4 should state how many cells were sorted and describe the appearance of the cells. Is it possible that rare populations of cells pre-exist or are already apparent on day 1 (thus, what are the “dots” of Fig. 1?). The authors will argue that, indeed, under certain circumstances, they were able to reprogram terminally differentiated cells, and that this was attributable to TCR recombination. I think, ideally, that the cells should be experimentally tagged and traced. This would unequivocally clarify the source of the cells and, further, would exclude the possibility that some cells pre-existed in a pluripotent state.

Critically, it is necessary to determine whether SAC cells can propagate stably in culture and whether such cells can be passaged.

 

Experimental tagging and tracing of the cells would have been a major step forward for clarifying whether the SAC/STAP phenomenon was real. STAP/SAC cells should have been made in parallel to iPS cells as well for direct comparison.

One has to wonder how the Nature reviewers and editors could not have picked up on so many problems that were apparent to the Science reviewers. Every review at a different journal of the identical paper will be distinct of course, but this data seemed inherently flawed in a systematic way. This was no ordinary paper either. It was a no-brainer that this kind of paper with revolutionary claims required extraordinary, very meticulous editorial oversight. It is therefore not an unreasonable expectation that the Nature review process of the STAP papers should have picked up on some of these serious problems.

Nobody likes to get a harsh review of a submitted manuscript, but it’s crucial after you calm down in that situation to consider that some of the comments by the reviewers likely raised legitimate, important issues to address before resubmission. This way you can avoid problems and improve your paper. Apparently to a large extent that didn’t happen between the SAC paper and STAP paper stages.

In the end these Science reviews of the rejected SAC paper indicate that the STAP manuscript and data were problematic in fundamental ways back in 2012.