STAP cells (stap細胞) are real deal says new Vacanti patent declaration

STAP is back?vacanti-stap-figure-2017

Really?

No, I don’t believe so, but there’s an interesting development and twist on the STAP cell front.

Just a few days ago on January 4, 2017 Dr. Charles Vacanti, the originator of the STAP cells concept, submitted a declaration to the USPTO affirming the belief that STAP cells are real and requesting that the patent office allow the rejected STAP patent application to be reconsidered.

I find a number of aspects of this development notable:

  • The declaration says they have generated new data supporting STAP, but the two figures shown are in my opinion unconvincing. More specifically, just showing some floating spheres and an image of a single cell (not even stained for a marker) doesn’t really prove anything. You can see a snapshot of Figure 1 above. Note that in May 2016 an Obokata-associated website posted some supposed STAP validation data as well, but in my view it too wasn’t at all convincing.
  • qPCR results on induced expression of pluripotency genes are mentioned, but I didn’t see that actual data in the document or other related documents so as far as I can tell it can’t be evaluated at this point. Update: I’m still searching to see if I can find a patent document that shows the new qPCR and it may be in there somewhere. Stay tuned. BTW, you can look at the patent documents directly yourself at this USPTO website. Plug in patent application #14/397,080 and click on the tab at the top that reads “Image File Wrapper”. I’m not a patent expert so there may be other useful tabs at the top as well where for instance the qPCR data could be found or other information.
  • The declaration expresses concern with how Nature handled the STAP cell situation with the retractions, indicating that in the view of some of the authors there should have been an indication that the authors believed the concept was real.
  • Why do some of the STAP authors believe in it still but many others in the stem cell field don’t? Apparently, according to the declaration, the other labs who tried the STAP method just didn’t use the proper technique. I have doubts about that explanation. For instance, Vacanti’s own Harvard/B&W’s colleague George Daley and other top stem cell scientists published two BCA pieces in Nature refuting the existence of STAP. Reportedly they even did some of this work in Vacanti’s own lab with someone who was an author on the STAP papers.
  • The STAP cell patent application has been transferred to a private company called Vcell Therapeutics, Inc., which seems somewhat obscure. A Japanese blog has dug into this situation and mentions a J. Kelly Ganjei, a name I’m not familiar with, as a leader of Vcell. There’s even some speculation that Vcell may be short for “Vacanti cell”, but I don’t know about that. Given the sound of the company’s name I can’t help but think of VSELs, another controversial kind of stem cell, when reading the word “Vcell”.

Continue reading

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.

STAP Cell Update: New STAP-like paper, Obokata, Vacanti, Real Origin of STAP cells, & More

The STAP cell mess that began in January of this year has in some ways quieted down.

In a broader sense, I believe that STAP is now and will be in the future viewed as a scandal that revealed some less than ideal aspects to the world of biomedical science and publishing.

Where does STAP stand today?

A New STAP-Like Paper?electric iPSC

The most recent development is the publication of a new paper pointed out by a number of people to me as perhaps STAP-like. It is entitled “Electromagnetic Fields Mediate Efficient Cell Reprogramming into a Pluripotent State”. It was published in the journal ACS Nano.

This Baek, et al. paper suggests that you can dramatically more efficiently create induced pluripotent stem cells (iPSC) by exposing somatic cells to an electromagnetic field (see graphical abstract above). My reaction? Let’s see if another lab can reproduce this, but I’m not terribly optimistic. Derek Lowe weighed in on this paper here. The Pubpeer folks have some concerns too and the authors have responded (which is a good thing) there as well.

STAP stem cellsObokata Thesis in Jeopardy

At this time, first author Haruko Obokata is faced with more immediate issues such as her future at RIKEN and her thesis. She must correct her Waseda University thesis or it may be revoked. The University did an abrupt U-turn on this as earlier they had said that while the Obokata thesis had problems it was not that big a deal. Now they are requiring a correction. Given the apparent massive plagiarism in it and re-used figures, I don’t see how a correction is possible frankly.

Vacanti still believes in STAP, issues new protocol

Obokata’s former mentor at Harvard/Brigham Women’s, Charles Vacanti, recently reaffirmed his belief in STAP and along with his lab member Koji Kojima, published yet another STAP protocol this time detailing that the addition of ATP might help other labs make it work. I’m skeptical. I do find it fascinating that Vacanti still believes in STAP despite all the evidence to the contrary. Otherwise in the STAP news, it’s interesting to speculate that during his sabbatical that he may continue working on STAP.

Nature‘s role in STAP

I still think that Nature has not come to terms with its role in STAP. As has been said many times, no journal, editors, or reviewers can catch all problems in a paper, but given the released STAP reviews of previous versions of the STAP papers including one at Nature that wasn’t initially accepted and received pretty harsh reviews, it sure seems the overall review process at Nature should have done better. All things considered, I kinda doubt we’ll hear anything else from the journal on STAP. If the trend of a surging number of overall retractions at Nature continues, however, there may be more of an impetus for change.

Remaining STAP mystery: where did STAP cells really come from?

If acid and other stressors (now perhaps including electricity) do not really make pluripotent or totipotent stem cells, then where did the alleged STAP cells/STAP stem cells come from that seemed in the mouse assays to have pluripotency or totipotency? There have been some indications that STAP cells have a different genetic make up or transcriptomic profile than they were “supposed to” as the authors reported these features in the retracted STAP papers. Were STAP cells actually a mixture of ES cells and trophoblastic stem cells? Some kind of iPS cells? We still do not know.

TGIF! Some attempts at humor to release STAP cell stress

Sometimes a situation is so bad or stressful that it just calls out for some comic relief.

STAP seems to be one of those.

Below are various silly attempts at STAP humor to hopefully release some of that stress.

Some doodling of hypothetical Dr. Bob and Dr. Sue trying to replicate STAP in a lab and being super stressed with a surprising consequence…
STAP cell cartoon 2014Other names for STAP stem cells?

Some said we should call them “SWAP cells” because of the image mixups.

Instead of “Oh snap!”, maybe the new expression is going to be “Oh STAP!”

Jim Woodgett

Jim Woodgett called the situation a “STAP in the back” on Twitter (see above).

Alan Boltz

Alan Boltz came up for a new meaning for the STAP acronym on Twitter above.

I’ve heard other new definitions for STAP:

  • Stressful Time After Paper
  • Stress-Triggering, Aggravating Publications
  • Stop Talking About these Papers

Please leave over alternative, funny definitions for the STAP acronym in the comments.

It’s ironic that STAP as an acronym can really stand for “Scientific and Technical Advisory Panel”.

An entire parody article was posted on another blog entitled “Stem cells created by dipping researchers in coffee”. It’s kinda humorous in a geeky way.

I’ve also seen STAP compared to the process by which mild-mannered Peter Banner turns into the Incredible Hulk (which is appropriately enough also green) when he’s stressed out.

Other attempts at STAP humor to help deal with the stress?

RIKEN rejects Obokata appeal on alleged STAP cell misconduct

Obokata press conferenceA RIKEN committee has rejected an appeal by Dr. Haruko Obokata regarding its finding of research misconduct related to two papers in Nature claiming the production of so-called STAP cells and STAP stem cells.

Earlier the committee had ruled that Obokata had allegedly engaged in misconduct and that there problems with the research. Obokata appealed this ruling on April 8 and now the committee has rejected her appeal. The results of their deliberations were summarized succinctly thusly:

The committee, taking into account the points and rationales presented in Dr. Obokata’s appeal filed on April 8, 2014, along with the supplementary rationales submitted on April 20 and May 4, has concluded that there is no need to re-investigate the results of the committee’s investigation issued on March 31, 2014.

It is notable that some members of the committee themselves have been accused of having issues of their own with past publications (e.g. see this Nature News piece). This is also mentioned in the statement of today from RIKEN’s President, Ryoji Noyori:

As regards the allegations of research misconduct in past papers published by members of the investigative committee, we believe the committee has nevertheless carried out its investigation appropriately and have concluded that the allegations do not affect the committee’s findings concerning the STAP cell papers. Members of the committee who are affiliated with RIKEN whose own papers have been called into question will be investigated separately as per RIKEN’s regulations. Committee members who are not affiliated with RIKEN will be investigated as per the regulations of their own institutions.

Obokata’s future at RIKEN remains uncertain at this time. With the rejection of her appeal, RIKEN may soon make a decision about what to do next.

This is all likely to end up in court as well.

The committee’s full report is not yet available in English, but commenter Ken has apparently read it and has raised some concerns about it already (BTW a hat tip to Ken on today’s RIKEN release of the decision and reports).

What a stressful mess, huh?