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.

5 new cool stem cell papers worth a look for weekend reading

Some diverse new stem cell papers worth a peek this weekend?

Direct reprogramming hits crest: Generation of Multipotent Induced Neural Crest by Direct Reprogramming of Human Postnatal Fibroblasts with a Single Transcription Factor, Cell Stem Cell 

Hormone receptors in prostate cancer cells versus stem cells: Concise Review: Androgen Receptor Differential Roles in Stem/Progenitor Cells Including Prostate, Embryonic, Stromal, and Hematopoietic LineagesStem Cells

Remember Me-thylation: Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells, Nature

A Variant Path to Pluripotency: Histone Variant H2A.X Deposition Pattern Serves as a Functional Epigenetic Mark for Distinguishing the Developmental Potentials of iPSCs, Cell Stem Cell

Making targeted human organs from PSCs in animals. Targeted Organ Generation Using Mixl1-Inducible Mouse Pluripotent Stem Cells in Blastocyst Complementation, Stem Cells & Development

 

 

Five stem cell legends & a blogger walk into a bar: the increasing influence of social media

stem cell leaders

Five legends and a blogger walk into a bar together.

The bartender asks the first legend “What can I get for you?”

The legend orders their drink.

The bartender eventually serves up drinks to all five legends and turns to the blogger, “And what can I get for you?”

The blogger replies, “Do you have Wi-Fi?

“…..and a beer.”

I’ve now been doing my stem cell blog for about 2 1/2 years.

It started as an experiment and sort of took on a life of its own.

I find it very rewarding, but does all this blogging mean anything real and substantial?

Traffic continues to increase on this blog and it seems that the blog still has a who’s who audience of the stem cell world. So I guess the answer is “yes” to many people.

I’m very proud of the research that my lab does and I believe in making a difference through this research, but my hope is that this blog also makes a difference and means something to readers.

This past week we had a company announce the 50 most influential people in the stem cell world.

I was very skeptical of such a list, but curious who they had picked and why. So I opened it up and was very surprised that there I was at the very top….no, not #1, but #50.

However, they chose to put #50 first at the top of the first page of the PDF.

Funny.

Heck, I’m not complaining. I don’t totally understand how this group picked the most influential stem cell people and such lists are clearly arbitrary in some ways, but it’s neat to be on the list.

I think this blog had a lot to do with me being there.

CIRM recently ran a piece on this Top 50 stem cell influencers and included a picture of some CIRM-related folks including me (see pic at the top of this piece.)

What an honor it is for me to be with those 5 legends in the stem cell field in that montage.

In case you are not in the stem cell field or if you are you have been doing research on stem cells on Mars for a few decades, I can tell you who the other 5 are.

Starting at the top left is Nobel Laureate Shinya Yamanaka, then to his right is CIRM President Alan Trounson, and then we have Bob Klein who made Prop 71 a reality and is Chairman Emeritus of the CIRM Board. Then the next row starts with me on the left, then stem cell legend Jan Nolta who is Editor-in-Chief of the fantastic journal Stem Cells (and my colleague here at UCD), and finally Fred Gage, who has been doing pioneering stem cell work for decades and is the past President of ISSCR.

This montage reminds of that song on Sesame Street “…which of these things do not belong” where they have pictures of maybe five balls of different shapes and sizes, and then a zebra. I feel kinda like that zebra. Yeah, you can tell I’m a dad from the Sesame Street reference.

I can think of many others who did not even make the top 50 in this particular list who I believe are amazing stem cell stars that could and arguably should have been included: Irv Weissman, George Daly, Len Zon, Sean Morrison, Konrad Hochedlinger, Jeanne Loring, and Rudy Jaenisch, just to name a few, but there dozens more I could list. I could probably list 50 people just in the state of California here in the US.

Do I belong there with those 5 stars in that photo montage above? Or on that list of top 50?

I don’t know, but I think one message from all of this is that social media is increasingly influential in science and in the stem cell field.

A stem cell blog can have a powerful impact on the field. I didn’t remotely imagine that in 2010.