Closing the Door on the STAP Episode

Last year, a group of Japanese researchers, led by scientists from the high-regarded RIKEN Center for Developmental Biology, reported a break-through in stem cell technology. Their so-called STAP or stimulus-triggered acquisition of pluripotency cells could be derived from mature, adult cells by exposing those cells to stressful conditions. Even though the papers that reported these advances were published in the prestigious journal Nature, immediately, people found problems in the papers that could not be easily resolved. Several laboratories tried to replicate the STAP results, with no success. The papers were eventually retracted and an internal investigation by the RIKEN Center also suggested that foul play might have been at work. Amidst all this, a question that hung in the air was this, “Was there something to the original discoveries but it was overstated?”

That question has now been definitely answered in the negative, thus closing the door for good on this whole sordid affair. Two papers were published on 23 September in the journal Nature, which was the same journal that published the original, ill-fated papers early last year that showed that STAP cells should be called NE (never existed) cells.

The original STAP papers were published in January 2014 by a team led by researchers at the RIKEN Center for Developmental Biology (CDB) in Kobe, Japan, in collaboration with scientists from Harvard Medical School in Boston, Massachusetts. These two papers claimed that embryonic-like stem cells could be produced by exposing adult body cells to stress, such as acidic conditions or physical pressure. These papers dubbed their technology “stimulus-triggered acquisition of pluripotency,” or STAP. Unfortunately, other scientists quickly discovered problems with data in the research. These problems then generated an investigation, and these papers were eventually retracted.

The paper retraction, however, did not answer the nagging questions as to whether or not the STAP procedure might have worked, and where the pluripotent stem cells labelled STAP in the RIKEN laboratory came from.

Such questions were addressed by seven teams in four countries who tried to replicate the procedure under various conditions (De Los Angeles, A. et al. Nature http://dx.doi.org/10.1038/nature15513 (2015). These teams collaborated to generate 133 attempts to produce STAP cells, and all of these attempts failed. One of these teams was led by researchers at Harvard Medical School who had worked with one of the original STAP co-authors. In this laboratory, cells were engineered to express a fluorescent protein when a gene related to pluripotency was expressed. When cells were exposed to stressful conditions, they did find some fluorescence, which suggested that pluripotency genes were expressed when cells were subjected to such conditions. However further testing showed this result to be an artifact since cells can naturally emit light; a phenomenon known as autofluorescence. Six other groups also observed autofluorescence in stressed cells, but no convincing evidence of STAP conversion.

A group of RIKEN researchers that did not include any authors of the original STAP papers analyzed the genomes of purported STAP cell lines that had be derived at the CDB. These scientists discovered multiple instances of contradictory data that probably resulted from contamination of purported STAP cells by other known cell types. The RIKEN group’s analyses showed that all remaining purported STAP stem cell lines, for example, were genetically identical to embryonic stem cell lines that already existed in the laboratory.

Additionally the “chimeric” mice that were reportedly produced by injecting STAP cells into the embryo of a developing mouse were found to have been produced by injecting pre-existing embryonic cell lines, rather than STAP cells, into the embryo. The production of chimeric mouse embryos is an experiment that definitively shows that particular cells are truly pluripotent.

Cell contamination also explains one of the most puzzling features of the original work, and that has to do with why the alleged STAP cells were reported to be capable of forming placental tissue, which is something that embryonic stem cells are not able to do (De Los Angeles, A. et al. Nature 525, 469–478 (2015)). These most recent analyses show that mixtures of trophoblast stem cells (which form the placenta in a developing embryo) were mixed with embryonic stem cells and that this mixture was used in the mouse chimeric experiments, leading to the production of mouse placental and embryonic tissue.

Stem-cell scientist Rudolf Jaenisch of the Massachusetts of Technology in Cambridge, who was part of the replication efforts, originally suggested in April 2014 to Nature’s news team that contamination was the reason for the results in the STAP papers. Unfortunately, he did not have evidence at the time for his hypothesis, but this most recent work has vindicated Jaenisch’s hypothesis.

A lingering question is how these embryonic stem cells and trophoblast stem cells came to replace purported STAP cells when the chimeric mouse experiments were performed. So-called cross-examination, which is the accidental contamination of one cell culture by another type of cell, is a well-known problem in cell culture experiments and biological research that depends on cultured cells. However, to properly explain the results in the original STAP papers, multiple independent contamination events must be invoked. “It is very difficult to reconcile the data with simple contamination or careless mislabeling,” says stem-cell scientist George Daley at Harvard Medical School. Unfortunately, requests for clarifying comments from corresponding authors of the original papers went unanswered.

In a review article published in Nature, Daley, Jaenisch argue that all new reports of new types of pluripotency should be subjected to rigorous “forensic” analysis that examines the genomes of the cells under consideration before publication. According to the authors, besides the failed STAP papers, “numerous groups are reporting ever more nuanced states of pluripotency.” In particular, the article focuses on genomic analyses, which are enabled by advances in sequencing technology, that will help evaluate such cell types.

Daley says that these experiments bring some well-desired closure to the STAP. He ended, however, with a warning to scientists who are looking for ways to reprogram cells to an embryonic-like state: “We will all be a tad more cautious in evaluating such claims.”

Embryonic Stem Cell Contamination Responsible for STAP Research Snafu

STAP or stimulus-triggered acquisition of pluripotency cells were allegedly derived from mature, adult cells by simply subjecting those cells to environmental stresses. These environmental stresses, such as low pH treatments and so on, were thought to cause cells to express genes that pushed them into an embryonic stem cell-like state. Researchers from the RIKEN institute reported these reports in the prestigious international journal Nature, and these advances were hailed as a stupendous advancement in stem cell biology.

However, as soon as stem cell scientists tried to repeat the results from these papers and failed, trouble started. Major laboratories had no success in recapitulating the results in the RIKEN institute papers, and, on-line post-publication reviews noticed some nagging problems in the published papers. RIKEN institute launched an investigation into the matter, and concluded that the lead researcher in these papers was guilty of scientific misconduct.

Now, new work as suggested that the whole thing was the result of contamination of the RIKEN group cells with embryonic stem cells. How that contamination occurred, however, remains unknown.

The RIKEN institute investigation was instigated by the institute and was carried out by a committee composed of seven outsiders. The committee analyzed DNA samples and laboratory records from two research teams who had participated in the STAP cell research. Those Nature papers have been retracted, but were once thought to provide a shortcut to producing pluripotent stem cells. The latest investigation suggests that the STAP findings resulted from contamination by embryonic stem cells. The investigation found signs of three separate embryonic stem cell lines, and they noted that it is difficult to imagine how contamination by three distinct lines could be accidental, but that they could also not be certain that it was intentional.

“We cannot, therefore, conclude that there was research misconduct in this instance,” the committee wrote. It did, however, find evidence that lead investigator Haruko Obokata, the lead author of the STAP papers, who formerly worked at the RIKEN Center for Developmental Biology in Kobe, Japan, had fabricated data for two figures in the original STAP publications.

Attempts to Recapitulate STAP Cells Fail

Japanese stem cell scientist Haruko Obokata was the first author of two papers that appeared in the journal Nature earlier this year that described the derivation of pluripotent stem cells from mature cells without the use of genetic manipulation. Instead, these cells were subjected to environmental stresses such as physical pressure or exposure to acid that, according to these papers, caused the cells to express genes associated with pluripotency. Culturing of these cells led to the derivation of pluripotent stem cells lines. Thus were born STAP or stimulus-triggered acquisition of pluripotency cells. Needless to say, these results were hailed as a remarkable advance in stem cell biology.

Unfortunately, as soon as the papers were published, several high-level laboratories tried to recapitulate these results and universally failed. Even more troubling were some of the inconsistencies that came to the forefront in the published papers that the reviews had apparently missed or were ignored by the journal. The RIKEN center where this work was done even launched an internal investigation that concluded that Dr. Obokata was guilty of scientific misconduct.  Obokata gave approval to formally retract her Nature papers.  However, the RIKEN Center gave Obokata and her colleagues until the end of November to prove that she could reproduce STAP cell derivation.

Now the jury is in – Obokata has been unable to replicate her results. In the original experiments, Obokata used a gene fusion that caused the cells to glow green if they expressed genes related to pluripotency. In her replication of her original experiments, Obokata produced such green glowing cells when she subjected to environmental stresses. However, this is only a preliminary test that only involved a few such cells. More rigorous tests that were conducted, however, failed. In this case, Obokata’s stressed adult cells were introduced into a mouse embryo to see whether they could contribute to the development of various tissues during animal development. Obokata’s stressed cells, however, were unable to integrate into the developing embryos. Since this is the ultimate test for pluripotency, and since these cells were not able to pass this test, it seems virtually certain that Obokata’s original results were completely bogus.

With her signature conclusions in tatters, Obokata has resigned from the RIKEN center. In a very emotional resignation letter, Obokata wrote she could not “find words enough to apologize… for troubling so many people at RIKEN and other places.”  The RIKEN president, Ryoji Noyori, wrote in an accompanying statement that Dr. Obokata had been subjected to horrible psychological stress as a result of this affair.  Noyori added that he accepted her resignation to hopefully save her from suffering further from a severe “mental burden.”  One the co-authors of the STAP papers, Japanese stem cell scientist Yoshiki Sasai, committed suicide a few weeks after the retraction of the paper.

Hopefully, RIKEN and the other scientists who were involved in this venture move on and continue with the business of pushing back the frontiers of science.  It is entirely possible that intentional fraud was involved, but ultimately, we will never know.  For now, it is clear that sloppiness and a lack of skepticism about one’s own results contributed to this fiasco.  I think most people simply want to put this whole sordid event behind them.  However, there are pointed lessons to be learned and we will be better investigators if we learn them.

For one, peer review is not omnipotent.  Post-publication review is important and will continue to be important.  Secondly, journals need to be willing to solicit outside opinions to ensure the quality of high-level publications.  Third, the majority of scientists publish in journals that most people will never read.  Their work is not glamorous, but instead document tedious, high-quality, detailed, scientific research.  The majority of such work will never appear in Nature or Science or Cell, but that’s alright because good solid research is still good solid research regardless of where it appears.  It is really too bad that the push for high-visibility publications can cause people to publish too quickly before results have been properly vetted.  The STAP episode might be a reminder for journals to take greater care with the review of original research.

STAP Papers Retracted

The two papers that appeared in the journal Nature that described the derivation of embryonic stem cell-like cells simply by exposing cells to environmental stresses have been formally retracted. In a notice of retraction from the Riken Center’s Haruko Obokata, who was the lead author of these papers, and her colleagues said that “[s]everal critical errors have been found in our Article and Letter.” The notice also pointed out that a subsequent investigation of those errors by an internal Riken Center investigation found evidence of research misconduct.

“The STAP technology, indeed, sounded too good to be true,” said Dusko Ilic, from King’s College London, to the Reuters news group. “I hoped that Haruko Obokata would prove at the end all those naysayers wrong. Unfortunately, she did not.”

In an editorial that appeared in Nature, Ivan Oransky from a blog site known as Retraction Watch, argue that it couldn’t have caught the errors. Oransky wrote: We at Nature have examined the reports about the two papers from our referees and our own editorial records,” the editorial notes. “Before publishing, we had checked that the results had been independently replicated in the laboratories of the co-authors.” Nevertheless, the journal says this incident has highlighted flaws in the peer-review publishing process.

“We — research funders, research practitioners, institutions and journals — need to put quality assurance and laboratory professionalism ever higher on our agendas, to ensure that the money entrusted by governments is not squandered, and that citizens’ trust in science is not betrayed,” it adds.

The simple fact is that reviewers examine data, figures and materials and methods, but they have no gift of ESP to determine is the authors are telling the truth.  Truth-telling and honesty are virtues without which science cannot exist.  What is the basis of honesty and truth-telling?  Well, the secular, pragmatic worldview would suggest that truth-telling works and without it we cannot do science without it.  However, if truth-telling gets the individual scientist ahead for a time, then why shouldn’t they prevaricate?  What should the individual worry about what the collective thinks or needs?

It is at this point that I must interject that the Christian worldview provides the foundation for honesty and truth-telling.  The Christian tells the truth because God is the author of all truth and is by His very nature, the truth (see John 14:6).  To not tell the truth is to dishonor God and not live in accordance with his revealed prescriptions.  Therefore, the Christian worldview explains why we should tell the truth when reporting our experiments.

Lead Author On STAP Papers Publicly Apologizes in Press Conference

On April 9th, the Japanese scientist at the center of a controversy over studies purporting to turn mature cells to stem cells simply by bathing them in acid or subjecting them to mechanical stress, Haruko Obokata, publicly apologized for her errors associated with the published work.

In a press conference in Osaka, Japan, with a crowd of voracious reporters flashing their cameras, Obokata blamed her scientific immaturity and lack of awareness of research protocols for the errors that were found in her two high-profile papers on the studies that were published in the journal Nature in January, which included the use of a duplicated image. With Obokata were two lawyers who are representing her.

To her credit, Obokata took full responsibility for the errors in the papers and apologized to her co-authors for the messy situation in which they presently find themselves. She also apologized to the RIKEN Center for Developmental Biology, where she did her work, for the embarrassing press this ordeal had brought upon it. Additionally, she sought forgiveness from the RIKEN committee whose report earlier this month found her guilty of scientific misconduct. At the time, Obokata had attacked the report.

This is Obokata’s first public statement in more than two months, and she held the press conference to apologize for the errors and to make the case that her research, despite the caveats and mistakes, was still valid. Also, Obokata wanted to establish that the inaccuracies in the papers were not deliberate. The day before the press conference, Obokata submitted a formal appeal to RIKEN for their committee to retract its misconduct findings. She insisted that the “stimulus-triggered activation pluripotency” or STAP phenomenon, as it has been dubbed, exists. RIKEN has 50 days to respond to her appeal.

In the STAP work, lead author Obokata, along with Japanese and US colleagues, described remarkable experiments in which she reprogrammed mature mouse cells to an embryonic state merely by stressing them. Unfortunately, she her two papers soon fell under suspicion and last month a RIKEN-appointed investigative committee found in a preliminary report that they contained numerous errors. A further report on 1 April by the RIKEN committee concluded that two of the errors in this paper constituted a case of scientific misconduct. Obokata aggressively responded on the same day in a written statement in which she expressed “shock and anger” at these conclusions. She also thought that the committee had unfairly come to their conclusions without giving her a chance to explain herself. On this day, however, Obokata’s seemed to sing a very different tune in which she pleaded for forgiveness and presented several apologies. However, she steadfastly maintains that her primary findings are true.

Obokata continues to insist that the two problems that the committee declared cases of scientific misconduct (the duplicated image and the swapping of a diagram of an electrophoresis gel) were honest mistakes, and that she had not been given enough time to explain her side to the committee.

After her brief introductory remarks, Obokata’s lawyer gave a 20-minute presentation to make the case that neither problem constituted misconduct. Defining fraud as fabrication, he countered that in both cases Obokata had the original data that should have been used but merely added the wrong data by mistake. For the more damning finding — an image of teratomas that had appeared in her doctoral dissertation and then again in the recent papers — the committee had found that she had changed a caption, which made it look intentional. The lawyer however traced the image back to a slide, part of a presentation that Obokata had continually updated and reused, until its origin became obscured. In one of her many apologies, Obokata said, “If I had gone back to carefully check the original data, there wouldn’t have been this problem.”

After the lawyer’s presentation, Obokata responded to journalists’ questions for more than 2 hours. Why had she only handed two laboratory notebooks over to the committee looking into her research? She said that she said she had four or five more that the committee hadn’t requested. Obokata denied that she ever agreed to retract the papers. Had she asked to retract her PhD dissertation? No, she merely sought advice on how to proceed Obokata’s dissertation is under investigation at Waseda University, where she studied for her doctorate).

Obokata also denied the possibility that the STAP cells had resulted from contamination from embryonic stem cells, saying that she had not allowed embryonic cells in the same laboratory and that she had carried out tests which precluded that possibility.

She said that she had created STAP cells more than 200 times, adding that she knows someone who has independently achieved it but refused to give the name (citing privacy). She believes that a RIKEN group trying to demonstrate STAP cells will help her. She has not, she said, been asked to participate in those efforts. She added that she would consider doing a public replication experiment but that it was not up to her whether she could.

Two hours into the questioning, her lawyer cut off journalists, citing concern for Obokata’s frail emotional state, and said she had to return to the hospital where she has been staying. She bowed, apologized, then bowed again and left with the reporter’s cameras flashing away as she retreated.

I feel genuinely sorry for this young lady.  Her career in science is essentially over.  It is within the realm of possibility that her mistakes were unintentional and were the result of a hurry to publish.  In this case, her adviser does bear some of the blame for her mistakes.  However, at this point it seems more likely that her mistakes were probably intentional.  If that is the case she should have known that such a high-prolife paper describing such a novel finding would be subjected to intense scrutiny and repeated attempts to verify it.  I am reminder of Moses’ admonition to the tribes that had settled on the East side of the Jordan River if they do not help the other tribes fight for their lands.  In Numbers 32:22-24, Moses said, “then when the land is subdued before the Lord, you may return and be free from your obligation to the Lord and to Israel. And this land will be your possession before the Lord.  But if you fail to do this, you will be sinning against the Lord; and you may be sure that your sin will find you out. ²⁴ Build cities for your women and children, and pens for your flocks, but do what you have promised.”

Indeed your sin will find you out, and if Ms. Obakata intentionally attempted to deceive her colleagues, then it would appear that her sin has found her out.  At the moment I am willing to give her the benefit of the doubt, but if further evidence emerges that the whole thing is bogus, then I will retract my half-hearted support.  It is entirely possible that she found something novel and interesting that happens to cells when they are stresses.  However, it seems equally clear that a conversion into an embryonic stem cell-like state is probably not one of these things.  I reiterate my original belief – the original STAP paper should be retracted.