Mystery Lingers Over STAP “Acid Bath” Stem Cells
An investigatory panel hired by the Riken Institute recently issued reports finding that STAP “acid bath” stem cells were, in the main, simply garden-variety embryonic stem (ES) cell lines.
The panel could not prove that Riken’s Haruko Obokata, lead author of two now-retracted STAP cell Nature papers—an article and a letter—deliberately contaminated STAP cultures with ES cells. But the panel did add two more instances of research misconduct to two earlier instances found to be committed by Obokata, Riken spokesperson Jens Wilkinson confirmed to Bioscience Technology. Obokata did not contest the conclusions by Riken's Monday deadline, "so now the disciplinary committee will meet," Wilkinson said.
Haruko Obokata resigned from Riken’s Center for Developmental Biology (CDB) earlier in December 2014 after she and other Riken scientists announced they could not reproduce the results she and other Riken and Harvard University scientists had claimed to achieve in the Nature papers.
But mysteries remain, keeping the saga alive around water coolers—and in classrooms—worldwide. “I don't think this story will end until we get Obokata's side of the story,” Chinese University of Hong Kong stem cell researcher Kenneth Lee told Bioscience Technology. “This story has been used by several UK universities as part of their Bioethics teaching!”
STAP history
In January 2014, Riken and Harvard scientists published two papers in Nature reporting the creation of extraordinary stem cells (STAP or “stimulus triggered acquisition of totipotency” cells) from ordinary mature cells by stressing them with acid. Such a plentiful source of stem cells could have accelerated regenerative medicine research. There was global acclaim.
But almost immediately there were global questions, as irregularities were unearthed first by scientist bloggers, and then by Riken panels. In the spring, Riken charged Obokata with research misconduct on two images in the papers, and the papers were retracted in July 2014. Obokata’s supervisor, the widely-revered Riken stem cell expert Yoshiki Sasai, committed suicide shortly after.
The most recent report
Starting in September 2014, a different Riken panel performed genetic analyses as well as additional interviews and analyses of notes. In late December 2014, the group reported it found that three of the STAP lines were commonly used ES cell lines.
In particular, the new report found (according to the summary):
“a) The three STAP stem cells, FLS, GLS, and AC129, were actually derived from the three ES cells FES1, GOF-ES, and 129B6F1-ES1, respectively.
b) The FI stem cell CTS was actually derived from an ES cell FES1.
c) It is highly probable that the chimera mice claimed to be developed from STAP cells were actually developed from ES cells FES1.
d) It is highly probable that the teratomas claimed to be developed from STAP cells were actually developed from ES cells FES1.
e) The STAP cell samples given to GRAS for Chip-seq analysis were actually 129B6F1-ES1 cells.”
The new report also found two other images were tampered with in such a way as to qualify as “research misconduct involving fabrication.” One figure was article Figure 5c, “Growth curves of STAP stem cells.” In that figure, the panel found: “No measurements were submitted of the cell numbers, and in the interview with Obokata, it was found that she had created the figure without measuring the cell numbers.”
The second involved article Figure 2c, “DNA methylation.” About this, the panel wrote: “It was not possible to reproduce this figure from the sequence data kept by GRAS [Riken CDB’s Genome Resource Analysis Unit], and in the interview with Obokata, it was found that she had created the figure with deliberately selected data.”
Therefore, the panel wrote, “The STAP stem cell growth experiments were not properly performed. The figure of DNA methylation was not correctly made using original data. We therefore conclude that these two figures represent research misconduct involving fabrication. Both figures were created by Obokata and she bears responsibility for them.”
In summary, the panel wrote: “We have concluded that there was research misconduct by Obokata on two points. More important is that all of the STAP stem cells, FI stem cells, chimera mice, and teratomas originated in cultures contaminated with ES cells, a fact that refutes all of the main conclusions of the two papers. We have been able to confirm the existence of very little original data for the figures in the papers, and the responsibility for this rests primarily with Obokata who created the figures. Nevertheless, it is a serious problem that the collaborators and co-authors overlooked this point. In particular, (Terukiko) Wakayama who headed the laboratory in which Obokata worked, and Sasai, who played a major role in compiling the final version of the STAP cell papers, both bear heavy responsibility.”
Remaining mysteries
Mystery remains, say Lee and others. Lee was the first scientist to publish a paper finding his crew could not replicate the Nature STAP claims.
"The panel found that three STAP stem cell lines that Obokata said she created were actually three different ES cell lines,” Lee noted to Bioscience Technology. Lee said this seemed to him to be “committed by Obokata, but she may have accomplices” as she was inexperienced, and did not seem qualified to pull off such an act. Lee asked, Did Obokata take “these ES cells lines from Riken’s cell depository” or was she “given” them?
Then there were the mouse embryos and placentas that Obokata reported she made from STAP cells. They glowed green, supposedly because the STAP cells were genetically altered to express green fluorescent protein (GFP). “How the green placenta was formed has not been addressed,” Lee said. Standard “ES cells can only contribute a few cells to the placenta. The placenta comes from trophoblasts. So the green embryo and placenta could only come from a mixture of ES cells plus trophoblasts, both GFP positive. I don’t think Obokata has the embryonic knowledge to add trophoblasts to her ES cells.”
Did Obokata have “help from an embryologist?” Lee asked. Did she extract “embryos from GFP transgenic pregnant mice and claim they were produced from STAP cells?”
Another researcher, who is familiar with the players but spoke to Bioscience Technology on condition of anonymity, said that “as soon as STAP began to unravel, I thought the starting cells may have been ES cells, and I'm sure I wasn't the only one who suspected this. Whether there is anything interesting occurring at a low frequency when all of the fraudulent representations and claims are deleted from STAP is another question.”
For that researcher, “the bigger question now concerns nailing who knew what and how this happened; which individuals and processes were responsible. Without an honest attempt comprehensively and transparently to answer these questions, something similar will happen again, perhaps involving the same individuals and processes. Inaction—not being prepared or able to bring people and processes to account and punish them appropriately will also, I think, tend to corrupt the practice of science more broadly.”
The researcher continued: “How could such momentous experiments be performed by a single scientific ingénue, with no one knowing what was going on? Just think about it…then ask why reviewers' comments pertaining to image manipulation from previous submissions were apparently ignored when the manuscript was submitted in March 2013 to Nature?” The latter refers to a Riken committee report finding that a Science reviewer had, when the papers were submitted to that journal, unearthed an image manipulation that remained in the Nature work.
“Who,” the researcher asked, “knew what?”
Other researchers told Bioscience Technology they believed it was possible Obokata worked alone, and was simply poorly supervised. Wilkinson confirmed that Wakayama, and co-author Hitoshi Niwa, were cleared of misconduct by the new panel. Sasai was not investigated by the new panel, but was cleared of misconduct by an earlier Riken panel.
