From the ‘ScienceInsider' column in ‘Science', 4 October 2011 (story by Jon Cohen).
Chronic Fatigue Syndrome Researcher Fired Amidst New Controversy
Judy Mikovits has had a rough few weeks. On 22 September, Science published online a nine-lab study widely seen as the final blow to the theory, championed by Mikovits and colleagues in an October 2009 Science paper, that a recently detected mouse retrovirus might play a causal role in chronic fatigue syndrome (CFS). A letter in the same issue of Science from one of the contributing labs to the 2009 report revealed that a contamination had marred its contribution—PCR detection and sequencing of the mouse virus, dubbed XMRV. Mikovits and colleagues defended the validity of the rest of the study, known as Lombardi et al., which detected the virus by several other methods, so Science issued a rare partial retraction of the original paper.
Then on 29 September, Mikovits was fired from her job as research director of the Whittemore Peterson Institute for Neuro-Immune Disease (WPI), a private organization in Reno, Nevada, devoted to CFS research and treatment. Both Mikovits and WPI's CEO, Annette Whittemore, say the firing was not related to the XMRV theory's demise.
The very next day, a graduate student who writes a snarky blog that has been highly critical of Mikovits and the XMRV theory raised questions about whether a figure in Lombardi et al. had been misrepresented. Science Executive Editor Monica Bradford said in a statement that the journal is investigating the allegation. “As is our policy in cases of alleged figure manipulation, we follow up with the research authors as soon as our own review of the allegation is complete,” said Bradford. “Science takes all such matters seriously and seeks to respond thoroughly and efficiently.”
The furore revolves around an image—the bottom half of Figure 2C in Lombardi et al.—that shows XMRV proteins in CFS patients but not healthy controls. In her blog known as ERV (endogenous retroviruses), Abbie Smith on 30 September noted the striking similarities between Figure 2C and a slide Mikovits presented at a CFS meeting in Ottawa, Canada, on 23 September. Smith, who is working on her doctoral dissertation at the University of Oklahoma, Oklahoma City, and studies HIV, wrote that an anonymous tipster had pointed out to her that the two images looked identical but had different patient numbers and experimental conditions. Smith questioned whether this was a simple mistake or an attempt to recycle old data to make a new argument.
The Ottawa slide supported Mikovits's contention that even if XMRV could not be detected in CFS patients, other gammaretroviruses still lurked in their chromosomes. Mikovits described how she had treated cells from two CFS patients with a chemical, 5-Azacytidine, that takes methyl groups off DNA. This procedure prods cells that harbor latent versions of retroviruses to produce them, and the image on the slide showed the resultant proteins in what's known as a Western blot gel. In Lombardi et al. what appears to be the same image shows “XMRV proteins” and makes no mention of 5-Azacytidine use.
Mikovits's collaborator, Francis Ruscetti of the National Cancer Institute (NCI) in Frederick, Maryland, who ran all of the Western blots, confirms that the Ottawa slide uses the same image that appears in Lombardi et al. Ruscetti and Mikovits, in a joint e-mail to Science for this article, said many patients and their doctor, Daniel Peterson (who since has had a falling out with WPI), knew the original coded numbers, so the researchers changed them for the Science publication to “protect the patient privacy.” Ruscetti says it was a mistake for Mikovits to have used the original patient codes in Ottawa. “We were under so much pressure, we missed it,” says Ruscetti.
As far as the use of 5-Azacytidine, Ruscetti and Mikovits stressed in their e-mail that “there was no attempt in the original paper to hide anything.” They say for the purposes of Lombardi et al., the use of 5-Azacytidine was not germane: They were simply trying to demonstrate that CFS patients had viral proteins not seen in controls. By the time of the Ottawa meeting, they say they realized that this experiment did not in fact show XMRV but proteins from a broader family of gammaretroviruses.
After Lombardi et al. appeared, several laboratories had reported that they could not detect XMRV in CFS patients. But Ruscetti and Mikovits note that most of these studies relied on polymerase chain reaction, which used DNA sequences of XMRV to fish out pieces of the virus from blood samples. Those tests, they point out, would have missed other gammaretroviruses with different sequences. The Western blot assay they used in Lombardi et al. just so happened to cast a wider net that uncovered proteins from any member of the gammaretrovirus family. In addition, they say, the use of 5-Azacytidine made clear that these infections would be missed in routine assays, as these viruses often exist in a latent state.
On the ERV blog, Smith and others also argued that the study lacked proper controls: the healthy controls in this experiment did not have 5-Azacytidine added to their samples. “My [principal investigator] would say ‘Why did you run this gel?' if I handed it to him,” wrote Smith.
Vinay Pathak, a retrovirologist at NCI who earlier damaged the XMRV/CFS theory with a study in published in Science that documented how the virus was accidentally created in laboratory experiments, says he is “bewildered” by Ruscetti's and Mikovits's explanations about Figure 2C. “If [5-Azacytidine] was used in the original experiment, it's an egregious error to leave it out of the Science paper,” says Pathak. “It makes a difference how I would interpret the results.”
Jonathan Stoye, a retrovirologist who once supported the XMRV/CFS hypothesis but subsequently changed his mind after his own studies failed to replicate the finding, says its time to retract Lombardi et al. in its entirety. “I think there's a point where Science has to say, there is no substance to this paper,” says Stoye. “It was published with a message, and that message is gone.”
Neither Lombardi et al. nor the questions about the slides were mentioned in Whittemore's 30 September letter formally terminating Mikovits's contract, sent the day after the two had a heated phone conversation. In that letter Whittemore charged her high-profile researcher with being “insubordinate and insolent.” Mikovits was immediately locked out of her lab.
Three letters between Whittemore and Mikovits say the firing hinged on Mikovits's failure to pass on a cell line that was sent to Vincent Lombardi, the first author of the October 2009 Science paper who runs UNEVX (formerly known as VIPDx), a diagnostic laboratory owned by WPI. Until recently, the lab sold a test for XMRV and related viruses.
In a 1 October written response to Whittemore, Mikovits contended that it was “completely appropriate” for her, as research director, not to give Lombardi the cell line. The cell line was not related to studies of the gammaretroviruses, but Lombardi wanted to use it for experiments connected to a grant Mikovits had secured from the U.S. National Institutes of Health to study possible causes of CFS. Mikovits contended that Lombardi “was unwilling to take my direction” and should not be undertaking a new project “while neglecting his other duties.” She also questioned his ability to carry out that experiment.
Annette Whittemore issued a statement to Science in which she strongly defended Lombardi's performance. “Dr. Lombardi is a valued and important part of our team, and conducts his research work accordingly,” wrote Whittemore. “While personnel matters are generally confidential, the statements made by Judy Mikovits are wrong, without merit and those of a disgruntled former employee.”
In an interview with Science, Mikovits contended that her firing was also linked to a longstanding battle about WPI's decision to sell, through VIPDx/UNEVX, a test for human gammaretroviruses. The lab began offering the tests, which cost around $500, shortly after Lombardi et al. reported a link between XMRV and CFS. Some patients who tested positive went on to take antiretroviral drugs. “I said, ‘No, no, no, no,' ” says Mikovits of the test. “I've asked them for the better part of 2 years to show me that what we got in Lombardi et al. is the same thing they're selling to patients.”
The issue came to a head with the recent publication by Science of the nine-lab study. The so-called Blood Working Group, which included the labs run by Mikovits and Ruscetti, failed to reliably find XMRV or other gammaretroviruses in blinded samples from people who previously had tested positive for these viruses. Both Mikovits and Ruscetti co-authored the paper, which invalidated their own assays for XMRV. WPI says UNEVX has stopped offering the diagnostic tests, but did not give details about the timing or reasons.
Whittemore, who refers to CFS as myalgic encephalomyelitis (ME)—a common name for CFS in Europe—stressed that the institute remains devoted to studying human gammaretroviruses in “ME and related diseases” and that no one there “would ever put self interest ahead of research or finding the causes of ME.”
Mikovits, who says she currently does not even have access to her laboratory notebooks, is looking for another institution to continue her work.
With reporting by Martin Enserink.
It is very apparent that people like Jonathan Stoye and John Coffin are using their positions to further their own agenda by try to get Lombardi et al. retracted. As their only reason to retract a paper is fraud, then they may as well be accusing Frank Ruscetti of fraud as he performed all the western blots for the paper.