In June of 2020, officials from the Veterans Affairs Medical Center of San Francisco and the University of California, San Francisco, sent a letter to the journal Oncogene with the findings of an investigation of scientific misconduct: A paper the journal had published in 2007 contained “falsified data,” and the officials recommended the journal “assess this paper for retraction.”
The 2020 letter – which we obtained through a public records request – was the second time the institutions had alerted the journal. As the officials stated, a previous investigation had found issues in the 2007 paper, and UCSF-VA had communicated “earlier evidence that this same paper had data fabrication and/or falsification constituting research misconduct” to the journal in 2017.
“Even though the journal has been notified after the last investigation and not taken action,” the 2020 letter stated, “they should be notified again because additional research misconduct has been found.”
In fact, a journal staffer was in the midst of discussing the issues in the article with Rajivir Dahiya, the corresponding author and then director of UCSF’s Urology Research Center with an appointment at the San Francisco VA Medical Center, according to emails seen by Retraction Watch.
As we’ve reported previously, Dahiya, who retired in 2020 and is now a professor emeritus of urology, has had four papers retracted after UCSF and the VA sent letters to journal editors saying that an investigation had found “fabrication or falsification of data” in the articles.
The 2020 letter from UCSF-VA officials confirms that the institutions conducted two investigations that found research misconduct, although neither inquiry could determine who was responsible for the faked data.
Judging from Dahiya’s correspondence with Oncogene, the letter also appears to have been a decisive factor for the journal’s editors. After receiving it, they moved forward with retracting the paper in question, despite the researcher’s objections. The emails also indicate the journal has been investigating another paper of Dahiya’s since at least 2019, with no resolution yet.
The retracted paper, “Knockdown of astrocyte-elevated gene-1 inhibits prostate cancer progression through upregulation of FOXO3a activity,” was pulled last October, and has been cited nearly 200 times, according to Clarivate’s Web of Science.
“The major problem was that this paper is about 16 years old and the investigation started in 2016,” Dahiya told us.
When the investigation committee asked for the original data, the authors couldn’t provide them. The first author who did the experiments had left for another institution, and Dahiya’s lab had moved. The lab’s notebooks had been stored in a centralized location, he said, and the VA/UCSF discarded the materials after the National Institutes of Health’s mandated five year data retention period.
Dahiya blamed the retractions on the VA/UCSF not keeping the old notebooks:
All the journals that published our papers did not have any problems with the data. But the VA/UCSF committee members forced these journals to retract our papers. It is strange that on one hand VA/UCSF discarded our original research data notebooks and on the other hand they blamed us that we did not have original data and thus we falsified the data.
It seems Oncogene’s editors did have questions about the data, according to Dahiya’s emails with the journal that he shared with Retraction Watch.
In November 2019, Dahiya sent a journal staffer new data from experiments he and his coauthors had repeated in response to questions about the 2007 paper. “The results are consistent with the results given in Paper and thus does not change the results or the conclusion of the paper,” he wrote.
Six months later, in May 2020, the staffer responded with “sincere apologies for not getting back to you sooner” and several detailed questions from the editors about the new data compared to the original.
For some of the new figures, the editors pointed out that the result “goes against what is written in the original paper.” Other figures were “not that convincing and as clear as the original ones.”
Dahiya sent a point-by-point response 10 days later. He concluded:
We believe that your editorial members will find our responses satisfactory and resolve these issues.
The next email from the journal, which came a week later, indicated the editor still had some questions:
Unless sufficient responses can be made to the editors questions, it is likely that the next course of action will be to retract this paper.
After a few weeks, during which Dahiya wrote that he could not go into the lab “due to COVID-19 lockdown and protests,” he sent additional data and responses to the editors’ comments. On July 20, 2020, he wrote:
We are highly grateful to the editorial board members for giving us a chance to address the concerns. We have really worked very hard and sincerely put all efforts to address each and every comment and generated new data using all appropriate controls. We hope that these responses are satisfactory to the reviewers.
Nearly a year later, Dahiya heard back from the journal:
Sincere apologies for the time taken to get back to you regarding the below response you sent to the latest round of comments from the editors.
Just prior to receipt of your last email, we received a report from the Investigation Committee on Scientific Misconduct of the Veterans Affair Medical Center, San Francisco, and the University of California San Francisco, which concludes that that [sic] several figures are the result of fabrication or falsification. Following receipt of this report the Editors propose that your paper be retracted.
The email included a draft of the retraction note that was later published. It stated that each author would need to communicate whether or not they agreed with the retraction. Dahiya responded on July 8, 2021:
We have carried out a series of experiments during the last two years to address all the concerns raised by the UCSF / VA investigation committee. All the original data was submitted to your journal and all concerns were addressed. Now under the pressure of UCSF/VA committee, the Editor has decided to retract our paper.
We (all authors) do not agree with the decision to retract our article by the Editors-in-Chief.
The retraction notice appeared online more than a year later, in October 2022, and referenced the committee’s findings “that Figures 2b, 4b, 4c, 5a and 5c are the results of fabrication or falsification of data.”
Commenters on PubPeer had drawn attention to those figures in the paper as far back as December 2013, but none of the authors responded on the site.
The recent letter from the VA/UCSF to Oncogene, dated June 30, 2020, stated that the investigation committee had found falsified data in figures 4b, 4c, 5a, and 5c. The committee concluded “that falsification occurred because the same bands were used to represent different experimental conditions,” and that the “nature of this manipulation makes it unlikely to have occurred by error.”
The letter also noted that the committee “could not determine who was responsible for the falsification of data,” and that none of the original data was available.
In a passage that echoed the investigation report, the letter detailed Dahiya’s defense of the paper, which the committee did not find convincing:
The senior author, Dr. Rajvir Dahiya, “provided line scans of the analysis given to him by the first author of the published figures” Dr. Noboyuki Kikuno. The Committee reported that “Dr. Dahiya has corresponded with first author, Dr. Kikuno, and claims he has forwarded the densitometry readings of the published blots, not the original data and is convinced that the bands are different.” However, the “Investigation Committee does not accept the densitometry as valid but rather finds the forensic analyses (Exhibit 1, pp. 2, 3) more compelling.” Therefore, the Committee did not make a definitive determination of who was responsible for the falsification of data that constitutes Research Misconduct.
The VA/UCSF officials concluded with their recommendation to retract the paper, and reiterated the findings sent to the journal in 2017.
Despite the 2020 letter’s statement that the journal had “not taken action” after the 2017 letter, a spokesperson for Springer Nature, which publishes Oncogene, told us that the editors of the journal and the research integrity group had launched an investigation in response:
Unfortunately, the investigation took somewhat longer than anticipated to complete. For context, while we appreciate that delays can be frustrating, there are a variety of reasons why our investigations can sometimes take longer to complete. When looking into issues, we may need to consult external experts, liaise with author institutions or COPE, or wait for authors to confer with their colleagues, prepare responses and, where appropriate, provide additional materials. Analysing raw data or assessing other evidence, which may require technical translations, can also be a lengthy process.
While we endeavour to proceed with investigations as swiftly and efficiently as possible, these factors, among others, can mean that it is not possible to update our readers as quickly as we would prefer.
Once we had completed our investigation and considered all options, we concluded that retracting the paper was the appropriate course of action to take.
The investigation into another of Dahiya’s papers at Oncogene, “Promoter CpG hypomethylation and transcription factor EGR1 hyperactivate heparanase expression in bladder cancer,” is taking even longer.
The article was published in 2005, and has been cited 74 times. In 2013, a PubPeer commenter pointed out “many similarities” between two panels of figure 6a in the paper.
Dahiya’s emails with the journal included one with new data and a response to the observation that bands in the 2005 paper’s figure 6 “are similar with different exposures,” which he sent on Sept. 18, 2019. He later sent the new data and responses to comments on the 2007 paper in the same thread, with the subject line “Two Oncogene articles under investigation.” None of the journal’s responses we saw seem to address the 2005 paper.
The Springer Nature spokesperson confirmed that the investigation into the 2005 paper, which remains intact without an editor’s note of any kind, “is still ongoing.”
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No doubt the Oncogene editors have had other important matters on their plates.
From https://retractionwatch.com/2022/12/08/professor-emeritus-loses-fourth-paper-after-ucsf-va-investigation-five-years-after-other-retractions/
“[Co-Editor in Charge Justin] Stebbing did not respond directly to our questions, but instead noted our previous story about an Oncogene retraction in which we mentioned he had been suspended from practicing medicine for nine months last year – which he called “my previous regulatory issues” – and that he’d had a paper retracted after readers raised questions about the data.”