Some quick background: the sequence hypothesis
central hypothesis dogma of biology states that DNA gets transcribed to RNA that gets translated into proteins. Some RNAs, however, don’t code for proteins, but instead help to regulate gene expression. These microRNAs are tiny in size, but can regulate gene expression across animal and plant kingdoms.
In September 2011, the Molecular Cell published an entire issue with regulatory RNA as its theme. V. Narry Kim, associate professor at Seoul National University and high-profile microRNA researcher contributed a study that her group has now retracted just months later on June 29.
The problem? A reagent used to purify miRNAs favors some miRNAs and fails to isolate those
rich low in guanine and cytosine — two of the four building blocks of RNA — or those with few secondary folding structures.
In this paper, we reported that the levels of specific microRNAs (miRNAs) decrease when cells are grown at low density or when cells are detached from a culture dish. Based on our results, we proposed that some miRNAs are selectively destabilized depending on the adhesion status of the cells. However, in subsequent studies, we discovered that structured miRNAs with low GC content, such as miR-141, miR-29b, miR-21, miR-106b, miR-15a, and miR-34a, are selectively lost during sample preparation rather than degraded in the cell. The small RNA loss occurs when a small number of cells is used for RNA preparation using the standard TRIzol protocol (see Kim et al. [pp. 893–895] in this issue for details). These findings provide an alternative explanation for our original data. While the original data are all reproducible, we are retracting the paper because we feel the main conclusions have been compromised. We apologize for any inconvenience this may have caused.
The group took their observation that led to the retraction one step further and conducted experiments to show how different reagents will isolate different populations of RNAs from small sample sizes. This is important since research before assumed that protocols isolated all kinds of RNA equally.
Along with the retraction notice, the group published a three-page letter to the editor with one figure that concludes:
Our current analyses indicate that structured small RNAs with low GC content are recovered inefficiently when a small number of cells is used for RNA isolation with TRIzol.
A spokesperson for Cell, the publisher of Molecular Cell, declined to comment. And we haven’t had a response from Life Technologies, which makes TRIzol. (Life Technologies, we should note, was the company that last year asked two of its employees to retract a paper because they’d submitted it without approval.)
Kim, however, was very forthcoming. She wrote us this email in response to our questions:
In brief, we found after publishing the original paper that our results were due to a technical problem associated with widely used Trizol reagent. When we used a different protocol (which is infrequently used in the field), we did not observe the same phenomenon. It turned out that small RNAs with low GC contents and/or secondary structure are lost from RNA purification when a small number of cells are used (miR-141 was a typical case). This is not due to a biological regulation, but a technical problem associated with Trizol reagent.
Our original data are reproducible regardless of scale. But we decided to retract the paper because the conclusion of the paper was mistaken. We interpreted the results based on an assumption that Trizol extracts all sorts of RNAs with equal yield. In fact, Trizol reagent has been used for decades to extract “total RNA” and has been the standard RNA extraction reagent. No one in the field has realized this problem before. My group found this problem from our own experiments without a help or notification from other groups.
After finding this problem, I contacted John Pham, an editor of Molecular Cell, who had handled our original paper. John was very surprised to hear the news but helped us enthusiastically in the process of retraction and publication of another article.
The new article was published as a Letter to the editor format, which is a type of peer-reviewed paper. The reviewers commended our new findings and were highly supportive of publishing the new article…I also received a number of supportive emails from scientists in the field regarding the publication of retraction.
Kim also had some thoughts on how retractions should be handled, and explained how this situation was very different from some other recent cases involving Seoul National University:
Although the whole process of finding the mistake and publishing a retraction was painful to my group, I strongly believe that scientists should not be afraid of retracting their own papers. Scientists inevitably live with a number of assumptions that may turn out to be wrong later. We also have a number of technical limitations which are unrecognized at the time of the study. So, making a mistaken conclusion is sometimes unavoidable. What is important is to be honest and to correct the mistake as soon as we realize it. I am very proud of my people who were smart enough to find and dissect the problem and brave enough to carry out additional experiments and retract the paper.
In this particular case, we and the reviewers felt that sharing the information is important because the technical issue is a general one and affects not only ours but also potentially many other people’s work. So we decided to publish the new article to warn the colleagues in the field.
This incident does not affect my research program. The particular project was just a part of my group’s research subjects. We continuously work on microRNAs to understand their regulation and function.
The SNU ethics committee was not involved in the retraction process at all. I did not notify them because there is no ethical violation here. My people and I have kept the highest standard of scientific integrity. This should be clearly distinguished from scientific misconduct. I believe that research community should respect and encourage honest retractions, instead of automatically associating retraction with misconduct.
We couldn’t agree more. Kudos to Kim for a transparent move that corrects the literature.