Déjà vu: JBC epigenetics paper is retracted, then largely re-published with fewer authors

A group of authors have withdrawn a 2011 Journal of Biological Chemistry paper, but then appear to have re-published almost the same paper a month later, only this time with just five of the original nine authors.

The paper, “HDAC3-dependent reversible lysine acetylation of cardiac myosin heavy chain isoforms modulates their enzymatic and motor activity,” concerns a type of protein regulation important to cardiac stress. Written by researchers at the University of Chicago and the University of Pittsburgh, it has been cited 16 times, according to Thomson Scientific’s Web of Knowledge. It was rated “Exceptional” by a reviewer on the Faculty of 1000 website.

As we’ve come to expect from the JBC, here’s the full retraction notice, in all its inexplicit glory:

This article has been withdrawn by the authors.

Here’s where it gets strange: As far as we can tell, the 2011 paper was retracted in March, but then re-published, with the same title and almost exact same text, in April.

The single major difference we can find between the two papers is that the 2015 version leaves out four of the 2011 authors: David S. Courson, Minjia Tan, Yingming Zhao, and Ronald S. Rock, all of the University of Chicago.

For an example of the similarity between the two papers, here’s the abstract of the retracted December 21, 2010 paper:

Reversible lysine acetylation is a widespread post-translational modification controlling the activity of proteins in different subcellular compartments. We previously demonstrated that a class II histone deacetylase (HDAC), HDAC4, and a histone acetyltransferase, PCAF, associate with cardiac sarcomeres, and a class I and II HDAC inhibitor, trichostatin A, enhances contractile activity of myofilaments. In this study, we show that a class I HDAC, HDAC3, is also present at cardiac sarcomeres. By immunohistochemical and electron microscopic analyses, we found that HDAC3 was localized to the A band of sarcomeres and was capable of deacetylating myosin heavy chain (MHC) isoforms. The motor domains of both cardiac – and -MHC isoforms were found to be reversibly acetylated. Biomechanical studies revealed that lysine acetylation significantly decreased the Km for the actin-activated ATPase activity of both – and -MHC isoforms. By an in vitro motility assay, we found that lysine acetylation increased the actin sliding velocity of -myosin by 20% and -myosin by 36%, compared to their respective non-acetylated isoforms. Moreover, myosin acetylation was found to be sensitive to cardiac stress. During induction of hypertrophy, myosin isoform acetylation increased progressively with duration of stress stimuli, independent of isoform shift, suggesting that lysine acetylation of myosin could be an early response of myofilaments to increase contractile performance of the heart. These studies provide the first evidence for localization of HDAC3 at myofilaments and uncover a novel mechanism modulating the motor activity of cardiac MHC isoforms.

And here’s the abstract of the April 24, 2015 paper. The differences, which we’ve highlighted in bold, are only cosmetic:

Reversible lysine acetylation is a widespread post-translational modification controlling the activity of proteins in different sub-cellular compartments. We previously demonstrated that a class–II HDAC, HDAC4 and a HAT, PCAF associate with cardiac sarcomeres, and a class-I and -II HDAC inhibitor, trichostatin A, enhances contractile activity of myofilaments. In this study we show that a class-I HDAC, HDAC3 is also present at cardiac sarcomeres. By immuno-histochemical and electron microscopic analyses we found that HDAC3 was localized to A–band of sarcomeres, and was capable of deacetylating myosin heavy chain (MHC) isoforms. The motor domains of both cardiac α- and β-MHC isoforms were found to be reversibly acetylated. Biomechanical studies revealed that lysine acetylation significantly decreased the Km for the actin-activated ATPase activity of MHC isoforms. By in vitro motility assay we found that lysine acetylation increased the actin-sliding velocity of α-myosin by 20% and β-myosin by 36%, compared to their respective non-acetylated isoforms. Moreover, myosin acetylation was found to be sensitive to cardiac stress. During induction of hypertrophy, myosin isoform acetylation increased progressively with duration of stress-stimuli, independent of isoform shift, suggesting that lysine acetylation of myosin could be an early response of myofilaments to increase contractile performance of the heart. These studies provide first evidence for localization of HDAC3 at myofilaments and uncover a novel mechanism modulating the motor activity of cardiac MHC isoforms.

We asked the JBC to explain what happened. Karou Sakabe, manager of publication issues at the American Society for Biochemistry and Molecular Biology, the publisher of the JBC, wrote:

It is JBC policy to maintain confidentiality in such matters.  Please direct your inquiry to Dr. Gupta.

We should note that although this is what we’ve come to expect from the JBC, it’s nonetheless disappointing that they continue to squander an opportunity. In 2012, the ASBMB created a new position, “manager of publication ethics,” with a job description that included “Write and/or help authors write corrections and retractions.” We were hopeful that it would lead to appropriately detailed retraction notices, but with rare exception, that has not been the case. (The position no longer appears on their staff list, but Sakabe’s role would appear to have taken its place. ) We recognize that opaque notices aren’t the fault of the person in that job, but of senior ASBMB management who stubbornly stick to policies that aren’t good for science.

In any case, we have repeatedly reached out to corresponding author Mahesh P. Gupta (the last author on both versions) and co-author of paper #1 Ronald Rock in the hopes of more information. We’ll update if we hear back.

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