Stem cell researchers fix two papers following PubPeer comments

Screen Shot 2016-04-13 at 5.56.09 PMA pair of stem cell researchers have earned two corrections, the result of images that were mislabeled, distorted, or compiled incorrectly, according to the notices.

Kang Cheng prepared the gels when he was a research fellow in last author Sanjeev Gupta‘s lab at the Albert Einstein College of Medicine. Gupta told us he reviewed the original gels, and the errors didn’t affect the conclusions in the papers, which were reproducible. He noted he believes the problems are the result of honest mistakes:

The errors did not confer any benefits whatsoever either for the papers or for Dr. Cheng.

On PubPeer, commenters have raised questions about the now corrected papers — along with several others on which Gupta is the senior author, but Cheng is not a co-author.

Edward Burns, research integrity officer at Einstein, told us that the medical school looked into an allegation of misconduct against Gupta:  

Our committee, after extensive review of primary data concluded that Dr. Gupta was not at fault but one of his lab staff had been sloppy in the preparation of gels.

Here’s the erratum (published in 2015) for “Switching of mesodermal and endodermal properties in hTERT-modified and expanded fetal human pancreatic progenitor cells,” by Stem Cell Research & Therapy:

After publication of our article [1], errors were noticed in the composition of data in Figures threeC, fiveD and sixA (Figs. 1c,2d and 3a here respectively). The data from original gels were incorrectly compiled or modified by the first author, Dr. K. Cheng, which was not noticed by the other authors.

The erratum includes new versions of each gel, and explains what was wrong with the originals:

In figure threeC (Fig. 1c here) the original gels for the following genes were incorrectly represented – GATA-2, GATA-6, ISL-1, Pdx1, CGA, GK, TGF-α, TGF-β1, TGF-β2, TGF-β2R, and GAPDH. Expression of these genes in mature islets was verified by additional studies.

In figure fiveD (Fig. 2d here) some of the lanes were cut out of the composition, and others were mislabeled.

In figure sixA (Fig. 3a here) the published figure was erroneously composed with incorrect or distorted images.

The correct figures are provided here. These errors do not affect the results or conclusions of our study.

The 2010 paper has been cited once, according to Thomson Reuters Web of Science.

The correction addresses issues that were raised by commenters on PubPeer in 2014.

The authors have also corrected “Hepatic targeting and biodistribution of human fetal liver stem/progenitor cells and adult hepatocytes in mice,” published in 2009 by Hepatology and cited 23 times.

Here’s the full erratum, also issued in 2015:

…errors in composition of Fig. 5A,B were noted recently. In column 6 of Fig. 5A, GAPDH band for intestine was from a separate part of the gel, as correctly shown below. In Fig 5B for 1h, GAPDH band for liver was not included, leading to incorrect ordering of subsequent lanes, which should have been provided as shown below. In column 2 of Fig. 5B for 1wk, CMT1A and GAPDH bands for spleen were from a different gel, as correctly shown below. These errors did not affect data interpretation or conclusions.

hep27697-fig-0001

The erratum also addresses concerns raised on PubPeer in 2014.

Gupta told us how he found out about the issues in the papers:

These came to my notice through communications from editors of the journals. They indicated concerns were raised by undisclosed reader or readers.

We asked if Cheng was still in Gupta’s lab; he said:

No, Kang Cheng left my lab in 2009 after completing his contract and is no longer in science.

Gupta also told us:

I believe Kang Cheng performed his work with honesty. Obviously, some of the gels in these two papers were not properly represented, which certainly escaped my notice. However, review of original gels for the papers, including various replicates that approached nearly a hundred gels, indicated the findings, conclusions and discussion in the papers were all correct and had been reproducible. The errors did not confer any benefits whatsoever either for the papers or for Dr. Cheng. The editors of both journals reviewed original gels and were also in agreement with that determination.

He added that he has learned from the experience:

I think it’s very important to make distinctions between fraud and deceit versus genuine quality control issues or errors related to data compilations, gels, microphotographs, etc. Needless to say, we at Einstein make efforts continuously  to inculcate sound practices and conduct in our trainees and colleagues, including by personal examples and formal coursework, but the process does require trust at multiple levels without the big brother (or sister) watching over the shoulder at all times. In my own case, these instances have been learning experiences for enhancing oversight of trainees.

We asked Gupta about the papers questioned on PubPeer that don’t list Cheng as a co-author; he has not yet replied to that question.

We reached out to the editors of both journals for more information. The editor of Stem Cell Research & Therapy passed our query on to a spokesperson for the journal’s publisher, BioMed Central, who declined to comment.

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3 thoughts on “Stem cell researchers fix two papers following PubPeer comments”

  1. “Phenotype reversion in fetal human liver epithelial cells identifies the role of an intermediate meso-endodermal stage before hepatic maturation”
    Mari Inada, Antonia Follenzi, Kang Cheng, Manju Surana, Brigid Joseph, Daniel Benten, Sriram Bandi, Hong Qian, Sanjeev Gupta, J. Cell. Sci., 121 (2008)
    http://jcs.biologists.org/content/121/7/1002
    https://www.pubpeer.com/publications/18319302

    “Isolated small intestinal segments support auxiliary livers with maintenance of hepatic functions”
    Brigid Joseph, Ekaterine Berishvili, Daniel Benten, Vinay Kumaran, Ekaterine Liponava, Kuldeep Bhargava, Christopher Palestro, Zurab Kakabadze, Sanjeev Gupta, Nat. Med., 10 (2004)
    http://www.nature.com/nm/journal/v10/n7/full/nm1057.html
    https://www.pubpeer.com/publications/15170210

    “Immunosuppression using the mTOR inhibition mechanism affects replacement of rat liver with transplanted cells”
    Yao-Ming Wu, Brigid Joseph, Sanjeev Gupta, Hepatology, 44 (2006)
    http://onlinelibrary.wiley.com/doi/10.1002/hep.21277/abstract
    https://www.pubpeer.com/publications/16871590

    “Transplantation of bone marrow-derived MSCs improves cisplatinum-induced renal injury through paracrine mechanisms”
    Kang Cheng, Partab Rai, Andrei Plagov, Xiqian Lan, Dileep Kumar, Divya Salhan, Shabina Rehman, Ashwani Malhotra, Kuldeep Bhargava, Christopher J. Palestro, Sanjeev Gupta, Pravin C. Singhal, Experimental and Molecular Pathology (2013)
    http://www.sciencedirect.com/science/article/pii/S0014480013000403
    https://www.pubpeer.com/publications/35AE81DBE3A6A9383268F8131917A1

    “Transplanted endothelial cells repopulate the liver endothelium and correct the phenotype of hemophilia A mice”
    Antonia Follenzi, Daniel Benten, Phyllis Novikoff, Louisa Faulkner, Sanj Raut, Sanjeev Gupta, Journal of Clinical Investigation (2008)
    http://www.jci.org/articles/view/32748
    https://www.pubpeer.com/publications/2C093420143131124E4B20672C3FB4

    “TGF-β and Iron Differently Alter HBV Replication in Human Hepatocytes through TGF-β/BMP Signaling and Cellular MicroRNA Expression”
    Sun O. Park, Mukesh Kumar, Sanjeev Gupta, PLoS ONE (2012)
    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039276
    https://www.pubpeer.com/publications/89AC6C5BBE86BA006AD61ADD772769

    “Novel hepatic progenitor cell surface markers in the adult rat liver”
    Mladen I Yovchev, Petar N Grozdanov, Brigid Joseph, Sanjeev Gupta, Mariana D Dabeva, Hepatology, 45 (2007)
    http://onlinelibrary.wiley.com/doi/10.1002/hep.21448/pdf
    https://www.pubpeer.com/publications/17187413

    “Embryonic mouse STO cell-derived xenografts express hepatocytic functions in the livers of nonimmunosuppressed adult rats”
    Mingjun Zhang, Brigid Joseph, Sanjeev Gupta, I Guest, Meng Xu, Stewart Sell, Kyung-Hwa Son, Katherine S Koch, Hyam L Leffert, Stem Cells, 23 (2005)
    http://onlinelibrary.wiley.com/doi/10.1634/stemcells.2004-0129/abstract
    https://www.pubpeer.com/publications/15671142

  2. 2nd author on

    Switching of mesodermal and endodermal properties in hTERT-modified and expanded fetal human pancreatic progenitor cells.
    Cheng K, Follenzi A, Surana M, Fleischer N, Gupta S.
    Stem Cell Res Ther. 2010 Mar 15;1(1):6.

    Antonia Follenzi, has Pubpeer entries without S Gupta.

    J Biol Chem. 2007 Nov 2;282(44):31900-8. Epub 2007 Sep 11.
    Role of MAPK phosphatase-1 in sustained activation of JNK during ethanol-induced apoptosis in hepatocyte-like VL-17A cells.
    Venugopal SK1, Chen J, Zhang Y, Clemens D, Follenzi A, Zern MA.
    Author information
    1Department of Internal Medicine, Transplant Research Program, UC Davis Medical Center, Sacramento, California 95817, USA.

    https://pubpeer.com/publications/17848570
    Figure 1A.
    http://i.imgur.com/EizauY2.jpg

    Figures 1A and 5C.
    http://i.imgur.com/NAde3RU.jpg

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