“All very painful:” Two retractions to watch for, in eLife and PLOS ONE

We have news of two upcoming retractions, both following critiques on PubPeer.

PLOS ONE is retracting a 2012 paper by researchers at the Istituto Superiore di Sanità in Rome and the World Health Organization’s International Agency for Research on Cancer in Lyon, France, “Interferon-β Induces Cellular Senescence in Cutaneous Human Papilloma Virus-Transformed Human Keratinocytes by Affecting p53 Transactivating Activity.”

PubPeer commenters first left critiques of the paper on August 6 of last year, noting likely splicing and other manipulation of images. Several days later, pseudonymous whistleblower Claire Francis contacted the journal to flag similar issues. On Wednesday of this week, a journal representative emailed Francis to say the paper would be retracted:

I am sorry we have not provided an update on this case much sooner. We completed our follow-up on this matter, and in light of the concerns you raised and other issues that came to light in our editorial assessment we retracted the above article. In about two weeks, you will be able to view the retraction notice through the article’s webpage or at doi.org/10.1371/journal.pone.0214341.

The paper has been cited 21 times, according to Clarivate Analytics’ Web of Science. The corresponding author, Giovanna Romeo, has not responded to a request for comment.

‘This was all very painful….!’

Separately, Karin Schumacher, of Heidelberg University, announced on Twitter Wednesday that she would be retracting a paper she and colleagues published in eLife in February. The move followed comments on PubPeer about potential manipulation of images in the paper, “Pyrophosphate modulates plant stress responses via SUMOylation.”

Schumacher had responded to the comments within days, first sending the original images and then writing:

I finally had the chance to discuss the matter with my colleagues. The blots in Figure 3E have indeed been manipulated in an inappropriate manner and we are very grateful that you brought this to our attention. However, the manipulation does not affect the outcome of the experiment. Our conclusion that SUMOylation is reduced in fugu5 is based on the quantification of independent replicate experiments. In the meantime, we are running another repetition of the experiment to be able to provide a suitable blot for the figure. Beyond that, everybody involved has learned a very painful lesson and we all hope to proof in the future that this was an exceptional break of the rules of good scientific practice and does not at all reflect how we do science!

On Wednesday of this week, Schumacher posted:

Update: We have initiated retraction of eLife 2019;8:e44213 based on irregularities associated with the Western Blots shown in Figures 3D and E as well as Figures 4C and D performed by Gorkem Patir-Nebioglu (GPN). Initiated by reports on PubPeer, we have further investigated the matter and have found that in both Figures 3 and 4 blots were spliced together from different original images without indication and a single lane was copied twice in Figure 3E. In addition, GPN has admitted to have intentionally loaded less protein for fugu5 at 4°C (Figure 3) and 40°C (Figure 4). Both issues represent severe violations of the rules of good scientific practice and retraction of the manuscript is thus mandatory.

We are currently running independent repetitions of the experiments in question and hope to be able to clarify the situation in the near future. In the meantime, our sincere apologies go to all of our collaborators and readers of our manuscript.

Schumacher, who did not respond to a request for comment, earned plaudits on Twitter for the move.

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8 thoughts on ““All very painful:” Two retractions to watch for, in eLife and PLOS ONE”

  1. More worrying are problematic data from the World Health Organization’s International Agency for Research on Cancer in Lyon, France.

    This paper includes data which appeared 2 years earlier in another journal. See comments #5, #6 and #16 (#6 and #16 are different illustrations showing the same thing) for the Pubpeer page below. There are also internal problematic data.
    https://pubpeer.com/publications/7954D730B35DF13A053ACA5B301779

  2. Another Giovanna Romeo/Massimo Tommasino co-production.
    J Cancer Res Clin Oncol. 2016 Aug;142(8):1751-63.

    https://pubpeer.com/publications/DD9B9F8212398AB85858299126AC96

    Most problematic is figure 3E.
    https://pubpeer.com/publications/DD9B9F8212398AB85858299126AC96#4

    J Cancer Res Clin Oncol. 2016 Aug;142(8):1751-63. doi: 10.1007/s00432-016-2189-1. Epub 2016 Jun 14.
    Human papillomavirus E6 and E7 oncoproteins affect the expression of cancer-related microRNAs: additional evidence in HPV-induced tumorigenesis.
    Chiantore MV1, Mangino G2, Iuliano M2, Zangrillo MS2, De Lillis I3, Vaccari G4, Accardi R5, Tommasino M5, Columba Cabezas S6, Federico M7, Fiorucci G3,8, Romeo G3,2,8.
    Author information
    1
    Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy. mariavincenza.chiantore@iss.it.
    2
    Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100, Latina, Italy.
    3
    Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
    4
    Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, 00161, Rome, Italy.
    5
    Infections and Cancer Biology Group, International Agency for Research on Cancer, 69372, Lyon, France.
    6
    Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, 00161, Rome, Italy.
    7
    National AIDS Center, Istituto Superiore di Sanità, 00161, Rome, Italy.
    8
    Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, 00161, Rome, Italy.

  3. Another problematic Massimo Tomassino, Infections and Cancer Biology Group, IARC-WHO, Lyon, France, publication.
    https://journals.plos.org/plosone/article/authors?id=10.1371/journal.pone.0003529

    PLoS One. 2008;3(10):e3529.
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003529
    HPV16 E7-Dependent Transformation Activates NHE1 through a PKA-RhoA-Iinduced Inhibition of p38alpha
    Rosa A. Cardone, Giovanni Busco, Maria R. Greco, Antonia Bellizzi, Rosita Accardi, Antonella Cafarelli, Stefania Monterisi, Pierluigi Carratù, Valeria Casavola, Angelo Paradiso, Massimo Tommasino, Stephan J. Reshkin
    Published: October 27, 2008https://doi.org/10.1371/journal.pone.0003529

    Pubpeer: https://pubpeer.com/publications/9557CE3A5261A9E78327D48F4F1409#2
    https://pubpeer.com/publications/9557CE3A5261A9E78327D48F4F1409#4

  4. J Exp Med. 2013 Jul 1;210(7):1369-87. doi: 10.1084/jem.20122394. Epub 2013 Jun 10.
    The human papillomavirus type 16 E7 oncoprotein induces a transcriptional repressor complex on the Toll-like receptor 9 promoter.
    Hasan UA1, Zannetti C, Parroche P, Goutagny N, Malfroy M, Roblot G, Carreira C, Hussain I, Müller M, Taylor-Papadimitriou J, Picard D, Sylla BS, Trinchieri G, Medzhitov R, Tommasino M.
    Author information
    1
    Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon 69008, France.

    https://pubpeer.com/publications/6C356C3FF471E2A7336C26468D762D

  5. Virology. 2007 Oct 10;367(1):1-9. Epub 2007 Jun 12.
    E7 properties of mucosal human papillomavirus types 26, 53 and 66 correlate with their intermediate risk for cervical cancer development.
    Mansour M1, Touka M, Hasan U, Bellopede A, Smet A, Accardi R, Gabet AS, Sylla BS, Tommasino M.
    Author information
    1
    Infections and Cancer Biology Group, International Agency for Research on Cancer, 150 cours Albert-Thomas, 69008 Lyon, France.

    https://pubpeer.com/publications/8B9BBDB02738F9DEB83FEF92464424

  6. J Immunol. 2007 Mar 1;178(5):3186-97.
    TLR9 expression and function is abolished by the cervical cancer-associated human papillomavirus type 16.
    Hasan UA1, Bates E, Takeshita F, Biliato A, Accardi R, Bouvard V, Mansour M, Vincent I, Gissmann L, Iftner T, Sideri M, Stubenrauch F, Tommasino M.
    Author information
    1
    International Agency for Research on Cancer-World Health Organization, 150 Cours Albert-Thomas, 69372 Lyon Cedex 08, France.

    https://pubpeer.com/publications/691F44D1935B173551D378F7491CBB

  7. J Biol Chem. 1985 Mar 25;260(6):3833-8.
    From PDF.
    Establishment of the Antiviral State in a,@-Interferon-resistant Friend
    Cells Treated with alpha,beta-Interferon
    INDUCTION OF 67-KILODALTON PROTEIN KINASE ACTIVITY IN ABSENCE OF DETECTABLE 2-5A
    SYNTHETASE*
    (Received for publication, August 2, 1984)
    Giovanna Romeo$, Elisabetta AffabrisS, Maurizio FedericoS, Nadir MechtiP, Eliana M. Coccia$,
    Cristina Jemma$, and Giovanni B. Rossi$
    From the $Departments of Virology, Zstituto Superiore di Sanita, and of Cellular and Developmental Biology, University of Rome, Rome, Italy and the SLaboratoire de Biochimie des Proteines, Equipe de Recherche Associee Centre Nationale de la Recherche Scientifique 482, University of Montpellier IZ, Montpellier, France.

    https://pubpeer.com/publications/DE4CB5B9D1AF19857026264682E2F2

  8. 2nd 2019 retraction Massimo Tommasino.
    PLoS One. 2008;3(10):e3529. doi: 10.1371/journal.pone.0003529. Epub 2008 Oct 27.
    HPV16 E7-dependent transformation activates NHE1 through a PKA-RhoA-induced inhibition of p38alpha.
    Cardone RA1, Busco G, Greco MR, Bellizzi A, Accardi R, Cafarelli A, Monterisi S, Carratù P, Casavola V, Paradiso A, Tommasino M, Reshkin SJ.
    https://journals.plos.org/plosone/article/authors?id=10.1371/journal.pone.0003529
    Rosa A. Cardone
    AFFILIATION Department of General and Environmental Physiology, University of Bari, Bari, Italy

    Giovanni Busco
    AFFILIATION Department of General and Environmental Physiology, University of Bari, Bari, Italy

    Maria R. Greco
    AFFILIATION Department of General and Environmental Physiology, University of Bari, Bari, Italy

    Antonia Bellizzi
    AFFILIATION Clinical Experimental Oncology Laboratory, National Cancer Institute Giovanni Paolo II, Bari, Italy

    Rosita Accardi
    AFFILIATION Infections and Cancer Biology Group, IARC-WHO, Lyon, France

    Antonella Cafarelli
    AFFILIATION Department of General and Environmental Physiology, University of Bari, Bari, Italy

    Stefania Monterisi
    AFFILIATION Department of General and Environmental Physiology, University of Bari, Bari, Italy

    Pierluigi Carratù
    AFFILIATION Department of Respiratory Medicine, University of Bari, Bari, Italy

    Valeria Casavola
    AFFILIATION Department of General and Environmental Physiology, University of Bari, Bari, Italy

    Angelo Paradiso
    AFFILIATION Clinical Experimental Oncology Laboratory, National Cancer Institute Giovanni Paolo II, Bari, Italy

    Massimo Tommasino
    AFFILIATION Infections and Cancer Biology Group, IARC-WHO, Lyon, France

    Stephan J. Reshkin
    * E-mail: reshkin@biologia.uniba.it

    AFFILIATION Department of General and Environmental Physiology, University of Bari, Bari, Italy

    2019 retraction notice 2nd retraction.
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0218402

    Following publication of [1], the following concerns were noted:

    Figure 1A: E7 and GAPDH panels appear to contain background irregularities;
    Figure 1B: the bands in the total p38 and total JNK panels appear similar, cropped and adjusted for brightness and contrast;
    Figure 1C: total ERK1/2 panel contains vertical discontinuities;
    Figure 1C: GAPDH panel appears similar to the Figure 1B GAPDH panel 1B;
    Figure 2A: E7 panel has a vertical change in background between the nc and +tet lanes;
    Figure 2A: GAPDH panel background appears dissimilar between bands;
    Figure 4B: Phospho-p38 panel has a vertical change in background between the middle lanes;
    Figure 5A: Phospho RhoA and total RhoA panels have been heavily adjusted for brightness/contrast;
    Figure 6A: Active RhoA panel has vertical discontinuities between the 3 and 6 hr bands.
    The corresponding author does not agree with the concerns raised and provided images in relation to Figure 1B totp38 and totJNK panels, Figure 1C total ERK panel, Figure 2A GAPDH and E7 panels, Figure 4B Phospho-p38 panel, Figure 5A phospho RhoA panel and Figure 6A Active RhoA panel, but these do not satisfactorily resolve the concerns raised for these items. The primary data underlying other figure panels has not been provided, which was attributed to the time that has passed since publication.

    In light of the unresolved concerns that question the validity of the study’s findings, the PLOS ONE Editors retract the article.

    RAC, MRG, PC, VC, MT, and SJR did not agree with retraction. GB, AB, RA, AC, SM, and AP did not respond.

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