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Lopez-Otin and Daley retract Nature Cell Biology paper

The 2015 Nature Cell Biology paper by the Spanish cancer researcher Carlos Lopez-Otin and his US partner George Q Daley, stem cell titan and dean of Harvard Medical School, is being retracted. First author and Lopez-Otin's student Clara Soria-Valles caused Daley even more trouble: her next groundbreaking paper was meant to be already published, but it is not even submitted and might never be.

Boom, the 2015 Nature Cell Biology paper by the famous, award-winning and now fugitive Spanish cancer and ageing researcher Carlos Lopez-Otin and his US partner George Q Daley, stem cell titan and dean of Harvard Medical School, is retracted. That happens because correct original data was unavailable, prompted by a prolonged debate on PubPeer (which in turn followed my reporting on Lopez-Otin’s data integrity practices), which established that the figures do not match what the authors deposited as supplement.

The paper Soria-Valles et al 2015 established the role of the transcription factor protein NF-kB in cellular senescence and cell reprogramming, while offering a potential cure to child patients suffering from the deadly premature ageing syndrome, such as Néstor–Guillermo or Hutchinson–Gilford progeria. Under this premise, the impactful Nature-themed paper earned Lopez-Otin in 2017 an ERC grant of €2.5 million, for a project named “Deconstructing Ageing: from molecular mechanisms to intervention strategies“. Earlier this year however, Lopez-Otin abandoned his ERC funded lab at University of Oviedo and escaped to Paris, to stay with his Photoshop expert friend Guido Kroemer. If past behaviour is anything to go by, ERC will now probably again play three monkeys and pretend that Lopez-Otin is still in Spain and his grant-deciding Nature Cell Biology paper was never retracted.

Another Soria-Valles et al paper from Daley lab, which proposed a way to produce haematopoietic stem cells via iPS technology and save people with leukaemia, was meant to be already published, but it is not even submitted and might never be. This and the retracted study’s first author Clara Soria-Valles was a former PhD student of Lopez-Otin, funded by EMBO postdoctoral fellowship and delegated to the Harvard labs of Daley and his junior partner Thorsten Schlaeger, to learn cellular reprogramming technique. Daley and Schlaeger are reported to be all but ready to apply the blood cell making technique in the clinic, at Boston Children’s Hospital, but now nobody knows if Soria-Valles’ preclinical data is anywhere near reproducible.

It is indeed difficult to find out what results still might be reliable. Soria-Valles disappeared already in April 2018 on a medical leave, though Daley still pays her (neither Daley nor Harvard normally pays any medical leaves for other sick lab members). Nobody else on that manuscript is available, because the Schlaeger lab people involved also left since. Money to try and reproduce it is not an issue though: the research project was funded from Daley’s biggest grant, the NHLBI Progenitor Cell Translational Consortium (NIH U01), which is worth almost $50 million.

Screenshot_2018-12-05 Blood stem cell breakthrough 'tantalizingly close'
Breakthrough manuscript as yet not even submitted to a journal. Screenshot: UBS

As I was informed, that Soria-Valles paper on haematopoietic reprogramming was meant to be originally submitted to the elite Cell family journal Cell Stem Cell (this is how the circulated draft was labelled in April 2018). Later on, roughly in August 2018, when my article appeared, the chosen target journal was Stem Cell Reports (published by International Society for Stem Cell Research, ISSCR). For someone like Daley this is a huge status reduction of journal venue. The results were presented earlier by Soria-Valles at the ISSCR annual meeting in 2017:

INTEGRATION-FREE SYSTEM FOR GENERATION OF HEMATOPOIETIC STEM AND PROGENITOR CELLS FROM HUMAN PLURIPOTENT STEM CELLS
Soria-Valles, Clara 1 , Sugimura, Ryohichi 1 , Kumar Jha, Deepak 1 , Lummertz da Rocha, Edroaldo 1 and Daley, George 2
1 Boston Children’s Hospital, Boston, MA, USA, 2 Stem Cell Program, Boston Children´s Hospital, Boston, MA, USA
The generation of hematopoietic stem cells (HSCs) from human pluripotent stem cells (PSCs) constitutes a valuable tool with promising applications for research and therapy. However, derivation of HSCs with in vivo long-term engraftment and multi-lineage potential remains elusive. We have described a combinatorial approach, based on the directed differentiation of hemogenic endothelium (HE) and transduction with five transcription factors (TF) (RUNX1, ERG, LCOR, HOXA5 and HOXA9) expressed in lentiviral vectors that allowed the conversion of human PSCs into hematopoietic stem
and progenitor cells (HSPCs). The resulted cells exhibited long-term and multi-lineage hematopoietic capabilities when injected into irradiated immune-deficient mice.
Despite this proof of principle, the engineered cells have a limited self-renewal capacity due to the integration of the transgenes and are still molecularly distinct from bona fide HSCs. Thus, in an attempt to achieve bona fide HSCs and make them safer for future therapeutic interventions, we have established integration-free systems that have shown comparable efficiency to the previously developed lentiviral strategy through in vitro and in vivo experiments. Therefore, this new method may overcome some limitations of the lentiviral approach and hold the key for future regenerative medicine advances in blood diseases.

Soria-Valles however was not present at the 2018 ISSCR meeting (a conference which I incidentally wrote about here, in a story about another dishonest stem cell researcher, who was set to be ISSCR 2018 keynote speaker). Nobody knows how much of Soria-Valles’ claim to make haematopoietic stem cells via iPS technology is still valid. Sources were quoted with estimates of too low a yield or even not sure of producing any haematopoietic stem cells at all. Yet just this September 2018, Daley spoke at a lecture at Dana-Farber-Institute of his future Stem Cell Reports paper and even of his plans to apply the method to treat paediatric patients with congenital bone marrow deficiencies, in particular Shwachman Diamond Syndrome and Diamond Blackfan Anemia.

Screenshot_2018-12-05 University of Oviedo - nueva terapia logra reprogramar envejecimiento celular - News
Press release by University of Oviedo. Photo shows Soria-Valles with her fiancée and co-author Fernando Garcia Osorio

But now back to the main subject, the Nature Cell Biology retraction. The journal warned readers on 4 October 2018 with an editorial note that “that the reliability of data presented in this manuscript has been the subject of criticisms“. 4 December 2018 was the deadline imposed by the publisher to submit signatures from co-authors for a retraction. Lopez-Otin’s Oviedo colleague Jose Maria Perez Freije collected the signatures of all authors, including the elusive Soria-Valles, and submitted them to the publisher Nature.

This is the retraction notice:

“We, the authors, are retracting this Article due to issues that have come to our attention regarding data availability, data description and figure assembly. Specifically, original numerical data are not available for the majority of the graphs presented in the paper. Although original data were available for most EMSA and immunoblot experiments, those corresponding to the published EMSA data of Supplementary Fig. 8a, the independent replicate immunoblots of Fig. 8b and Supplementary Fig. 1e, and the independent replicate EMSA data of Supplementary Figs 6e, 8b, 8c and 8d, are unavailable. Mistakes were detected in the presentation of Figs 3c, 4i and Supplementary Figs 6a, 8a, 8d, 9, and in some cases the β-actin immunoblots were erroneously described in the figure legends as loading controls, rather than as sample processing controls that were run on separate gels. Although we, the authors, believe that the key findings of the paper are still valid, given the issues with data availability we have concluded that the most appropriate course of action is to retract the Article. We deeply regret these errors and apologize to the scientific community for any confusion this publication may have caused. All authors agree with the retraction.”

This slide show illustrates the data issues mentioned in the retraction notice. 

This slideshow requires JavaScript.

And this slide show illustrates the issues the retraction notice chose not to address at all. 

This slideshow requires JavaScript.

In Daley’s lab, more things do not work as expected. His most famous Nature paper, Park et al 2008 , meant to compete with Shinya Yamanaka for induced pluripotency (iPS) fame and the Nobel Prize, is being plucked apart on PubPeer, accused of not having delivered any pluripotency as such. The exogenously delivered reprogramming transgenes remained namely active, while they were supposed to become silenced as cells’ own pluripotency genes become active. Also, Daley’s method of using Large T Antigen and telomerase TERT in addition to Yamanaka’s four iPS reprogramming factors proved rather counterproductive.

Whom to believe? A retracted Soria-Valles paper? Or Daley’s 2008 Nature paper which desperately wanted to prove better than Yamanaka’s iPS discovery? Source: PubPeer.

For someone like Daley, all of this is not the end of the world. There are always new windows of opportunity. Just as Chinese scientist Jiankui He caused a worldwide scandal with his unethical human experiments with CRISPR-modified babies, Daley (and his Harvard colleague George Church) offered a more enthusiastic view: America cannot afford a CRISPR gap to China. Daley suggested that Harvard should take the lead and apply CRISPR eugenics to ensure the survival of the human race:

“There have even been discussions that we as a species need to maintain the flexibility in the face of future threats to take the control of our own heredity.”

Harvard’s CRISPR experiments on human germ line editing are already starting. An Alzheimer’s associated gene is to be edited in human sperm, while Daley announced big plans to design the children of the future to be resistant to various diseases. Ethics is something this Harvard dean is apparently less interested in.

Harvard recently received a $200 million donation to set up a new institute, the money came from a controversial tycoon Leonard Blavatnik with Russian origins, whose lawyers made The Guardian apologise for erroneously calling him a “Putin pal” and an oligarch. 

It is Daley’s Spanish collaborator, the fugitive Lopez-Otin, who is in deep trouble with that retraction now. Lopez-Otin did manage to bring himself into news recently with his new paper (in a Nature -themed journal!) where his Oviedo lab analysed the genome of Lonesome George, the last member of his giant tortoise species who died in 2012. The press release omitted to say whether he spoke from Oviedo or Paris, Lopez-Otin the turtle geriatrics researcher was quoted with:

“We had previously described nine hallmarks of aging, and after studying 500 genes on the basis of this classification, we found interesting variants potentially affecting six of those hallmarks in giant tortoises, opening new lines for aging research” 

Nature now probably deeply regrets having awarded him with a 2017 Mentoring Award. Maybe they can give next one to Daley? Maybe Daley can get Soria-Valles to CRISPR some of those turtle genes to create a new long-lived human race of Homo harvardiensis crispri?


Update 21.12.2018. My article was apparently well received in Harvard, according to this information I was privy to:

“Daley was complaining intensely at lab meeting in front of entire lab and his junior faculty labs (Trista North and Thorsten Schlaeger) about potential lab members who might have leaked Soria-Valles information to the German blogger. It was intense”

I also learned that the now retracted Soria-Valles Nature Cell Biology 2015 paper was originally submitted to Science, were it was rejected due to some statistics issues.

Update 5.01.19. I was recently alerted by a source:

“George [Daley, -LS] has scared the lab members and provoked Stockholm syndrome among members. The Daley lab is trying to figure out who the leaks are now. Some of the members are trying to crash the German website by sending Hakenkreuz images.”

This was exactly what happened. Commenters used several fake identities to post highly defamatory comments about Daley on my site, equalling his research to Macchiarini’s trachea transplants and, indeed, using Nazi Swastika armband photoshopped on a photo of Daley. Exactly same picture was shared by Daley lab members in preparation of the campaign, it was confirmed to me. I deleted all those comments, but made backup, also of IP addresses.

Specifically, those IP addresses were located in US to Connecticut, 06902 Stamford, and New York State, 10022 New York. My source suggested I contact these Daley lab alumni: In-Hyun Park at Yale, CT, and Kitai Kim at MSKCC in NY, as well as the person allegedly orchestrating the campaign, the current Daley postdoc Deepak Jha. None of them replied, but Jha immediately blocked me on Twitter. This is how some grown men behave to please their mighty (ex-)boss. Maybe they should rather relax and read the book by Daley’s wife, Amy C. Edmondson, “The Fearless Organization: Creating Psychological Safety in the Workplace for Learning, Innovation, and Growth“.

Daley will be opening the Blavantik institute in ceremony on February 5th, at 5:30 PM. Come to talk about plans of CRISPR babies!

image


 

 

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174 comments on “Lopez-Otin and Daley retract Nature Cell Biology paper

  1. Good news!
    It was good that other shameless Nature papers would be also retracted

    Like

  2. What will happen to Soria-Valles Stem Cell Reports? Given her Nature Cell Biology retracted, can the author with retraction history submit to other journals and continue research work?

    Like

    • Razielclein

      We should wait that cheater learn the lesson, and overall that the science has a powerful weapon to catch them.

      Like

  3. Indigofera Tanganyikensis

    Thank you Leonid for your tremendous contribution to science.

    I started the discussion regarding the Nature Cell Biology paper by Soria Valles on PubPeer one year ago after I got inspiration from your article about Lopez-Otin.

    I will continue to fight against the cheaters and will encourage all the vigilant scientist out there to stand up against the producers of fake science. Put pressure on those “scientist” and the journals and research institutes which protect them.

    Like

  4. First retraction ever from both Daley and Lopez-Otin.

    Like

  5. Another Daley’s most famous Nature paper to claim possible ectogenesis of life was under debate on PubPeer about its reproducibility and image fabrication.

    Derivation of embryonic germ cells and male gametes from embryonic stem cells
    Nature (2004) – 3 Comments
    pubmed: 14668819 doi: 10.1038/nature02247 issn: 1476-4687 issn: 0028-0836 issn: 1476-4679

    Niels Geijsen , Melissa Horoschak , Kitai Kim , Joost Gribnau , Kevin Eggan , George Q. Daley

    https://pubpeer.com/publications/A338DD5840B3ED818917AEB1B984C5

    “Indeed 10 years later and this method has not been adopted or reproduced. ”

    “The Daley group should have applied their guidelines for establishing provenance of pluripotent states
    ( https://pubpeer.com/publications/8029B0E58FBD9134E9AEA36BB096F9#fb37135 )
    ( https://pubpeer.com/publications/F92E647912A9DBF17A3319600A1945#fb37163 ), on their previous study claiming the generation of functional sperm from mouse ESCs published in Nature 2004, which remains to be reproduced!!!!

    They should have reproduced this controversial study and used “forensic genomics” to establish provenance of in vitro generated haploid male gametes and sperm. Alternatively, publishing “Failure to replicate the STAP cell phenomenon” in 2015, would have made a good occasion to retract Geijsen et al. 2004 paper. ”

    “Image splicing.”

    Like

  6. One of the current lab members at Daley’s lab is a postdoctoral fellow named Pavlos Missios. He did his PhD under Karl Lenhard Rudolph who was accused of profound scientific misconduct (https://forbetterscience.com/2017/06/27/german-leibniz-institute-director-karl-lenhard-rudolph-guilty-of-misconduct/) as 8 of Rudolph’s had evidence of data fabrication/manipulation. Pavlos Missios is the primary author of one of those 8 paper which also been criticized on pubpeer (https://pubpeer.com/publications/31B3D6A98C16815ABD9FAAC8364887?fbclid=IwAR0O5M0p6zN8SYZasEwgH5ThS0-KCs63RDxicohxt2zXel5zycyaJlyimA8).

    Collectively such incidences suggest that Daley is inclined in recruiting such postdocs.

    Like

  7. Why this retraction note avoided to address more issues? The notice only addressed superficially. Daley and Lopez-Otin still want to hide some worse detail of this paper?
    “And this slide show illustrates the issues the retraction notice chose not to address at all.”

    Like

  8. Unfortunately the truth behind many iconic papers maybe quite sinister and their revelation even a scandal to governments

    Like

  9. Comparing with Daley’s talk at DFCI this Sept. 2018, his following NIH talk Nov. 2018 dramatically shrunk Soria-Valles work. He did not repeat his claim that “(Soria-Valles’) haematopoietic stem cells showed similar capacity as cord blood haematopoietic stem cells” that was most outstanding point at DFCI talk.
    56-57: Soria-Valles work in three slides
    57-59: Daley proposed scale-up production strategy to test Soria-Valles haematopoietic stem cells in human patients.
    https://videocast.nih.gov/summary.asp?Live=28849&bhcp=1

    Like

  10. Apparently, the retraction note was written in too mild manner. As you described in the slide show, most of critical points from pubpeer were not chosen to address. These include progeria patients’ sample swapping in figure 6b; aged donors’ sample swapping in figure 7a, contradictory expression of pluripotent genes in adult cells in figures 6g, 7f; and band-donor films used throughout in entire paper.

    Like

  11. Pingback: Aperto al dibattito - Ocasapiens - Blog - Repubblica.it

  12. “award-winning and now fugitive Spanish cancer and ageing researcher”, now fugitive? Did I miss any fun here?

    Like

  13. Soria-Valles’ thesis was based on now retracted Nature Cell Biology paper and another PubPeer alleged Oncogene paper on which they deposited someone else’s irrelevant microarray data from irrelevant tissue as their own breast cancer microarray data. https://pubpeer.com/publications/8D0F4C1D83621DE5F72E92A4C39787

    The act of defending the Thesis of Dna. Clara Soria Valles, titled “Tissue remodeling and cell reprogramming in cancer and aging” directed by Dr. Carlos Lopez Otin and Dr. Ana Y. Gutierrez Fernandez, will take place on June 12 at 12.00 in the Sala de Grados of the Faculty of Medicine.

    http://bbm.uniovi.es/noticias/-/asset_publisher/0002/content/cara-soria?redirect=http://bbm.uniovi.es/inicio

    Like

    • A PhD thesis in Spain as far as I know is supposed to be an original, unpublished work with the exceptions of certain regions in Spain where they follow the Dutch model where a PhD thesis is a compilation of published papers
      If a PhD student comes from a big lab will be very difficult he/she gets enough attention from their supervisor which maybe just interested in adding more PhD theses to his/her CV as well as nature papers rather than conveniently forming someone to be a competent researcher

      Like

      • Razielclein

        Dear Ana, I don’t know if you are Spaniard or Hispanic, but as Spaniard, my thesis is the addition of 3 articles published on international peer-reviewed journals. I think that very probably in big labs and is not the case of the Otin one, the student can cheat easily the PI. Hence, in these cases, the punishment should lie on the student. If Otin is compulsively cheating then is when he should be investigated.

        Does somebody know what will happen to this young first author-researcher?

        Like

      • Razielclein,
        Lopez-Otin has 23 of problematic papers with copy-paste of images. The retracted Nature Cell Bio. paper was a flagship of a fleet of their problematic papers.
        https://forbetterscience.com/2018/05/07/the-perennial-northern-blot-of-lopez-otin/
        Soria-Valles mocked data deposition policy not only for Nature Cell Bio. but also for another npg journal Oncogene. They, instead of their own, linked microarray data of someone else’s lab of totally irrelevant samples.
        I assume all these papers are under investigation.

        Like

      • “Does somebody know what will happen to this young first author-researcher?”
        The first author Clara Soria-Valles safely returned back to her home university with fund from Spanish government called Juan de la Cierva-incorporación. The Spanish system encourages cheaters, rather giving them penalty.

        Like

      • Claire Francis

        G Marino is the first author of two retracted papers with Lopes-Otin as last author, both of which were part of his PhD thesis (https://www.educacion.gob.es/teseo/mostrarRef.do?ref=409845). Marino currently holds a Ramon y Canal grant from the Spanish Government. This is a very competitive position, and many other candidates have been rejected. What does happen now to his PhD thesis and grants? Should I have cheated in my papers????

        Like

  14. The Retraction Watch Database indexed this paper and all authors.

    Like

  15. I inquired Oncogene editors to dig into Soria-Valles’ microarray data and original numerical data to make graphs in the article.
    The chief editor Dr. Stebbing said he will deal with this.

    Like

  16. Another reader on PubPeer argues back that gel splicing seems nitpicky.

    Derivation of embryonic germ cells and male gametes from embryonic stem cells
    Nature (2004) – 4 Comments
    pubmed: 14668819 doi: 10.1038/nature02247 issn: 1476-4687 issn: 0028-0836 issn: 1476-4679

    Niels Geijsen , Melissa Horoschak , Kitai Kim , Joost Gribnau , Kevin Eggan , George Q. Daley

    https://pubpeer.com/publications/A338DD5840B3ED818917AEB1B984C5

    “Whether the findings in this paper are truly reproducible is a worrisome question, but it’s hard to see how the splicing in figure 2D is terribly problematic. I would imagine the gel comb has 24 wells and therefore some combining of non-adjacent images would be necessary here, either at the position shown or just before the controls. It’s actually better that the experimenter put some experimental lanes together with the control lanes, rather than probing the controls separately. No, there isn’t a separation between the non-contiguous membranes, but the splice is quite obvious and this is a 2004 paper. Seems nitpicky to me.”

    Like

    • If one has so many samples that a second gel is needed, one should also load control samples on both gels. Unless this is a Harvard paper meant for Nature, of course.

      Like

  17. Complex history of biorxiv pre-print from Daley. How many reincarnation this pre-print needs to be real print?

    Short hairpin RNAs artifactually impair cell growth and suppress clustered microRNA expression
    bioRxiv (2018) – 7 Comments
    doi: 10.1101/372920

    John Powers author has email , Edroaldo Lummertz Da Rocha , Daniel Pearson , Pavlos Missios , Tarja Yvanka De Soysa , Jessica Barragan , Patrick Cahan author has email , George Daley

    https://pubpeer.com/publications/5D8FDD6767EE6F2424B5D9B0164CF7

    “You can find the original version here. https://www.biorxiv.org/content/early/2018/12/11/372920.article-info I found the article has two older versions. The mistake of copy-paste and splicing was introduced in the first version (July 20, 2018), stil remained in the second version (July 26, 2018), and finally replaced with new images in the latest version (December 11, 2018). The second version added two missing references to introduce this sentence ” LentiCRISPRv2 was a gift from F. Zhang19,20.”

    Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. bioRxiv 11, 006726 (2014).
    Shalem, O. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84–7 (2014)."
    

    Like

  18. Soria-Valles’ NCB paper (2015) was retracted and finally removed from Lopez-Otin lab website.
    http://degradome.uniovi.es/publications.html

    Selected publications from our lab
    Ferrando, A. A. and Lopez-Otin, C. Clonal evolution in leukemia. Nature Med, 23, 1135-1145 (2017). PubMed
    de la Rosa, J., Weber, J., Friedrich, M. J., Li, Y., Rad, L., Ponstingl, H., Liang, Q., de Quiros, S. B., Noorani, I., Metzakopian, E., Strong, A., Li, M. A., Astudillo, A., Fernandez-Garcia, M. T., Fernandez-Garcia, M. S., Hoffman, G. J., Fuente, R., Vassiliou, G. S., Rad, R., Lopez-Otin, C., Bradley, A. and Cadinanos, J. A single-copy Sleeping Beauty transposon mutagenesis screen identifies new PTEN-cooperating tumor suppressor genes. Nature Genet, 49, 730-741 (2017). PubMed
    Lopez-Otin, C., Galluzzi, L., Freije, J. M., Madeo, F. and Kroemer, G. Metabolic Control of Longevity. Cell, 166, 802-21 (2016). PubMed
    Osorio, F. G., Soria-Valles, C., Santiago-Fernandez, O., Bernal, T., Mittelbrunn, M., Colado, E., Rodriguez, F., Bonzon-Kulichenko, E., Vazquez, J., Porta-de-la-Riva, M., Ceron, J., Fueyo, A., Li, J., Green, A. R., Freije, J. M. and Lopez-Otin, C. Loss of the proteostasis factor AIRAPL causes myeloid transformation by deregulating IGF-1 signaling. Nature Med, 22, 91-6 (2016). PubMed
    Puente, X. S., et al. Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature, 526, 519-24 (2015). PubMed
    Quiros, P. M., Langer, T. and Lopez-Otin, C. New roles for mitochondrial proteases in health, ageing and disease. Nature Rev Mol Cell Biol, 16, 345-59 (2015). PubMed
    Robles-Espinoza, C. D.,et al. POT1 loss-of-function variants predispose to familial melanoma. Nature Genet, 46, 478-81 (2014). PubMed

    2015
    Loi, M., Cenni, V., Duchi, S., Squarzoni, S., Lopez-Otin, C., Foisner, R., Lattanzi, G. and Capanni, C. Barrier-to-autointegration factor (BAF) involvement in prelamin A-related chromatin organization changes. Oncotarget, 7, 15662-77 (2016). PubMed
    Alioto, T. S., et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Commun, 6, 10001 (2015). PubMed
    Puente, X. S., et al. Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature, 526, 519-24 (2015). PubMed
    Xargay-Torrent, S., Lopez-Guerra, M., Rosich, L., Montraveta, A., Roldan, J., Rodriguez, V., Villamor, N., Aymerich, M., Lagisetti, C., Webb, T. R., Lopez-Otin, C., Campo, E. and Colomer, D. The splicing modulator sudemycin induces a specific antitumor response and cooperates with ibrutinib in chronic lymphocytic leukemia. Oncotarget, 6, 22734-49 (2015). PubMed
    Gutierrez-Fernandez, A., Soria-Valles, C., Osorio, F. G., Gutierrez-Abril, J., Garabaya, C., Aguirre, A., Fueyo, A., Fernandez-Garcia, M. S., Puente, X. S. and Lopez-Otin, C. Loss of MT1-MMP causes cell senescence and nuclear defects which can be reversed by retinoic acid. EMBO J, 34, 1875-88 (2015). PubMed
    Rodriguez, D., Bretones, G., Quesada, V., Villamor, N., Arango, J. R., Lopez-Guillermo, A., Ramsay, A. J., Baumann, T., Quiros, P. M., Navarro, A., Royo, C., Martin-Subero, J. I., Campo, E. and Lopez-Otin, C. Mutations in CHD2 cause defective association with active chromatin in chronic lymphocytic leukemia. Blood, 126, 195-202 (2015). PubMed
    Quiros, P. M., Langer, T. and Lopez-Otin, C. New roles for mitochondrial proteases in health, ageing and disease. Nature Rev Mol Cell Biol, 16, 345-59 (2015). PubMed
    Cal, S. and Lopez-Otin, C. ADAMTS proteases and cancer. Matrix Biol, 44-46C, 77-85 (2015). PubMed
    Cabrera, S., Maciel, M., Herrera, I., Nava, T., Vergara, F., Gaxiola, M., Lopez-Otin, C., Selman, M. and Pardo, A. Essential role for the ATG4B protease and autophagy in bleomycin-induced pulmonary fibrosis. Autophagy, 11, 670-84 (2015). PubMed
    Aguilera, O., Gonzalez-Sancho, J. M., Zazo, S., Rincon, R., Fernandez, A. F., Tapia, O., Canals, F., Morte, B., Calvanese, V., Orgaz, J. L., Niell, N., Aguilar, S., Freije, J. M., Grana, O., Pisano, D. G., Borrero, A., Martinez-Useros, J., Jimenez, B., Fraga, M. F., Garcia-Foncillas, J., Lopez-Otin, C., Lafarga, M., Rojo, F. and Munoz, A. Nuclear DICKKOPF-1 as a biomarker of chemoresistance and poor clinical outcome in colorectal cancer. Oncotarget, 6, 5903-17 (2015). PubMed
    Wallace, D. F., Secondes, E. S., Rishi, G., Ostini, L., McDonald, C. J., Lane, S. W., Vu, T., Hooper, J. D., Velasco, G., Ramsay, A. J., Lopez-Otin, C. and Subramaniam, V. N. A critical role for murine transferrin receptor 2 in erythropoiesis during iron restriction. Br J Haematol, 168, 891-901 (2015). PubMed
    Rodriguez, D., Bretones, G., Arango, J. R., Valdespino, V., Campo, E., Quesada, V. and Lopez-Otin, C. Molecular pathogenesis of CLL and its evolution. Int J Hematol, 101, 219-28 (2015). PubMed
    Bassaganyas, L., Bea, S., Escaramis, G., Tornador, C., Salaverria, I., Zapata, L., Drechsel, O., Ferreira, P. G., Rodriguez-Santiago, B., Tubio, J. M., Navarro, A., Martin-Garcia, D., Lopez, C., Martinez-Trillos, A., Lopez-Guillermo, A., Gut, M., Ossowski, S., Lopez-Otin, C., Campo, E. and Estivill, X. Sporadic and reversible chromothripsis in chronic lymphocytic leukemia revealed by longitudinal genomic analysis. Leukemia, 29, 758 (2015). PubMed
    Queiros, A. C., Villamor, N., Clot, G., Martinez-Trillos, A., Kulis, M., Navarro, A., Penas, E. M., Jayne, S., Majid, A., Richter, J., Bergmann, A. K., Kolarova, J., Royo, C., Russinol, N., Castellano, G., Pinyol, M., Bea, S., Salaverria, I., Lopez-Guerra, M., Colomer, D., Aymerich, M., Rozman, M., Delgado, J., Gine, E., Gonzalez-Diaz, M., Puente, X. S., Siebert, R., Dyer, M. J., Lopez-Otin, C., Rozman, C., Campo, E., Lopez-Guillermo, A. and Martin-Subero, J. I. A B-cell epigenetic signature defines three biologic subgroups of chronic lymphocytic leukemia with clinical impact. Leukemia, 29, 598-605 (2015). PubMed
    Keane, M., Semeiks, J., Webb, A. E., Li, Y. I., Quesada, V., Craig, T., Madsen, L. B., van Dam, S., Brawand, D., Marques, P. I., Michalak, P., Kang, L., Bhak, J., Yim, H. S., Grishin, N. V., Nielsen, N. H., Heide-Jorgensen, M. P., Oziolor, E. M., Matson, C. W., Church, G. M., Stuart, G. W., Patton, J. C., George, J. C., Suydam, R., Larsen, K., Lopez-Otin, C., O’Connell, M. J., Bickham, J. W., Thomsen, B. and de Magalhaes, J. P. Insights into the evolution of longevity from the bowhead whale genome. Cell Rep, 10, 112-22 (2015). PubMed
    Caravia, X. M. and Lopez-Otin, C. Regulatory Roles of miRNAs in Aging. Adv Exp Med Biol, 887, 213-30 (2015). PubMed
    Soria-Valles, C., Osorio, F. G. and Lopez-Otin, C. Reprogramming aging through DOT1L inhibition. Cell Cycle, 14, 3345-6 (2015). PubMed
    Galluzzi, L., et al. Essential versus accessory aspects of cell death: recommendations of the NCCD 2015. Cell Death Differ, 22, 58-73 (2015). PubMed
    Fernandez, A. F. and Lopez-Otin, C. The functional and pathologic relevance of autophagy proteases. J Clin Invest, 125, 33-41 (2015). PubMed
    Lopez-Guerra, M., Xargay-Torrent, S., Rosich, L., Montraveta, A., Roldan, J., Matas-Cespedes, A., Villamor, N., Aymerich, M., Lopez-Otin, C., Perez-Galan, P., Roue, G., Campo, E. and Colomer, D. The gamma-secretase inhibitor PF-03084014 combined with fludarabine antagonizes migration, invasion and angiogenesis in NOTCH1-mutated CLL cells. Leukemia, 29, 96-106 (2015). PubMed

    In contrast, Daley lab website still displays this paper in Publication section.
    https://daley.med.harvard.edu/publications

    Like

  19. Does anyone know there are any progeria patients and researchers associations in europe, Spain, US etc? They need to be alerted that Harvard, International society of stem cell research and uniovi produced a big fake hope using public fund of EMBO.

    Like

  20. Progeria Research Foundation has been operating clinical trials to progeria kids since 2007 at Boston Children’s Hospital, where Soria-Valles’ progeria study took place at the Daley lab located there. The study was published in Nature Cell Biology and retracted by now.

    https://www.progeriaresearch.org/clinical-trials/

    The clinical trial is based on 2003 discovery of progeria gene lamin A in HGPS progeria by Francis Collins, NIH director. Soria-Valles’ retracted study proposed a method to rejuvenate HGPS patients cells, where they swapped samples to make up the claim.

    “Twenty-eight (28) children from sixteen countries participated, ages 3 to 15 years. Children returned to Children’s Hospital Boston every four months, for testing and to receive new drug supply, and stayed in Boston for 4-8 days each visit. While at home, their doctors kept a close watch over the children and submitted periodic health reports to the Boston research team. For the duration of the trial, an average of 2 children per week traveled to Boston to participate.”

    Like

  21. Here are Supporting Organizations for progeria according to NORD website. https://rarediseases.org/rare-diseases/hutchinson-gilford-progeria/
    Ironically, Progeria Research Foundation (PRF) who runs clinical trials for progeria kids is based on Daley’s home ground Boston Children’s Hospital. There Soria-Valles and Daley worked for both retracted progeria paper and haematopoietic reprogramming to treat paediatric patients with Shwachman Diamond Syndrome (SDS) and Diamond Blackfan Anemia (DBA). For both diseases, Daley has been publishing intensively for years.

    Genetic and Rare Diseases (GARD) Information Center
    PO Box 8126
    Gaithersburg, MD 20898-8126
    Phone: (301) 251-4925
    Toll-free: (888) 205-2311
    Website: http://rarediseases.info.nih.gov/GARD/

    Progeria Research Foundation, Inc.
    P.O. Box 3453
    Peabody, MA 01961-3453 USA
    Phone: (978) 535-2594
    Email: info@progeriaresearch.org
    Website: http://www.progeriaresearch.org

    Like

  22. At NIH this November 2018, Daley shared his roadmap to inject Soria-Valles stem cells to pediatric patients.

    And graphs show that Soria-Valles stem cells successfully engrafted in mice for long-term.

    Like

    • Daley was promoting pipeline of Clara Soria-Valles to patients. Question is if he KNEW about Soria-Valles problems, yet still wanted to apply her research to children patients.

      Very concerning if true.

      Like

  23. The co-first author of retracted NCB paper, Fernando G. Osorio has just published a quick paper in Cell Reports with his current host lab Fernando Camargo (Boston Children’s Hospital) and Ruben van Boxtel (Princess Maxima Center).
    https://www.cell.com/cell-reports/fulltext/S2211-1247(18)31760-1
    Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Hematopoiesis
    Fernando G. Osorio, Axel Rosendahl Huber, Rurika Oka, Ignacio Varela, Fernando D. Camargo, Ruben van Boxtel
    Publication History
    Published: November 27, 2018
    Accepted: October 31, 2018
    Received in revised form: October 10, 2018
    Received: June 14, 2018

    Nicely free from any immunoblot!
    See his former research at Lopez-Otin lab.

    Like

  24. Soria-Valles retraction notice is saying that they did not have original numerical data for majority of graphs. So the graphs made from scratch? And there were lots of image problems. These are terrible fraud, cannot say honest mistakes at all. And they got fund because of this fraud paper. How much fund do they have to return to funding bodies?

    Like

  25. The funding source and amount of money related with Soria-Valles’ retracted NCB paper and haematopoietic stem cell paper she had done at Daley lab;
    – NIH U01 grant to Daley
    $1,044,680 as of the fiscal year 2016
    http://grantome.com/grant/NIH/U01-HL134812-01

    EMBO long-term fellowship to Soria-Valles
    $45,133/first year + $49,646/second year
    ERC grant to Lopez-Otin
    €2,500,000. Through 2017-2022

    Like

    • That is why I keep insisting if we all have to pay taxes and support this people minimally a list of all the expenses that were covered by these grants including raw data from the research that was conducted with conclusions should be available to public

      Like

  26. This means George Daley was presenting Soria-Valles’ work at NIH who is funding the project, him knowing that the work of Soria-Valles had been under investigation and been alerted by Nature Cell Biology. Knowingly presenting data which may not be right (or not exist) at the own funding body?

    Like

  27. More comment on Daley’s Nature paper about deriveration of human iPS cells. The paper lacks a significant evidence to validate pluripotency of their cells. Pluripotent reporter data is missing, while J. Thomson lab has the data. They used the same reporter line originally from Thomson..

    Reprogramming of human somatic cells to pluripotency with defined factors
    Nature (2008) – 12 Comments
    pubmed: 18157115 doi: 10.1038/nature06534 issn: 1476-4687 issn: 0028-0836

    In-Hyun Park author has email , Rui Zhao , Jason A. West , Akiko Yabuuchi , Hongguang Huo , Tan A. Ince , Paul H. Lerou author has email , M. William Lensch author has email , George Q. Dale
    https://pubpeer.com/publications/A600E09BABFB5C7A28B86BBA6F8AD9

    “I am curious why this paper did not show GFP data from reprogrammed H1-OGN cells? The line is made from Zwaka and Thomson and can report reprogramming by reactivation of GFP. The most convincing evidence at the time. Indeed both Daley and Thomson papers used the line. You can see GFP reactivation in Thomson 2007 Science, but not in this paper. ”

    Like

  28. That is the reality unfortunately of many powerful labs in USA…either you shut your mouth or you will get a ticket back to your home country or you will see your research career with no perspectives…that were the perspectives of the lab were I did my post doc

    Like

  29. I am just hoping all the postdocs from these labs don’t be afraid and start telling the truth, how they are under pressure to get certain results, how they are frightened with visa and other issues

    Like

  30. Hey Ana Pedro, could you give us more details on your experience as a postdoc in the USA and what happened to you?

    Like

    • Hi Sirgraphs,

      You can find a summary of what happened to me in the email bellow (a response to the email Lyden and Cardoso sent Dr. Inglis from BioRxiv) also published in this blog in comments. I recently wrote an email to Cornell RARC Department and I am waiting for their response

      Kind regards,

      Ana Pedro

      “fatimacardoso@fundacaochampalimaud.pt” fatimacardoso@fundacaochampalimaud.pt,
      “joaquim.teixeira@fundacaochampalimaud.pt” joaquim.teixeira@fundacaochampalimaud.pt,
      “irm2224@med.cornell.edu” irm2224@med.cornell.edu,
      “dcl2001@med.cornell.edu” dcl2001@med.cornell.edu,
      biorxiv biorxiv@cshl.edu,
      Rod Tucker rodtucker.tucker@gmail.com,
      Ronny Schmidt ronny.schmidt@sciomics.de

      Dear Dr Inglis

      The data published pertains to my post doc work at WCMC and Champalimaud Foundation. These data obtained before Ayuko et al 2015 was published clearly contradicts what was published in this manuscript stating that integrins determine cancer metastasis sites. I remember very well I had a meeting as well much time before Hoshino et al was published with Dr Lyden, Dr Hoshino and Dr Bruno Costa Silva and we clearly saw that sample CF33 didn’t have any integrins and the integrins content of CF27 sample was not consistent with Hoshino et al, 2015
      Moreover, given that I mentioned the origin of the samples and the founders and all the intelectual work was performed by myself including project writing (I can proof it and I can mention including that Dr Cardoso and Dr. Lyden did not wrote a line of the project that was approved for funding by FCT), sample processing and analysis I believe I am on the right of publushing these data
      Indeed I believe that instead the manuscript Hoshino et al 2015 should be removed by Nature as it is clearly cheated. Also I can proof there were mouse work irregularities corresponding to the period of time when Hoshino et al 2015 was published
      You can consult the the hotmail address reclamacao.anapedro@hotmail.com, password:recl@m@cao for details about mouse work issues and project authorship
      Given that Nature or WCMC did not undertook any measure given the mentioned misconduct allegations, instead Dr Inglis, I ask you what I can do in order to get justice and being able to publish my hard work which is a true, transparent work
      I also give permission to Leonid Schneider to publish this email in his site
      I also ask Dr Cardoso and Dr Lyden for some reasonability
      I thank you so much your help regarding the issues I raised above

      Looking forward to hearing from you
      Kind regards
      Ana Pedro

      Like

  31. Here are all four slides related with Daley’s data and roadmap to transplant Soria-Valles’ stem cells into pediatric patients at NIH talk this Nov. 1, 2018.
    .
    How to make Soria-Valles’ stem cells

    Long-term engraftment of Soria-Valles’ stem cells in mice

    FACS plots and DNA analysis of Soria-Valles’ stem cells

    Roadmap to transplant Soria-Valles’ stem cells into kids

    Link to NIH videocast of Daley, Nov. 2018
    https://videocast.nih.gov/summary.asp?Live=28849&bhcp=1

    Like

  32. Please, please stop him!
    Before experiments are done with patients pre-clinical data and data from non-invasive patient samples like blood samples, etc or patient samples obtained during standard treatment (for example tumor samples obtained during breast cancer surgery) also experiments in animals must clearly show that is both safe to test a treatment in humans and that there is a strong possibility the treatment will be an effective one

    Like

  33. I will be presenting the preliminary data from my “problematic” bioRXIv pre-print at the Frontiers Stem Cell 2019 meeting in the end of April in New York and I will add some independent preliminary data from Lyden lab regarding flow cytometry analysis of circulating HSCs and MDSCs in control and early and metastatic breast cancer patients. It is obvious for me that exosome integrins do not play a fundamental role in metastases and also by analysing the mentioned flow data (unfortunately I do not have the original flow cytometry files, I wrote down the flow results and returned the CDs containing the original data) if it seems obvious that MDSCs play a role in metastasis, this data does not clearly demonstrate that HSCs are involved in metastasis…if this is true we should see more HSCs in those early breast cancer patients who will develop metastases? And also in metastatic breast cancer patients? For sure MDSCs are derived from HSCs…so further experiments are needed
    Discussions are open

    Like

  34. “in some cases the β-actin immunoblots were erroneously described in the figure legends as loading controls, rather than as sample processing controls that were run on separate gels”
    Simply precious. Might as well have just used the blots on the manufacturer’s websites.
    Just once I would like to see a journal say this paper was retracted because the authors ignored our instructions for data presentation and faked most of the results. And for heaven’s sake, don’t let them get away with “we, the authors, believe that the key findings of the paper are still valid” when the whole thing is a sham.

    Like

  35. PubPeer readers are pointing out that Daley’s observation of telomere elongation in iPS cells may be due to artifact from vector system they chose. The other team Artandi at Stanford used the correct vectors and reported opposing results to Daley.

    Telomere elongation in induced pluripotent stem cells from dyskeratosis congenita patients
    Nature (2010) – 4 Comments
    pubmed: 20164838 doi: 10.1038/nature08792 issn: 1476-4687 issn: 0028-0836

    Suneet Agarwal , Yuin-Han Loh , Erin M. McLoughlin , Junjiu Huang , In-Hyun Park , Justine D. Miller , Hongguang Huo , Maja Okuka , Rosana Maria Dos Reis , Sabine Loewer , Huck-Hui Ng , David L. Keefe , Frederick D. Goldman , Aloysius J. Klingelhutz , Lin Liu , George Q. Daley

    https://pubpeer.com/publications/265A83EC56E557C8588D151FFEBBC0

    “The contradiction may come from vector method each paper used. Daley team used pMIG retroviral vectors which are tough to be silenced, and prevent complete reprogramming. And causing more artificial results from remaining transgenes. The issues of artificial observation using pMIG vector system are discussed here https://pubpeer.com/publications/A600E09BABFB5C7A28B86BBA6F8AD9
    Artandi team used pMX retroviral vectors which can be silenced, leading to complete reprogramming. This vector system was also used by Yamanaka team (Takahashi, Cell, 2007). Artandi’s obsservation of telomere shortening in dyskeratosis iPS cells is plausible.”

    Like

  36. Park (Nature 2008) Daley’s first claim of human reprogramming study, is argued intensely on PubPeer.
    The paper did not report crucial data that they should have, and probably negative. The validity of their claim is vague now.

    Reprogramming of human somatic cells to pluripotency with defined factors
    Nature (2008) – 15 Comments
    pubmed: 18157115 doi: 10.1038/nature06534 issn: 1476-4687 issn: 0028-0836

    In-Hyun Park , Rui Zhao , Jason A. West , Akiko Yabuuchi , Hongguang Huo , Tan A. Ince , Paul H. Lerou , M. William Lensch , George Q. Daley

    https://pubpeer.com/publications/A600E09BABFB5C7A28B86BBA6F8AD9

    “In addition, OCT4-neo (geneticin/G418 resistance) was practiced by Thomson to prove acquisition of pluripotency, while not by Daley. Both teams used the same cell line.
    Yu et al. (Thomson) “In this cell line, the expression of neomycin phosphotransferase, which makes cells resistant to geneticin, is driven by an endogenous OCT4 promoter, a gene that is highly expressed in pluripotent cells but not in differentiated cells. Thus, reprogramming events reactivating the OCT4 promoter can be recovered by geneticin selection….. These geneticin-resistant colonies expressed typical human ES cell–specific cell surface markers (fig. S2B) and formed teratomas when injected into immunocompromised severe combined immunodeficient–beige mice ”
    Park et al. (Daley) “Selection with G418 was not required to identify cells with ES-cell-like colony morphology””

    “Actually large T tends to be integrated in DNA during reprogramming. Johns Hopkins group reported that all five clones contained large T DNA in the genomic DNA.
    It is difficult to assume that large T transgene was absent in all the Daley lines.
    https://stemcellsjournals.onlinelibrary.wiley.com/doi/full/10.1634/stemcells.2008-0346 “When we analyzed the presence of the T transgene, we found that all five expanded clones contained the T DNA in the genomic DNA, as in the IL group with the same T vector. Similarly, all seven clones obtained by the NIL OSTM transduction (described above) also contained the T DNA. Considering that the integration rate of NIL vectors is supposed to be 104‐fold lower, these data strongly suggested that sustained presence of T is likely critical to the enhanced reprogramming of human fibroblasts under the conditions we used. ”
    According to Park et al., “the human ES-cell-like colonies that we ultimately isolated failed to show integration or expression of hTERT and SV40 large T (data not shown).””

    “Rudolf Jaenisch said that partially reprogrammed cells have retrovirus transgene on, lack of Oct4 reporter (Daley iPS cells). Fully reprogrammed cells have retrovirus silenced and Oct4 reporter (Yamanaka iPS cells, Thomson iPS cells). Therefore, Park et al. did not fully reprogrammed human cells. ”

    Like

  37. PubPeer comments on Soria-Valles’ Oncogene article. The link to their microarray data set is dead, or the authors did not upload the data set.

    https://pubpeer.com/publications/8D0F4C1D83621DE5F72E92A4C39787

    The anti-metastatic activity of collagenase-2 in breast cancer cells is mediated by a signaling pathway involving decorin and miR-21
    Oncogene (2014) – 3 Comments
    pubmed: 23851508 doi: 10.1038/onc.2013.267 issn: 1476-5594 issn: 0950-9232

    C Soria-Valles , A Gutiérrez-Fernández , M Guiu , B Mari , A Fueyo , R R Gomis , C López-Otín

    “Here is the link to accession number put on the paper. Actually, this is 2007 data of Kevin Lebrigand lab in France, the samples were of human lung cancer. Does not match with breast cancer cell line microarray conducted for this paper at 2014. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4718

    “Reading the text more carefully one finds that the microarray data “…are available on http://www.microarray.fr:8080/merge/index (follow the link to ‘microRNA’…”.
    This link seems to be dead (the same link is listed in GEO with GPL4718) – you should ask the authors to provide raw data or a working link.
    The link you report refers to the “…platform referenced in GEO accession numbers GPL4718…”.
    It is therefore a GEO platform ID and not a GEO data set ID and describes the type of microarray used. There are two data series in GEO using this platform, neither of which is associated with this publication.
    So: dead link to data set – ask authors. Nothing else to complain about here, apart maybe from the fact that authors did not upload the raw data to GEO, too – the journal should have insisted in case that it is required by data availability policy.”

    Like

    • Ana Pedro

      A message for the new year: Any researcher should be allowed to publish a paper without presenting the original data including clinical trial and animal trials protocols and the use of photoshop should be forbidden, WBs should be automated

      Like

  38. Let’s not raise the technical bar so high that the cheating megalabs get a further advantage. It is also important to distinguish legitimate scientific discussion of work such as other Daley lab outputs from detection of sloppiness and fraud as occurred in this paper. Not knowing something at the time that has come out later is not a retractable offense. Also worth noting is how prominent authors and major institutions like Harvard can assert their “five hundred pound gorilla” status. This turkey was in the literature for over 3 and a half years. It lumbered along with a mass of PubPeer baggage for over a year and dragged along an official cloud of suspicion from Nature for several months. That inertia indicates powerful backing, as does the mealy-mouthed retraction notice. Last but not least, we should consider the inconsistencies in how institutions and granting agencies deal with such matters. Anversa was canned and his papers were marked for bulk retraction because his institution eventually came to the conclusion that he had fabricated an entire field of research. There is no sign of similar investigations of the major players in this paper, who appear to have been up to similar shenanigans.

    Like

  39. Ana Pedro

    The point is these problems are global problems. What measures can the scientific community take to:

    The establishment of cheating megalabs or even cheating worldwide nets of labs?
    Inconsistencies how institutions, journals and granting agencies deal with these problems?

    Like

  40. Part of the solution is due diligence. If a funding agency finds out that a research group fraudulently obtained and/or used grant funding, they should cut off the offending researchers and host institutions while pursuing legal means to recover the money and punish those responsible. If research is funded by others, then research fraud is an intentional tort, and a misdemeanor or felony depending on the amounts involved. Yet in most tales of fraudulent research we find the punishments are so mild, avoidable and delayed that they offer no real deterrent, especially for those who gain the most from cheating. The top dogs get wrist slaps in the form of a temporary bans or supervision, and the worst culprits shuffle off to another plum post with minor inconvenience leaving a trail of wrecked lives behind. How else can we expect high-stakes gamblers to behave if we let them play for free?

    Like

    • Ana Pedro

      The main problem is that the so called top-dogs are intimately connected with/ get protected by governments and politicians worldwide…so to solve these problems we would need to start by changing science funding and publication policies worldwide

      With this goal a science petition should be organised worldwide and signatures from scientists worldwide should be obtained and this petition should be handed in at United Nations

      Like

  41. PubPeer comment on Soria-Valles’ Protocol Exchange. The validity of the protocol is being argued.

    Somatic cell reprogramming using NF-κB inhibitory strategies
    Protocol Exchange (2015) – 7 Comments
    doi: 10.1038/protex.2015.057 issn: 2043-0116

    Clara Soria-Valles , Fernando Osorio , José Freije , Carlos López-Otín

    https://pubpeer.com/publications/0DFD5A1F3303958FBBE3D562F455AE#7

    “The most crucial technical advance in this protocol is that one can achieve visible TRA1-60+ iPSC colonies in 1 weeks of induction, which is still elusive to others in the field. Please refer figure 3e from the original article for this protocol.”

    Like

  42. Soria-Valles has been selected for Juan de la Cierva-incorporación to bring her money to uniovi. 35,000 euro for 2019, and 29,000 euro for 2020. Information is as of nomination date at Sept. 28, 2018. Application number, IJCI-2017-31455, UNIVERSIDAD DE OVIED.
    https://www.ctt.upc.edu/arxius/ca/RESOLUCIO_DEFINITIVA_2017_arxiu_5689.pdf

    Like

  43. For the nomination of 2017 Juan de la Cierva-incorporación organized by Spanish ministry, Soria-Valles has been selected to be top ranked among 63 of Biomedicina candidates. 27 candidates were selected, and rest of 36 failed. Total 64,000 euros will be spent on Soria-Valles’ research back in uniovi from 2019.
    https://sede.micinn.gob.es/stfls/eSede/Ficheros/2018/PROPUESTA_RESOLUCION_PROVISIONAL_SELECCIONADOS_RESERVAS_IJCI2017.pdf

    Like

  44. PubPeer arguments over Daley’s 2008 Nature paper still continue.

    Reprogramming of human somatic cells to pluripotency with defined factors
    Nature (2008) – 17 Comments
    pubmed: 18157115 doi: 10.1038/nature06534 issn: 1476-4687 issn: 0028-0836

    In-Hyun Park author has email , Rui Zhao , Jason A. West , Akiko Yabuuchi , Hongguang Huo , Tan A. Ince , Paul H. Lerou author has email , M. William Lensch author has email , George Q. Daley

    https://www.pubpeer.com/publications/A600E09BABFB5C7A28B86BBA6F8AD9#17

    “The reprogramming knowledge and technology in 2008 was not as advanced as it is now. This paper is what it is for that time.

    However, what you need to know dear reader, is that almost the entire discussion above is from one single troll, recently also using cross-site posting tactics. I’ve been waiting to see if anyone would notice. And now they have! But, as has happened before, the wrong person has very regrettably been identified on teh intarwebs.

    Well done, very clever!

    And who fed this gullible tweeter with false information? Let’s just say that the correct troll is the one trying to defend bogus Mbd3-/- reprogramming. Perhaps Professor Daley is being trolled because he knows too much?”

    “Actually, the Jaenisch paper was published in 2008. Therefore, even by 2008 standards, the Park iPS cells are partially reprogrammed.”

    Like

  45. PubPeer reader found image duplication in Deepak Jha’s publication.
    Pictures were copied and pasted over Figures 1 and 2. They were supposed to be differentially treated samples.

    An RNA polymerase II-coupled function for histone H3K36 methylation in checkpoint activation and DSB repair
    Nature Communications (2014) – 2 Comments
    pubmed: 24910128 doi: 10.1038/ncomms4965 issn: 2041-1723

    Deepak Kumar Jha , Brian D. Strahl

    https://www.pubpeer.com/publications/42A80DA0DB5523DEEF61FEE107F982#2

    Figure 1

    Figure 2

    Like

  46. Gel splicing in Daley and Baltimore’s old article. PubPeer readers are arguing that it was acceptable practice 30 years ago.

    Transformation of an interleukin 3-dependent hematopoietic cell line by the chronic myelogenous leukemia-specific P210bcr/abl protein
    Proceedings of the National Academy of Sciences (1988) – 6 Comments
    pubmed: 3143116 issn: 0027-8424

    G Q Daley , D Baltimore

    https://www.pubpeer.com/publications/61226A71F74171D4410CB1B4916745#6

    Like

  47. University of Oviedo had awarded Soria-Valles “Premios Extraordinarios de Doctorado” for her outstanding Thesis study at Lopez-Otin lab based on her now retracted Nature Cell Biology.

    http://www.asturiasmundial.com/noticia/90228/uniovi-aprueba-plan-propio-investigacion-transferencia-20172020/

    Premios Extraordinarios de Doctorado

    Por otra parte, el Consejo de Gobierno ha aprobado la propuesta de Premios Extraordinarios de Doctorado para las tesis leídas en esta Universidad en el curso académico 2014-2015, abarcando dicho curso el periodo comprendido entre el 1 de septiembre de 2014 y el 31 de agosto del 2015. Estos premios se entregarán de forma solemne el próximo día 27 de enero en el acto conmemorativo de la festividad de Santo Tomás de Aquino. La relación de las candidaturas galardonadas es la siguiente:

    RAMA DE CIENCIAS DE LA SALUD

    Burón Fernández, Patricia
    García Inclán, María Cristina
    Méndez López, Marta
    Rodrígue Carrio, Javier
    Rodríguez García, Aida
    Sampedro Piquero, Patricia
    Soria Valles, Clara
    Weidberg López, Sara Eva
    

    Like

  48. Daley’s alumnus Kitai Kim published a mega-correction at Nature Cell Biology.
    They had reused bars and figure panels.
    Reminds now-retracted Soria-Valles’ case in the same journal. The only difference is that they own up before PubPeer detection.
    https://www.nature.com/articles/s41556-018-0269-y

    Author Correction: ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors

    Maria Skamagki, Cristina Correia, Percy Yeung, Timour Baslan, Samuel Beck, Cheng Zhang, Christian A. Ross, Lam Dang, Zhong Liu, Simona Giunta, Tzu-Pei Chang, Joye Wang, Aparna Ananthanarayanan, Martina Bohndorf, Benedikt Bosbach, James Adjaye, Hironori Funabiki, Jonghwan Kim, Scott Lowe, James J. Collins, Chi-Wei Lu, Hu Li, Rui Zhao & Kitai Kim 
    

    Nature Cell Biology (2019) |

    Correction to: Nature Cell Biology https://doi.org/10.1038/ncb3598, published online 28 August 2017.

    In the version of this Article originally published, Supplementary Fig. 6j showed incorrect values for the LS and AG4 glutathione samples, and Fig. 5c and Supplementary Fig. 6j did not include all n = 6 samples for the hESC, Y-hiPSC and AG4-ZSCAN10 groups as was stated in the legend. In addition, the bars for hESC, Y-hiPSC, AG4-ZCNAN10, AG4 and LS in Supplementary Fig. 6i and j have been reproduced from Fig. 5b and c, respectively. Figure 6e was also reproduced in the lower panel of Supplementary Fig. 6h, to enable direct comparison of the data, however this was not explained in the original figure legends. The correct versions of these figures and their legends are shown below, and Supplementary Table 5 has been updated with the source data for all numerical data in the manuscript.
    Corrected Fig . 6 legend:

    Impaired DNA damage response in human A-hiPSCs caused by deregulation of ZSCAN10 and GSS and recovered by ZSCAN10 expression. a, Excessive oxidation capacity with elevated glutathione in A-hiPSCs, and recovery by ZSCAN10 expression. The total glutathione level was measured to determine the maximum oxidation capacity. Excessive oxidation capacity of glutathione in A-hiPSCs is normalized to the level of hESCs and Y- hiPSCs by transient expression of ZSCAN10. Glutathione analysis was conducted with the glutathione fluorometric assay. Mean ± s.d. is plotted for three biological replicates with two independent clones (n = 6) in each sample group from each condition. Statistical significance was determined by two-sided t-test. b, ROS scavenging activity of hESCs, Y-hiPSCs, A-hiPSCs and A-hiPSCs–ZSCAN10. A cellular ROS assay kit (DCFDA assay) was used to measure H2O2 scavenging activity. A-hiPSCs show strong H2O2 scavenging activity, with a reduced response against treatment with TBHP (tert-butyl hydrogen peroxide; stable chemical form of H2O2, 3 h); the response is recovered by ZSCAN10 expression. Mean ± s.d. is plotted for four biological replicates in each sample group from each condition (n = 4). Statistical significance was determined by two-sided t-test. c, Immunoblot of pATM showing recovery of the DNA damage response after phleomycin treatment in three independent clones of A-hiPSCs with shRNA-mediated knockdown of GSS. d, Immunoblot of pATM showing that lentiviral expression of GSS cDNA impairs the DNA damage response in three independent clones of Y-hiPSCs after phleomycin treatment. e–g, Copy-number profiling analysis of human iPSCs43. Schematic diagrams represent seven rearranged A-hiPSCs, four non-rearranged A-hiPSCs and five non-rearranged A-hiPSCs– ZSCAN10 in the genetically controlled setting of A-hiPSCs. Ten non-rearranged Y-hiPSCs, which were generated from a different tissue donor, were also included. A-hiPSCs (n = 11 (7/11), P = 0.64), (These data are also presented in Supplementary Fig. 6h), A-hiPSCs–ZSCAN10 (n = 5 (0/5), P* = 6.3 × 10−3) and Y-hiPSCs (n = 10 (0/10), P* < 4 × 10−5). The number in parentheses represents detected rearrangements and P and P* are the observed and estimated likelihoods of detecting no rearrangements in the absence of lineage effects using a binomial distribution, respectively50. Unprocessed original scans of blots are shown in Supplementary Fig. 7.

    Like

  49. The latest Nature Communication paper from Daley group has been argued over image duplication and weird uniformity in data points.
    The first author Yermalovich received F99/K00 NIH’s career transition award for this project. Funded
    33,026 USD as of 2016. The support continues for 6 years.
    http://grantome.com/grant/NIH/F99-CA212487-01

    Lin28 and let-7 regulate the timing of cessation of murine nephrogenesis
    Nature Communications (2019) – 2 Comments
    pubmed: 30635573 doi: 10.1038/s41467-018-08127-4 issn: 2041-1723

    Alena V. Yermalovich , Jihan K. Osborne , Patricia Sousa , Areum Han , Melissa A. Kinney , Michael J. Chen , Daisy A. Robinton , Helen Montie , Dan S. Pearson , Sean B. Wilson , Alexander N. Combes author has email , Melissa H. Little author has email , George Q. Daley

    https://www.pubpeer.com/publications/730D5F3BC8FD82D483604CEE8442B9#2

    Image duplication.

    https://imgur.com/a/L3NOa0E

    “Unexpected uniformity in Serum creatinine level in fig. 3g. The data points are shown as in lattice points. The data points came from 14 independent animals, not mere technical replicates. I initially thought it would represent the feature of this assay. But the other data points of serum creatinine level at fig. 5k did not follow the the same rule… ”

    https://imgur.com/a/1FCkWlD

    Like

  50. It is interesting to see Lopez-Otin had actually associated his News&Views with this mega-corrected Kitai Kim’s article. Marveling lineage of Soria-Valles’ now-retracted paper.
    https://www.nature.com/articles/ncb3602

    Like

  51. Soria-Valles Thesis is losing credibility.
    The first half part is about Oncogene (2014) paper which was alleged for missing microarray data. https://pubpeer.com/publications/8D0F4C1D83621DE5F72E92A4C39787
    The later half part is about Nature Cell Biology (2015) paper which was retracted.

    http://digibuo.uniovi.es/dspace/handle/10651/34063

    A lo largo de esta Tesis doctoral, hemos estudiado la relevancia funcional y tumoral de varias proteasas así como las implicaciones del envejecimiento en el proceso de reprogramación celular. Así, empleando líneas celulares humanas de cáncer de mama, hemos estudiado el papel de la metaloproteasa MMP-8 en la progresión tumoral demostrando un mecanismo molecular responsable de las propiedades anti-metastásicas de MMP-8 en cáncer de mama. Por otra parte, hemos generado ratones deficientes en dos metaloproteasas, MMP-25 y MMP-14, que nos han permitido analizar su papel fisiológico y patológico. De esta manera, hemos comprobado que MMP-25 es una proteasa dispensable para el desarrollo de los ratones, pero clave en la respuesta inmune innata y en el desarrollo del cáncer colorrectal, donde ejerce una función supresora tumoral. Por otra parte, MMP-14 es indispensable para la vida y tiene una implicación en el desarrollo de senescencia celular debido a su capacidad de remodelar la matriz extracelular. Además, hemos demostrado que la senescencia generada por la ausencia de MMP-14 puede revertirse parcialmente mediante tratamiento con ácido retinoico. Para abordar los objetivos de la segunda parte de esta Tesis doctoral hemos generado un nuevo modelo de células madre pluripotentes inducidas (iPSCs) a partir de fibroblastos de pacientes con el síndrome progeroide Néstor-Guillermo (NGPS). Dado que las progerias son modelos de estudio del envejecimiento fisiológico, hemos podido estudiar las barreras que comprometen la eficiencia de la reprogramación celular de las células envejecidas, empleando células progeroides y modelos celulares de envejecimiento fisiológico. En este sentido, hemos podido describir una ruta de señalización directamente responsable de la reducida eficiencia de reprogramación que presentan las células envejecidas y cuyo estudio detallado nos ha permitido desarrollar nuevas terapias de rejuvenecimiento.

    Like

  52. What will happen to Soria-Valles’ Thesis? Both Soria-Valles’ PhD papers are retracted and in doubt now. And is she still eligible to receive Juan de la Cierva postdoc fellowship to bring back her work at uniovi? If so, how corrupt Spanish scientific system is.
    And what will happen to rest of Lopez-Otin papers flagged?

    Like

  53. PubPeer dates back to Soria-Valles’ very first paper before Soria-Valles joins to Lopez-Otin lab.

    Antioxidant responses to variations of oxygen by the Harderian gland of different species of the superspecies Spalax ehrenbergi
    Canadian Journal of Zoology (2010) – 1 Comment
    doi: 10.1139/z10-049 issn: 0008-4301 issn: 1480-3283

    C. Soria-Valles , B. Caballero , I. Vega-Naredo , V. Sierra , C. Huidobro-Fernández , D. D. Gonzalo-Calvo , D. Tolivia , M. J. Rodríguez-Colunga , A. Joel , A. Coto-Montes author has email , A. Avivi

    https://www.pubpeer.com/publications/6E08A10273C176E2A7DBE4A61D4022#1

    “This study measured the level of ROS, protein damages and lipid damages in animals housed in 6%, 21% and 85% oxygen condition. The authors found that animals kept under 21% oxygen condition showed highest levels of protein and lipid damages. However, it is intriguing to know how much impact tissue froze and thaw gave on results? According to the Method, all the animals were kept, sacrificed and tissue frozen at Israel. Then all the frozen samples flew to Spain where all the measures were conducted. The authors did not explain what would be anticipated effect of tissue freeze-thaw cycle on protein and lipid damages. And any special justification why all the tissues have to fly from Israel to Spain?”

    Like

  54. PubPeer reader comments uncertain identity of mice used in Soria-Valles’ Oncogene paper. Mice having identical pen marking supposed to be different.

    The anti-metastatic activity of collagenase-2 in breast cancer cells is mediated by a signaling pathway involving decorin and miR-21
    Oncogene (2014) – 4 Comments
    pubmed: 23851508 doi: 10.1038/onc.2013.267 issn: 1476-5594 issn: 0950-9232

    C Soria-Valles author has email , A Gutiérrez-Fernández author has email , M Guiu , B Mari , A Fueyo author has email , R R Gomis , C López-Otín

    https://www.pubpeer.com/publications/8D0F4C1D83621DE5F72E92A4C39787#4

    “Could the authors explain why all the mice in the different groups were having identical pen-marking on their back at day 1 of measurement? ”

    Like

  55. Eight 2019 Withdrawals/Retractions

    Withdrawal: Dm1-MMP, a matrix metalloproteinase from Drosophila with a potential role in extracellular matrix remodeling during neural development.
    Elena Llano, Alberto M. Pendás, Pedro Aza-Blanc, Thomas B. Kornberg, and Carlos López-Otín
    J. Biol. Chem. 2019 294: 1428. doi:10.1074/jbc.W118.007322

    Withdrawal: Identification, characterization, and intracellular processing of ADAM-TS12, a novel human disintegrin with a complex structural organization involving multiple thrombospondin-1 repeats.
    Santiago Cal, José M. Argüelles, Pedro L. Fernández, and Carlos López-Otín
    J. Biol. Chem. 2019 294: 1429. doi:10.1074/jbc.W118.007323

    Withdrawal: Matriptase-2, a membrane-bound mosaic serine proteinase predominantly expressed in human liver and showing degrading activity against extracellular matrix proteins.
    Gloria Velasco, Santiago Cal, Victor Quesada, Luis M. Sánchez, and Carlos López-Otín
    J. Biol. Chem. 2019 294: 1430. doi:10.1074/jbc.W118.007324

    Withdrawal: Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy.
    Guillermo Mariño, José A. Uría, Xose S. Puente, Víctor Quesada, Javier Bordallo, and Carlos López-Otín
    J. Biol. Chem. 2019 294: 1431. doi:10.1074/jbc.W118.007325

    Withdrawal: Identification and characterization of human and mouse ovastacin: A novel metalloproteinase similar to hatching enzymes from arthropods, birds, amphibians, and fish.
    Víctor Quesada, Luis M. Sánchez, Jesús Álvarez, and Carlos López-Otín
    J. Biol. Chem. 2019 294: 1432. doi:10.1074/jbc.W118.007326

    Withdrawal: Identification of human aminopeptidase O, a novel metalloprotease with structural similarity to aminopeptidase B and leukotriene A4 hydrolase.
    Araceli Díaz-Perales, Víctor Quesada, Luis M. Sánchez, Alejandro P. Ugalde, María F. Suárez, Antonio Fueyo, and Carlos López-Otín

    J. Biol. Chem. 2019 294: 1433. doi:10.1074/jbc.W118.007327
    Withdrawal: Identification and characterization of human archaemetzincin-1 and -2, two novel members of a family of metalloproteases widely distributed in Archaea.
    Araceli Díaz-Perales, Víctor Quesada, Juan R. Peinado, Alejandro P. Ugalde, Jesús Álvarez, María F. Suárez, F. Xavier Gomis-Rüth, and Carlos López-Otín

    J. Biol. Chem. 2019 294: 1434. doi:10.1074/jbc.W118.007328
    Withdrawal: Tissue-specific autophagy alterations and increased tumorigenesis in mice deficient in Atg4C/autophagin-3.
    Guillermo Mariño, Natalia Salvador-Montoliu, Antonio Fueyo, Erwin Knecht, Noboru Mizushima, and Carlos López-Otín
    J. Biol. Chem. 2019 294: 1435. doi:10.1074/jbc.W118.007329

    Like

  56. PubPeer comment suggested Soria-Valles to show all the data points used to make a table. Considering lack of numerical data in majority of graphs in Soria-Valles’ retracted NCB paper, it is sensible comment.

    Antioxidant responses to variations of oxygen by the Harderian gland of different species of the superspecies Spalax ehrenbergi
    Canadian Journal of Zoology (2010) – 2 Comments
    doi: 10.1139/z10-049 issn: 0008-4301 issn: 1480-3283

    C. Soria-Valles author has email , B. Caballero , I. Vega-Naredo , V. Sierra , C. Huidobro-Fernández , D. D. Gonzalo-Calvo , D. Tolivia , M. J. Rodríguez-Colunga , A. Joel , A. Coto-Montes author has email , A. Avivi

    https://www.pubpeer.com/publications/6E08A10273C176E2A7DBE4A61D4022

    “The data can be more appreciated and understandable if individual plots of measurement were shown. From Materials and Method, groups of three for each of the three oxygen conditions (hypoxia, normoxia, and hyperoxia) were used, means N=3.”

    Like

  57. After the crash of the C. Soria-Valles paper and the recent retraction of eight JBC articles, I am wondering if the University of Oviedo still fully support Lopez-Otin and his research group?

    From a letter from the “Ethics commitee” signed by vice-rector of research, José Ramón Obeso, addressing a report containing a long list of Pubpeer comments (please see https://forbetterscience.com/2018/05/07/the-perennial-northern-blot-of-lopez-otin/ ):

    “After listening to the experts in the field, this Committee has concluded that there are no relevant irregularities in the papers you mentioned and that the research has been performed following the standards established by the different journals.

    The University of Oviedo fully support professor Carlos López Otín and his research group and we are very concerned about the potential consequences of publishing this kind of doubts on the internet.”

    It clearly shows how currupt the research institutes in Spain have become.

    Like

    • “It clearly shows how currupt the research institutes in Spain have become.”

      What is the evidence that there has been any change? Most things continue as they have been before.
      Like Newton’s first law of motion

      Like

  58. I see you point Zebedee, but it all depends on from where you start the comparison. I don’t think (or hope) that the research insitutions in the beginning of 20th century at the time of Santiago Ramón Cajal were so totally currupted as they apparently are now.

    Today’s research is about getting the most prestige and recognition in a world where there is little more to discover, where researchers are driven by despair or the pursuit of honor to secure a career.

    There is a extreme mismatch between the number of journals/steadly increase in publications and the potential for new discoveries, which leads to the scholarly literature is being filled with nonsense and research institutions must pretend that they are running a serious business.

    Like

    • Academic institutions in Spain are very corrupt and it happens there things like sexual favours, etc in exchange of PhD thesis, etc. I know this by my own experience because I received some proposals which I refused but fortunately I also met a couple of professors which are capable, wise and with a lot of knowledge and honest who bothered that I learnt and did a good PhD thesis which was not published
      I only can tell these professors please be strong get together make the difference and change the system

      Like

      • Did you report it to the authorities?

        You make a blank statement about institutions, but I wonder what the extend of your experience is. The way you present pieces of data doesn’t help any one and it’s not the way to fix a system. You need to be specific with names, journals, and data if you want to be credible.

        Like

      • Gustavo A.

        That is bullshit. Stop taking advantage of a very unusual (and still under investigation) situation in the country to throw such a disgusting accusation.

        Like

  59. Antonio Herrera-Merchan

    Señor o señora Clare Francis.
    Creo que está usted muy equivocado. Muestre documentos, referencias e información que verifiquen lo que afirma porque de lo contrario usted solo sabe escupir acusaciones sin pruebas.
    Muy poco digno de alguien que se dedica a la ciencia (aunque se esconde bajo un seudónimo).
    Aquí estoy esperando. ⏲

    Like

  60. “These studies described the identification of novel protease-coding genes, and their preliminary characterization as proteolytic enzymes. There is no doubt in the scientific community that these human genes exist and have the nucleotide and amino acid sequences we had reported in these articles, that they are expressed in the tissues we showed, and that they constitute proteolytic enzymes. Therefore, the findings reported in these articles have been widely validated by the scientific community, with more than 800 citations altogether.”
    The genes exist, the proteins exist and the papers were cited, therefore we were correct despite the 9 and counting retractions. Interesting logic.

    Like

  61. Antonio Herrera-Merchan

    Pues usted mismo se desmiente. Porque yo no obtuve la JdC como usted literalmente dice:
    “got the Juan de la Cierva Fellowship using two retracted papers on his CV to score high and get a 3 years full-paid position.”
    Y usted mismo lo ha puesto en evidencia que falta a la verdad.
    Usted verá que quiere conseguir con esto.
    Sigo esperando pruebas de sus afirmaciones.

    Like

  62. Very similar to Antonio Herrera-Merchan case, Clara Soria-Valles chronological
    2015; published Nature Cell Biology paper
    2016; received EMBO fellowship and joined into George Daley lab at Harvard.
    2018 September; accepted to Juan de la Cierva Incorpolacion.
    2018 December; retracted Nature Cell Biology paper.
    2019; supposed to start receiving Juan de la Cierva fellowship through 2020.
    Soria-Valles already enjoyed EMBO fellowship and did not return the money. Juan de la Cierva is not yet funded, or at least beginning.
    It is not too late yet. Spanish government should consider.

    Like

    • Paper manipulations are like doping in the sports.
      With the doping you get unfairly medals. With paper manipulations you get unfairly grants.

      I just have read that Ruth Beitia has won the olympic medal after the discoverment of the doping of Shkolina. Shkolina has lost retroactively all theirs medals.
      https://elpais.com/deportes/2019/02/01/actualidad/1549038092_197645.html

      I think that Lopez-Otin grants that came from these manipulations should be removed as well.

      Like

  63. I have inquired Spanish Ministry of Science as below.
    “I would like to inquire again about IJCI-2017-31455. The selected recipient Clara Soria-Valles had retracted her research paper, and her host lab Carlos Lopez-Otin at University of Oviedo retracted another eight articles last week. Please refer El Pais. https://elpais.com/elpais/2019/01/27/ciencia/1548629779_450088.html Soria-Valles is supposed to receive two-years fund from IJCI for 2019-2020. The fellowship may not be fully funded to the person yet, I guess. And credibility of her candidacy is elusive. I wonder if your agency will explain about this in public. “

    Like

  64. https://www.abc.es/ciencia/abci-lopez-otin-errores-detectados-no-tienen-ningun-impacto-sobre-investigacion-201901282207_noticia.html

    “López Otín: «Los errores detectados no tienen ningún impacto sobre la investigación»”

    There we have it!

    Like

  65. https://www.20minutos.es/noticia/3548287/0/rector-muestra-total-apoyo-universidad-oviedo-lopez-otin/

    “El rector muestra el “total apoyo” de la Universidad de Oviedo a López Otín”

    The rector shows the “total support” of the University of Oviedo to López Otín

    Rector nailing his colors to the mast.

    Like

  66. https://www.asturiasmundial.com/noticia/105443/universidad-asturiana-cierra-filas-defensa-lopez-otin/

    University of Oviedo threatening legal action? It should think twice before defending the indefensible.
    Laughingstock already.

    “Oviedo.-La Universidad de Oviedo, por boca de su rector, Santiago García Granda, cerró filas este lunes en torno al investigador Carlos López Otín, algunos de cuyos artículos fueron cuestionados en una “extraña maniobra” secundada anónimamente en las redes sociales. La Universidad asturiana anuncia, así mismo, acciones judiciales “para preservar el buen nombre y reputación de nuestra institución, así como en defensa al derecho al honor y la propia imagen de las y los miembros de nuestra comunidad universitaria en el ejercicio de sus labores investigadoras, docentes y de gestión.”

    “Oviedo.-The University of Oviedo, through the mouth of its rector, Santiago García Granda, closed ranks on Monday around the researcher Carlos López Otín, some of whose articles were questioned in a “strange maneuver” anonymously seconded on social networks. The Asturian University also announces legal actions “to preserve the good name and reputation of our institution, as well as in defense of the right to honor and the image of the members of our university community in the exercise of their investigative work. , teachers and management. ”

    “En todo caso, la Universidad de Oviedo se reserva su derecho a emprender acciones judiciales para preservar el buen nombre y reputación de nuestra institución, así como en defensa al derecho al honor y la propia imagen de las y los miembros de nuestra comunidad universitaria en el ejercicio de sus labores investigadoras, docentes y de gestión.”

    “In any case, the University of Oviedo reserves the right to take legal action to preserve the good name and reputation of our institution, as well as in defense of the right to honor and the image of the members of our university community in the exercise of their research, teaching and management tasks.”

    Like

  67. Is the University of Oviedo threatening J Biol Chem for retracting 8 papers, and Nat Cell Biol for retracting 1 paper, with legal action?

    Like

  68. Like A Sandler refers I quite believe most of the fellowships in Spain are not fairly attributed…this includes countries like Portugal where Sonia Melo for example has been benefiting from the system

    Like

  69. https://www.elmundo.es/ciencia-y-salud/salud/2019/01/29/5c4f1ae121efa0466b8b4663.html

    “Más de 50 científicos defienden la validez del trabajo de López Otín tras la retirada de ocho de sus artículos”

    “More than 50 scientists defend the validity of López Otín’s work after the withdrawal of eight of his articles”

    “Los errores detectados no afectan de ninguna manera a las conclusiones de las investigaciones, que han sido validadas de forma independiente en múltiples ocasiones y han servido de base para otros trabajos, como el desarrollo de modelos animales para entender la progresión del cáncer. Nadie duda de su validez”, subraya el investigador.
    Junto a él, firman la carta personalidades de primer nivel en el ámbito de la ciencia como Margarita Salas, profesora Ad Honorem del Centro de Biología Molecular Severo Ochoa; Manuel Serrano, investigador del IRB de Barcelona; Elías Campo, científico del Instituto de Investigaciones Biomédicas Augus Pi i Sunyer de Barcelona; Cristina Garmendia, ex ministra de Ciencia; José López-Barneo, del Instituto de Biomedicina de Sevilla o Juan Bueren, del Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas de Madrid, entre otros.”

    “The errors detected do not affect in any way the conclusions of the investigations, which have been validated independently on multiple occasions and have served as the basis for other works, such as the development of animal models to understand the progression of cancer. of its validity “, emphasizes the researcher. Next to it, the letter signed personalities of first level in the field of science as Margarita Salas, professor Ad Honorem of the Severo Ochoa Molecular Biology Center; Manuel Serrano, researcher at the IRB of Barcelona; Elías Campo, a scientist at the Augus Pi i Sunyer Biomedical Research Institute in Barcelona; Cristina Garmendia, former Minister of Science; José López-Barneo, of the Institute of Biomedicine of Seville or Juan Bueren, of the Center for Energy, Environmental and Technological Research of Madrid, among others.”

    Like

  70. Besides 23 times reused blots in decades ago papers from Lopez-Otin including eight retracted JBC, we should keep in mind that another retracted Nature Cell biology paper of Soria-Valles had unique and worse problems. These involved both swapping patients samples and mocking up bands from artifacts. The retraction note did not address these problems.

    Like

    • “mocking up bands from artifacts”. That is really clever as the artefacts are unlikely to be the same and will not be detected when people look for duplicate images.

      Like

  71. Pingback: Spanish elites rally in support of data manipulation – For Better Science

  72. Antonio Herrera-Merchan

    Do you think that Soria-Valles and me are the same case?
    Do you know what I did?
    Please read, think and try to be honest.
    Best,

    Like

  73. Is there a distinction in Spanish between “error” and “fake shit”? We may be looking at a simple translation problem here, rather than a vast cultural chasm regarding the essentials of science.

    Like

    • adamselwith

      “error” is a valid formal word, “fake shit” is highly informal, actually an expletive and would be converted into “false faecal matter” in the formal register.

      You can qualify “error” with an adjective anyhow. On its own, it means an error of arbitrary size.

      Spanish of course has a rich informal register, but equally, as with English, its equivalent would need to be converted to be admissible in the formal register.

      Like

  74. Antonio Herrera-Merchan

    Morty, did you read these?

    https://elpais.com/elpais/2017/03/07/ciencia/1488903640_769865.html

    And

    https://www.tandfonline.com/doi/full/10.1080/15384101.2016.1205369

    And of course. I am real Antonio Herrera-Merchan.
    Please read both.

    Do you think are the same case? Really?

    Like

    • Life is not black and white. Many whistleblowers were part of a fraud, if you recall Karolinska sentenced Macchiarini whistleblowers for not speaking out fast enough. Was that just? No. Antonio as we all needed money to live on. As many whistleblowers do, who remain silent for years afraid for their jobs. It is important that people speak out. There are not many heroes, but not everyone is a villain. Btw, Susana still is in pay and tenure , despite everything, am I right?

      Like

  75. Antonio Herrera-Merchan

    So, you believe in the media that you want.
    But, do you believe in internal Investigation of CNIC and in legal process and judgment?

    Copy and paste of judgment:

    Los cuatro colaboradores/estudiantes entrevistados coinciden en manifestar que no han participado en ningún caso en la elaboración final de las figuras ni en la escritura de texto alguno, incluyendo materiales y métodos y pies de figura, de ninguno de los artículos de los que son autores. Ninguno de ellos dice haber leído el borrador final del artículo antes de ser enviado a su publicación a la revista, Estas declaraciones contradicen lo expuesto por Consuelo a este Comité. Por otro lado, se detectan además otras contradicciones entre Consuelo y los colaboradores / estudiantes sobre las autorías asignadas a los distintos paneles de figuras de las distintos manuscritos (ver Anexos III y IV).
    3. Todos los investigadores del CNIC que firman como co-autores del artículo de Nature Comm 2015 (P5) coinciden en reconocer que en realidad no se les dio la oportunidad de revisar el borrador final da este trabajo antes de ser enviado pare publicación en la revista (ver Anexo VI)

    Now, you and other can think whatever you want.
    I have researchers that believe me and trust me, CNIC people too.

    You dont have all information and you consider that you say ALL truth and of course you wrong.
    Best,

    Like

  76. Soria-Valles case told us both corrupt systems in Spain and US.
    1. one can publish fake and still hold grant, so as to Herrera-Merchan.
    2. one can disappear from the workplace while make your employer continue paying you during “medical leave” so as to Susana Gonzalez. And to surprise, it happened in Harvard in US where others won’t get payed during such leave.
    We should listen to Soria-Valles’s astonishing skill of how she managed to combine two of corrupt mechanics internationally.

    Like

    • I have discovered that my site was under a troll attack using scrambled IP addresses and fake email identities. I deleted a whole collection of comments by “Clare Francis” and “Morty” (both fake ones), “A.Sandler”, “Wanderer”, “Unicorn”, which used various emails and always new, scrambled IP addresses located all over the world.
      Their common target was Antonio Herrera-Merchan, a former student in the lab of Susana Gonzalez, who eventually reported her for misconduct and became a central whistleblower. I close this debate now and will delete all follow-up troll comments.
      I also point here to my Comments Policy: https://forbetterscience.com/comments-policy/
      and conclude with the remark that the world is not black and white, and whistleblowers should be respected even if they are not all angels and saints.

      Like

  77. And again, Soria-Valles fellowship Juan de la Cierva Incorporacion is starting this year 2019. It is still not too late. Before the money is consumed in place of others who are doing cleaner business, the Spanish ministry should take some action.

    Like

  78. Antonio Herrera-Merchan

    Si ustedes no quieren creer en mi, yo no puedo hacer nada por ello. Lamento que no me crean. Hay otros muchos que si me creen, además conocen más en profundidad todo lo que no se sabe, ni vosotros sabéis.
    Lo voy a decir una vez más. Luego crean lo que quieran. Y ojo, lo dice y lo demuestra la sentencia judicial y la investigación interna del CNIC, si no quieren creerme a mi ok, pero den credibilidad a la una investigación judicial y las pruebas que se acompañan y la del CNIC.
    YO NO CONOCÍA NI ERA PARTICIPE DE LAS MANIPULACIONES QUE SE REALIZARON EN TODAS LAS PUBLICACIONES HASTA SEPTIEMBRE DE 2014 (Congreso de SEBBM en Granada).
    Si usted no me cree ni a mi, ni al juez ni al CNIC… usted sabrá que intereses tiene.

    Like

  79. Pingback: El Teatro de la Ciencia y la Academia. El Otín-Gate – Investigadores En Paro

  80. Pingback: El Teatro de la Ciencia y la Academia. El Otín-Gate – Información Alternativa

  81. Pingback: “Manipular datos es fácil y muy tentador”. Entrevista a Leonid Schneider – Investigadores En Paro

  82. Pablo Menéndez comments ‘trolls are Russian maffias.
    Reminding that he is an author of retracted Nature Cell Biology paper (Soria-Valles, 2015), the paper not mentioned in his commment.
    I am seeing direct conflic of interest there…

    NF-κB activation impairs somatic cell reprogramming in ageing
    Nature Cell Biology (2015) – 168 Comments
    pubmed: 26214134 doi: 10.1038/ncb3207 issn: 1465-7392 issn: 1476-4679

    Clara Soria-Valles , Fernando G. Osorio , Ana Gutiérrez-Fernández , Alejandro De Los Angeles , Clara Bueno , Pablo Menéndez , José I. Martín-Subero , George Q. Daley , José M. P. Freije , Carlos López-Otín

    His comment.
    https://www.lavozdeasturias.es/amp/noticia/asturias/2019/02/17/pasado-otin-verguenza-pueden-ir-/00031550423048634231376.htm

    «Lo que le está pasando a Carlos López Otín es una vergüenza. Que esas mafías que todos conocemos se porten así… Los rusos y esa gente que sale rebotada de la ciencia porque no le va bien. Yo estoy acojonado. Ahora le tocó a Carlos. A mí me puede tocar el año que viene. Hay plataformas profesionales que se dedican a esto. Si quieren arruinarme la carrera, leerán mis publicaciones y algo encontrará. Es como si en un artículo periodístico encuentras una coma fuera de sitio o una errata». El que se expresa en estos términos es el científico asturiano Pablo Menéndez Buján, investigador de prestigio cuyas investigaciones relacionadas con la leucemia infantil, desde la Fundación Josep Carreras, están encontrando gran repercusión en los últimos meses. Menéndez Buján se confiesa discípulo de Otín y no se ahorra halagos. «Si hay alguien riguroso, riguroso, trabajador, humilde y sensato ese es Otín», señala. Está convencido de que lo único que le pasa al bioquímico es que está siendo víctima «de le envidia de los mediocres».

    English
    «What is happening to Carlos López Otín is a shame. That these mafias that we all know behave like this … The Russians and those people who come out bounced from science because it is not going well. I’m scared. Now it was Carlos’ turn. It can touch me next year. There are professional platforms that are dedicated to this. If they want to ruin my career, they will read my publications and find something. It’s as if in a newspaper article you find an out-of-site comma or an erratum. ” The one expressed in these terms is the Asturian scientist Pablo Menéndez Buján, a prestigious researcher whose research related to childhood leukemia, from the Josep Carreras Foundation, is finding great repercussion in recent months. Menéndez Buján confesses to being a disciple of Otín and does not save praise. “If there is someone rigorous, rigorous, hardworking, humble and sensible that is Otín,” he says. He is convinced that the only thing that happens to the biochemist is that he is being victim “of the envy of mediocre people”.

    La retirada de ocho artículos firmados por Carlos López Otín en la revista Journal of Biological Chemistry por fallos con las imágenes que soportan la investigación ha despertado una auténtica tormenta mediática y científica. El prestigioso bioquímico de la Universidad de Oviedo ha dado sobradas explicaciones. Ha reconocido la existencia de errores en las imágenes y ha señalado que incluso se ofreció a retirarlas. Pero también ha garantizado que esos fallos no comprometen el resultado de sus investigaciones. Tanto Otín como otros colegas de profesión han insinuado, de una manera más o menos directa, que está siendo víctima de una especie de trama, orquestada por plataformas especializadas en desacreditar a investigadores de todo el mundo. Esta es exactamente la misma tesis que sostiene Pablo Menéndez.

    English
    The withdrawal of eight articles signed by Carlos López Otín in the Journal of Biological Chemistry for failures with the images that support the investigation has awakened an authentic media and scientific storm. The prestigious biochemist at the University of Oviedo has given many explanations. He has acknowledged the existence of errors in the images and has indicated that he even offered to remove them. But he has also guaranteed that these failures do not compromise the results of his investigations. Both Otín and other colleagues have suggested, in a more or less direct way, that he is falling victim to a kind of plot, orchestrated by platforms specialized in discrediting researchers from all over the world. This is exactly the same thesis that Pablo Menéndez holds.

    «En el mundo de los mediocres cualquiera de los que destaca puede ser su víctima porque hace más mediocres a los demas», argumenta el asturiano que conjuga su doble formación como licenciado en Bioquímica y doctorado en Medicina. Menéndez explica que pasa en Oviedo, al igual que pasa en todo el mundo, que siempre hay gente «dispuesta a putear al vecino». El procedimiento que utilizan es de sobra conocido dentro del círculo científico. Existen plataformas que comienzan a repasar de manera minuciosa todos los papers. En investigadores prestigiosos con centenares de artículos, señala el asturiano, siempre se pueden encontrar algunos errores. Se publica en webs y se amplifica a través de las redes. «Se produce un retuir detrás de otro. Eso genera ruido y más retuits. Sale de los círculos académicos y llega a los medios. Se generan más retuirs… Y se hace un daño irreparable a alguien», explica.

    English
    “In the world of the mediocre any of the highlights can be his victim because it makes others more mediocre,” argues the Spaniard who combines his dual training as a graduate in Biochemistry and PhD in Medicine. Menéndez explains what happens in Oviedo, as happens throughout the world, that there are always people “willing to bitch the neighbor.” The procedure they use is well known within the scientific circle. There are platforms that begin to review all papers in detail. In prestigious researchers with hundreds of articles, notes the Asturian, you can always find some mistakes. It is published on websites and amplified through networks. «One retuir occurs after another. That generates noise and more retuits. It leaves the academic circles and reaches the media. More retuirs are generated … And irreparable damage is done to someone, “he explains.

    En este caso la persona a la que se ha dañado, Carlos López Otín. «Es una persona que lleva más de 40 años trabajando, con 400 publicaciones y con todos los premios, que imparte conferencias en todo el mundo. Ahora con 60 años van y le sacan cuatro paños. Es vergonzoso», insiste indignado Pablo Menéndez, quien sabe de primera mano lo que está sufriendo Otín y su círculo más cercano. Es más, indica que Asturias es tan conocida en el mundo por Fernando Alonso como por el propio Otín.

    English
    In this case the person who has been injured, Carlos López Otín. “He is a person who has been working for more than 40 years, with 400 publications and with all the awards, who gives lectures all over the world. Now with 60 years go and get four cloths. It’s shameful, “insists Pablo Menéndez indignantly, who knows first-hand what Otín and his closest circle are suffering. Moreover, it indicates that Asturias is as well known in the world by Fernando Alonso as by Otín himself.

    Like

    • If you read the original article, it might make you puke. Fake mafias and the usual bullshit tropes like posing with kids. No sane researcher could envy that fraud factory.
      Get one thing straight, muchachos: If it’s fake, it’s not a mistake.
      Or if you prefer: Si es falso, no es un error.
      Would make a nice tattoo, si?

      Like

  83. Damn mediocre Russians! I knew it!

    Like

  84. Senior authors of retracted papers, it is time to stop playing victim. All those “I am a victim” comments are throwing junior first authors under a bus. I am suspecting some hush up that none of junior authors have spoken up so far. The junior authors should own up how they had been treated by senior authors.

    Like

  85. PubPeer comments to CRISPR baby expert G. Q. Daley et al.

    After the Storm — A Responsible Path for Genome Editing
    New England Journal of Medicine (2019) – 3 Comments
    pubmed: 30649993 doi: 10.1056/NEJMp1900504 issn: 1533-4406 issn: 0028-4793

    George Q. Daley , Robin Lovell-Badge , Julie Steffann

    https://pubpeer.com/publications/9C98ECC3CAFADA1487FA4391B4BC7F#3

    “A very sensible remark from Jeanne F Loring on Paul Knoepfler’s site. https://ipscell.com/2019/02/counterpoints-to-lovell-badge-daleys-crispr-baby-rationales/ “Paul, if someone has a question about the technical challenges of CRISPR-Cas, George Daley, George Church, Robin Lovell-Badge, would NOT be the people to ask. Nor would I be, because I have no experience myself in designing or carrying out gene editing with CRISPR. They don’t either. I would ask younger scientists, those who are in the lab experimenting with these techniques, what they find to be the difficulties…do they see off-target effects? Do they do whole genome sequencing to look for other CRISPR-associated abnormalities, like the large deletions that have been reported in some cases in which people actually looked? How about mosaicism? We need to see the actual data, but those data are not generated by us. Invite the postdocs. This is not a matter of being pessimistic or optimistic…it’s just being a scientist. We have opinions, but we also have facts.””

    “Nature, 02 JANUARY 2019
    Human genome editing: ask whether, not how
    The scientific community’s response to the CRISPR twins should not pre-empt broader discussion across society, warns J. Benjamin Hurlbut.
    Nature 565, 135 (2019)
    doi: 10.1038/d41586-018-07881-1 https://www.nature.com/articles/d41586-018-07881-1

    “(to the first comment)
    I give this my strong endorse. It is time for scientists who have no experience with Cas9 to stop lecturing the rest of the field about Cas9. “

    Like

  86. The first author of the Rudolph’s Nature Communications paper Pavlos Mission is currently a postdoc at George Q. Daley lab where other current members are having prominent records on PubPeer.
    Clara Soria-Valles https://pubpeer.com/publications/836AB3A8AB4FD562A2D4CBFBF8ED18 Retracted.
    Deepak Kumar Jha https://pubpeer.com/publications/42A80DA0DB5523DEEF61FEE107F982 duplicated image uncorrected.
    Alena Yermalovich https://pubpeer.com/publications/730D5F3BC8FD82D483604CEE8442B9 duplicated image uncorrected.

    “Anyway, @dfg_public named to me 3 papers proven fabricated. One in @embojournal was corrected. Two others, in @CellCellPress & @NatureComms ? Pristine and untainted. A big f*** you to science from @SpringerNature & @ElsevierNews https://www.cell.com/cell/fulltext/“

    Like

  87. Since E. Pub. from last December, the retraction notice to Soria-Valles (2015, Nature Cell Bio.) finally came out physically on paper-based issue. Now people from some universities without online access, so not recognizing the retraction, can see.
    Retraction | 17 December 2018
    Retraction Note: NF-κB activation impairs somatic cell reprogramming in ageing

    Clara Soria-Valles, Fernando G. Osorio[…] & Carlos López-Otín
    

    https://www.nature.com/ncb/volumes/21/issues/3

    Like

  88. Intensive PubPeer discussion was going on a Cell paper from Marcella Cesana, an alumnus of Daley lab, currently a senior research scientist at TIGEM. The paper has image duplications, splicings and band erasures.

    https://pubpeer.com/publications/04C9D6AC1E5AFB2D80175A707E34EA

    A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA
    Cell (2011) – 12 Comments
    pubmed: 22000014 doi: 10.1016/j.cell.2011.09.028 issn: 1097-4172 issn: 0092-8674

    Marcella Cesana , Davide Cacchiarelli , Ivano Legnini , Tiziana Santini , Olga Sthandier , Mauro Chinappi , Anna Tramontano , Irene Bozzoni

    “Excuse me, it is Figure 6B and Figure 6D, not Figure 6A.

    Control bands are identical in Figure 4B, Figure 6B/D.

    This is the corrected image:”

    “Identical control HPRT bands are present in Figure 4B and Figure 6A and 6B.

    Bands in Figure 4B were rotated 180 degrees and flipped vertically and re-presented in Figure 6A,B, yet labeled differently. ”

    https://imgur.com/a/l6B7XbM

    “It looks like controls are recycled between what appear to be independent experiments.”

    “To be fair, the authors do not claim that the panels in question show independent experiments. Based on reading their discussion and legends, it seems likely that the HPRT control lanes are reused because the WBs for the different muscle proteins shown in the three panels were all done on lysates from the same perturbation experiments.

    Should the authors have been more explicit about what they did here? Yes!
    Is there any reason to believe that the presentation is intentionally misleading, or inconsistent with the authors’ claims or interpretations? I’d say no.”

    “I would agree, but it is puzzling why anyone would have to rotate and flip Western blot bands.

    I’ve never rotated or flipped any gel or WB data in my career.”

    “Not intentionally misleading, but just pure sloppiness.”

    “How can you be so sure?!
    As a senior scientist I have never flipped a western blot and duplicated it, and
    never duplicated a western blot. The manuscript preparation and reviewing/submitting
    process is so rigorous that it should be impossible to end up with these irregularities in
    the final print!”

    “What you have or have not done in your esteemed career is better discussed in threads relating to your own papers.”

    “Why do you find it so hard to agree that it is NOT OK to flip blots as you duplicate them?”

    “Duplications and evidence for splicing in Figure 1C.”

    https://imgur.com/a/VeUKZ3q

    “Not convinced by the purported duplication. Bands rather fuzzy and generic, not identical, different relative orientations. Very weak.”

    “I too did not find either the duplications or splices to be very convincing. There are probably more clear examples of splicing elsewhere in the panel (e.g., between lanes 5-6 in the bottom panel) and in panel 1E.

    But, I am more troubled by possible band erasure efforts in Figure 1C. In one case it looks like a remnant of a band has been lightened in the center (row 3, lane 5), and in another it looks as if a swirly erasure or dodging has been applied (row 2, lane 7). Illustrated in this linked image.”

    https://imgur.com/a/trS8sKF

    Like

  89. A PubPeer comment compares both Daley lab and Hanna lab Nature papers. Each result is conflicting. Daley has that Soria-Valles; Nature Cell Biology paper as a follow-up paper retracted by now, and Hanna has 2 of follow-up Cell Stem Cell papers.

    Chromatin-modifying enzymes as modulators of reprogramming
    Nature (2012) – 1 Comment
    pubmed: 22388813 doi: 10.1038/nature10953 issn: 1476-4687 issn: 0028-0836

    Tamer T. Onder , Nergis Kara , Anne Cherry , Amit U. Sinha , Nan Zhu , Kathrin M. Bernt , Patrick Cahan , B. Ogan Marcarci , Juli Unternaehrer , Piyush B. Gupta , Eric S. Lander , Scott A. Armstrong , George Q. Daley

    https://pubpeer.com/publications/7E225EFEC338C6D184033584EA2E28

    This study from Daley and colleagues demonstrated that the depletion of MBD3 suppressed reprogramming efficiency, which actually contradits with another prominent paper from Hanna and colleagues (Rais 2013). According to Rais et al., the depletion of MBD3 promoted reprogramming efficiency. These conflicting results could question the reliability of experimental platform from the Daley group where another gene (DOT1L) but not MBD3 came up as an obstacle to efficient reprogramming.

    https://pubpeer.com/publications/1F7040DCBE8DB35DAA1328CF8B4219#100

    We should take into consideration that experimental platform might differ between two groups, so even the same gene might work differentially in the same type of cells…? And we expect that further replication may resolve the conflicting conclusions.

    While, Hanna group has published 2 follow-up papers back to back in Cell Stem Cells to underpin their observations in MBD3 :

    https://www.ncbi.nlm.nih.gov/pubmed/30554962 Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules. Cell Stem Cell. 2018 Dec 10. pii: S1934-5909(18)30550-2. doi: 10.1016/j.stem.2018.11.014. [Epub ahead of print]

    https://www.ncbi.nlm.nih.gov/pubmed/30122475 Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency. Cell Stem Cell. 2018 Sep 6;23(3):412-425.e10. doi: 10.1016/j.stem.2018.07.004. Epub 2018 Aug 16.

    And Daley group published one follow-up paper in Nature Cell Biology to reinforce that their original experimental platform picked up the right target. But we need to note that this paper was retracted due to multiple issues in data integrity :

    https://www.ncbi.nlm.nih.gov/pubmed/26214134 NF-κB activation impairs somatic cell reprogramming in ageing. Nat Cell Biol. 2015 Aug;17(8):1004-13. doi: 10.1038/ncb3207. Epub 2015 Jul 27.

    Like

  90. A.Sandler

    The Daley lab website still lists Soria-Valles as an active member of the lab. Despite the trouble to the lab she made, she seems to be very special.
    Is she still receiving EMBO fellowship, and started receiving Juan de la Cierva Incorporacion?

    Clara Soria Valles, Ph.D.
    First Name:
    Clara
    Last Name:
    Soria Valles, Ph.D.
    Position:
    Postdoctoral Fellow

    https://daley.med.harvard.edu/people/clara-soria-valles-phd

    Like

  91. Close examination reveals they are distinct bands. I see no problems in this figure.

    Like

  92. CRISPR baby expert George Q. Daley comments against moratorium on creating CRISPR babies. Yes, we have Bravatnik money.
    “But I’m concerned a moratorium complicates future discussions rather than clarifies them. How long should a moratorium last? How is it enforced? Who gets to decide when to rescind it?”

    After the Storm — A Responsible Path for Genome Editing
    New England Journal of Medicine (2019) – 8 Comments
    pubmed: 30649993 doi: 10.1056/NEJMp1900504 issn: 1533-4406 issn: 0028-4793

    George Q. Daley , Robin Lovell-Badge , Julie Steffann

    https://pubpeer.com/publications/9C98ECC3CAFADA1487FA4391B4BC7F#8

    Stat News, 13 March 2019
    Leading scientists, backed by NIH, call for a global moratorium on creating ‘CRISPR babies’ By Sharon Begley
    Expert opinion nonetheless remains divided on the wisdom of a moratorium. Opponents fear that a formal ban, perhaps backed up with country-by-country laws prohibiting germline editing for baby-making, would be hard to undo. The current “effective moratorium,” as** Doudna** calls it, the one every scientist supposedly recognizes, can more easily melt away if the regulated community itself — genome scientists — reaches a consensus that the technique has cleared the hurdles of safety, efficacy, benefit, and societal support. “We didn’t call for a moratorium because we didn’t think it was the right thing to do,” said Richard Hynes of the Massachusetts Institute of Technology, who co-chaired the National Academies 2017 report on genome editing. “We specified what would be required to move forward.” “I don’t disagree with the call for an international framework to set standards for both the scientific hurdles and the ethical and social concerns,” said Harvard Medical School Dean Dr. George Daley. “But I’m concerned a moratorium complicates future discussions rather than clarifies them. How long should a moratorium last? How is it enforced? Who gets to decide when to rescind it?”
    https://www.statnews.com/2019/03/13/crispr-babies-germline-editing-moratorium/

    Like

  93. “You think Croce lost in court? He did not, he is so obscenely rich, the money was well invested. He proved to everyone he means business. Did you read a single bad word about him since, anywhere? Did he lose his job? No and No”.

    Most of his claims against the New York Times were thrown out.
    The added bonus is that co-authors cannot distance themselves from the paper (in the U.S.).

    Carlo Maria Croce is not longer head of department. This may have been on the cards.
    https://retractionwatch.com/2019/02/04/carlo-croce-loses-a-round-in-legal-bid-to-be-reinstated-as-dept-chair/

    Like

    • Croce is 74, what is he doing heading a department? And you still didn’t point me to any follow-up articles criticising his science.
      Ever been in court? I was, several times. I leave scared for my own future and for the future of democracy if media stops watching over what judges do there.

      Like

  94. The Nature Communication paper from Deepak Jha, current postdoc at George Daley lab, is getting more attentions at PubPeer. A reader criticized that Brian Strahl has not addressed their image duplication.

    An RNA polymerase II-coupled function for histone H3K36 methylation in checkpoint activation and DSB repair
    Nature Communications (2014) – 3 Comments
    pubmed: 24910128 doi: 10.1038/ncomms4965 issn: 2041-1723

    Deepak Kumar Jha , Brian D. Strahl

    https://pubpeer.com/publications/42A80DA0DB5523DEEF61FEE107F982

    “The erratum has not corrected the image duplication pointed by Adiantum Serratodentatum. https://www.nature.com/articles/ncomms7015

    Like

    • This obvious image duplication made by Deepak Jha, current member at the Daley lab, and former student of Brian Strahl, has not been corrected for long. To whom should bring the attention? Current/old PIs? Editors of Nature Communication?

      Like

  95. Lopez-Otin’s progeria Nature Medicine paper gets criticized “completely unacceptable”
    https://pubpeer.com/publications/11210396030EFC51C75D1AC048553E#1

    Development of a CRISPR/Cas9-based therapy for Hutchinson–Gilford progeria syndrome
    Nature Medicine (2019) – 1 Comment
    doi: 10.1038/s41591-018-0338-6 issn: 1078-8956 issn: 1546-170x pubmed: 30778239

    Olaya Santiago-Fernández , Fernando G. Osorio , Víctor Quesada , Francisco Rodríguez , Sammy Basso , Daniel Maeso , Loïc Rolas , Anna Barkaway , Sussan Nourshargh , Alicia R. Folgueras , José M. P. Freije , Carlos López-Otín

    “Both AAV and the Cas9 are integrating in the genome. This should be completely unacceptable Patients should be told
    Data from 5 diff studies (till date) can be found here.
    https://sanchakblog.wordpress.com/2019/03/08/adeno-associated-virus-vector-delivery-method-in-gene-editing-is-not-safe-it-inserts-the-vector-including-the-bacterial-nuclease-in-the-genome-5-studies-in-mice/
    Here is an example of a read has both Cas9 and target gene
    SRR8205688.506.1 CAGTTGTGACACTGGAGGCAGAAGAGCCAGAGGAGATGGATCCACCCACCTGGGCTCCCGCTCCACCGGCAG CCTTGTCAGCAGGCTGCCCACACGTCCCGCACAGCACGGTGCGTGAGCGCAGGTTGTACTCTCTGGTGGCGTA TCTGGTATCCACCAGGTTCCGGTTGATGAAGTCTTTCTGCACGGAGAACCTGTTGATGTCCCGTTCTTCCAGCA GATACTCTTTCTTGGTCTTGCTGGTCCCCCGAGCCGCTGCAGTGGGAACCCTGGGAAGGGAGACAAGGCCCA GGAGGGACAG

    https://imgur.com/a/Q69KA3l

    The insertion encodes the 36 aa SKTKKEYLLEERDINRFSVQKDFINRNLVDTRYATR from the SaCas9 gene
    Here is data from all sequencing samples … ”

    https://imgur.com/a/Vcuc8pR

    Like

  96. A.Sandler

    What is going with Soria-Valles et al. paper about blood stem cells from George Daley lab? Did they publish something already? Or they have started to inject Soria-Valles stem cells to patients without publication evidence?

    Like

  97. Soria-Valles stem cell transplantation work has not been published yet on any source, PubMed indexed journals, biorxiv, Stem Cell Reports, Stemjournal, Lancet’s eBiomedicine, CellPress’ iScience etc. The last time it appeared on Daley’s talk at NIH videocast, November 2018. It will very likely reappear at ISSCR2019, never know if Soria-Valles herself will present or someone replaced Soria-Valles will present.

    Like

    • Ana Pedro

      Yes very probably will reappear…if just only to keep justifying spending grant funding… curiously for funding agencies retractions, misconduct, seems not be important enough to cancel grants although granting agencies may mentioned this in their regulations

      Like

      • A.Sandler

        After several inquiries, I received responses from Juan de la Cierva regarding decision on Soria-Valles’ funding number IJCI-2017-31455. Agencia Estatal de investigacion jdcincorp.seg@aei.gob.es CCed unidad responsable de la Evaluacion s.evaluacion@aei.gob.es to investigate how the funding is processed.

        Like

  98. Inigo Santamaria, former staff at Lopez-Otin lab and passed away last month, had PubPeer records on two of his JBC papers. Neither of them had been corrected or retracted. JBC, why you concluded there is no more papers to be investigated after retractions of eight papers (and one retraction at NCB).

    Molecular cloning and structural and functional characterization of human cathepsin F, a new cysteine proteinase of the papain family with a long propeptide domain
    Journal of Biological Chemistry (1999) – 6 Comments
    pubmed: 10318784 issn: 0021-9258

    I Santamaría , Gloria Velasco , Alberto M. Pendás , Ana Paz , C López-Otín
    https://pubpeer.com/publications/E28349CFF14CE804CF0ADD14128D31

    Cathepsin Z, a novel human cysteine proteinase with a short propeptide domain and a unique chromosomal location
    Journal of Biological Chemistry (1998) – 1 Comment
    pubmed: 9642240 issn: 0021-9258

    I Santamaría , G Velasco , A M Pendás , A Fueyo , C López-Otín
    https://pubpeer.com/publications/0E0C1F23E551921ED211BF524EF95D

    https://www.lne.es/oviedo/2019/02/28/muere-49-anos-inigo-santamaria/2433784.html

    Like

  99. A.Sandler

    So more than 3 months past since retraction of nine papers of Lopez-Otin. We know Lopez-Otin is back to uniovi. What happens to first authors afterwards? Did decade ago JBC authors get faculty jobs? Did recent one Soria-Valles get Juan de la Cierva fellowship?

    Like

  100. American Association for Cancer Research (AACR) has nomiated George Q. Daley as a 2019 class of fellow according to his pioneer work in earlier days.
    https://imgur.com/a/vTJYZ6p#pfxHJ5P

    https://pubpeer.com/publications/61226A71F74171D4410CB1B4916745
    https://pubpeer.com/publications/32494494DF1BA35389D4DD4215FDB6

    “George Q. Daley, MD, PhD, Dean, Faculty of Medicine; Caroline Shields Walker Professor of Medicine; Professor of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, Massachusetts
    For demonstrating the role of the BCR/ABL oncogene in the pathogenesis of chronic myeloid leukemia, and for his creation of pluripotent stem cell-based disease models to improve drug and transplantation therapies for malignant and genetic diseases.”

    https://www.aacr.org/Newsroom/Pages/News-Release-Detail.aspx?ItemID=1284

    Like

  101. Lopez-Otin’s told Elpais that they could not locate only one of triplicate, which contradicted with Retraction Notice from Nature Cell Biology where majority of original numerical data were missing.

    Lopez-Otin interview (Elpais)
    https://elpais.com/elpais/2019/04/10/ciencia/1554916951_385474.html
    Después de un año de pedirles los datos de los experimentos, no encontraron unos triplicados de uno de ellos. Habían hecho los experimentos hacía más de cinco años y no estaban los triplicados de uno. La presión era tal que decidimos retirar ese trabajo.

    English
    “After a year of asking them for the data of the experiments, they did not find a triplicate of one of them. They had done the experiments more than five years ago and they were not tripled by one. The pressure was such that we decided to withdraw that job.”

    Retraction Notice (Nature Cell Biology)
    https://www.nature.com/articles/s41556-018-0259-0
    -original numerical data are not available for the majority of the graphs

    Like

  102. A.Sandler

    If Lopez-Otin leaves uniovi by June, what will happen to his lab? Closed and get lost? And what will happen to retracted Nature Cell Biology author Clara Soria-Valles, she is supposed to bring Juan de la Cierva money there?
    https://www.lne.es/asturias/2019/04/10/otin-estudia-tres-ofertas-gente/2455007.html

    Like

  103. Unaddressed image duplications in three Nature and its associate papers from Daley lab. Is HMS Dean status so powerful that can sweep the dirts under rug?

    Reprogramming of human somatic cells to pluripotency with defined factors
    Nature (2008) – 19 Comments
    pubmed: 18157115 doi: 10.1038/nature06534 issn: 1476-4687 issn: 0028-0836

    In-Hyun Park , Rui Zhao , Jason A. West , Akiko Yabuuchi , Hongguang Huo , Tan A. Ince , Paul H. Lerou , M. William Lensch , George Q. Daley
    https://pubpeer.com/publications/A600E09BABFB5C7A28B86BBA6F8AD9#19

    Epigenetic memory in induced pluripotent stem cells
    Nature (2010) – 2 Comments
    pubmed: 20644535 doi: 10.1038/nature09342 issn: 1476-4687 issn: 0028-0836

    K. Kim , A. Doi , B. Wen , K. Ng , R. Zhao , P. Cahan , J. Kim , M. J. Aryee , H. Ji , L. I. R. Ehrlich , A. Yabuuchi , A. Takeuchi , K. C. Cunniff , H. Hongguang , S. Mckinney-Freeman , O. Naveiras , T. J. Yoon , R. A. Irizarry , N. Jung , J. Seita , J. Hanna , P. Murakami , R. Jaenisch , R. Weissleder , S. H. Orkin , I. L. Weissman , A. P. Feinberg , G. Q. Daley
    https://pubpeer.com/publications/E8874B8B02107526F141197718C646#1

    Lin28 and let-7 regulate the timing of cessation of murine nephrogenesis
    Nature Communications (2019) – 2 Comments
    pubmed: 30635573 doi: 10.1038/s41467-018-08127-4 issn: 2041-1723

    Alena V. Yermalovich , Jihan K. Osborne , Patricia Sousa , Areum Han , Melissa A. Kinney , Michael J. Chen , Daisy A. Robinton , Helen Montie , Dan S. Pearson , Sean B. Wilson , Alexander N. Combes , Melissa H. Little , George Q. Daley
    https://pubpeer.com/publications/730D5F3BC8FD82D483604CEE8442B9#1

    Like

  104. Unaddressed gel splicings from Daley himself and his lab.

    Transformation of an interleukin 3-dependent hematopoietic cell line by the chronic myelogenous leukemia-specific P210bcr/abl protein
    Proceedings of the National Academy of Sciences (1988) – 5 Comments
    pubmed: 3143116 issn: 0027-8424

    G Q Daley , D Baltimore
    https://pubpeer.com/publications/61226A71F74171D4410CB1B4916745#1

    Induction of chronic myelogenous leukemia in mice by the P210bcr/abl gene of the Philadelphia chromosome
    Science (1990) – 7 Comments
    pubmed: 2406902 issn: 0036-8075

    G Q Daley , R A Van Etten , D Baltimore
    https://pubpeer.com/publications/32494494DF1BA35389D4DD4215FDB6#6

    Derivation of embryonic germ cells and male gametes from embryonic stem cells
    Nature (2004) – 4 Comments
    pubmed: 14668819 doi: 10.1038/nature02247 issn: 1476-4687 issn: 0028-0836 issn: 1476-4679

    Niels Geijsen , Melissa Horoschak , Kitai Kim , Joost Gribnau , Kevin Eggan , George Q. Daley
    https://pubpeer.com/publications/A338DD5840B3ED818917AEB1B984C5#3

    Like

  105. Retraction worthy contamination in Daley iPSC studies in both Nature (Park, 2008) and Cell (Park, 2008).

    Reprogramming of human somatic cells to pluripotency with defined factors
    Nature (2008) – 23 Comments
    pubmed: 18157115 doi: 10.1038/nature06534 issn: 1476-4687 issn: 0028-0836

    In-Hyun Park , Rui Zhao , Jason A. West , Akiko Yabuuchi , Hongguang Huo , Tan A. Ince , Paul H. Lerou , M. William Lensch , George Q. Dale

    and

    Disease-specific induced pluripotent stem cells
    Cell (2008) – 4 Comments
    pubmed: 18691744 doi: 10.1016/j.cell.2008.07.041 issn: 1097-4172 issn: 0092-8674

    In-Hyun Park , Natasha Arora , Hongguang Huo , Nimet Maherali , Tim Ahfeldt , Akiko Shimamura , M. William Lensch , Chad Cowan , Konrad Hochedlinger , George Q. Daley

    https://pubpeer.com/publications/A600E09BABFB5C7A28B86BBA6F8AD9

    DNA fingerprint mismatch-1, Daley lab (Park, 2008, Cell, Nature)

    //s.imgur.com/min/embed.js

    DNA fingerprint mismatch-2, Daley lab (Park, 2008, Cell, Nature)

    //s.imgur.com/min/embed.js

    DNA fingerprint mismatch-3, Daley lab (Park, 2008, Cell, Nature)

    //s.imgur.com/min/embed.js

    DNA fingerprint mismatch, Daley lab (Park, 2008, Cell, Nature)

    //s.imgur.com/min/embed.js

    Like

  106. Soria-Valles et al. published Correction. Their 2014 Oncogene paper had been criticized for updating mock dataset of microarray. https://pubpeer.com/publications/8D0F4C1D83621DE5F72E92A4C39787

    Correction: The anti-metastatic activity of collagenase-2 in breast cancer cells is mediated by a signaling pathway involving decorin and miR-21

    “The original microRNA hybridization data for this article, which has been available for the scientific community upon request, has now been deposited in the GEO repository under accession number GSE124432.”

    https://www.nature.com/articles/s41388-019-0825-3

    Like

  107. Pingback: Does ERC help cheaters pay protection money? – For Better Science

  108. PubPeer somehow clears up comments to Soria-Valles’ Journal of Immunology article, that had been critiqued on suspicious tight error bars in graphs.
    https://blog.pubpeer.com/publications/46D48D7AB88DC28DD57C0CC1BF8DF9

    MMP-25 Metalloprotease Regulates Innate Immune Response through NF-κB Signaling
    The Journal of Immunology (2016)
    pubmed: 27259858 doi: 10.4049/jimmunol.1600094 issn: 1550-6606 issn: 0022-1767
    Clara Soria-Valles author has email , Ana Gutiérrez-Fernández , Fernando G. Osorio , Dido Carrero , Adolfo A. Ferrando , Enrique Colado , M. Soledad Fernández-García , Elena Bonzon-Kulichenko , Jesús Vázquez , Antonio Fueyo , Carlos López-Otín

    “The error bars of figure 3C, blood metabolites in six mice are too small. Based on physiological variability of these parameters, it is concerning. The authors could show source data of numerics.”

    Like

  109. Harvard Med School Dean George Daley still displays his Soria-Valles article, retracted half a year ago, as a representative publication on two of his webpages. Deanship is too busy to recognize his own retraction…? Even Lopez-Otin removed the Soria-Valles article from his website just after retraction.

    HMS Dean Webpage

    https://hms.harvard.edu/faculty-staff/george-q-daley

    HMS Dean Lab Webpage

    https://daley.med.harvard.edu/publications

    Like

  110. A.Sandler

    ISSCR meeting in LA is approaching. Could anyone please check if Soria-Valles stem cell transplantation is updated there?

    Like

  111. A.Sandler

    Soria-Valles’ thesis, composed from both retracted Nature Cell Biology and erratum Oncogene, is still valid? What will happen to her degree of PhD in Spanish system?

    Like

  112. ISSCR2019 abstracts are open to all registrants. There is no update of Soria-Valles stem cell injection work in either oral or poster. More information to be followed.
    Full schedule (need registration for full access).
    https://www.eventscribe.com/2019/ISSCR/agenda.asp?pfp=FullSchedule

    Like

  113. PubPeer commment on the latest paper from Daley (Rowe, 2019).

    The developmental stage of the hematopoietic niche regulates lineage in MLL-rearranged leukemia
    Journal of Experimental Medicine (2019) – 1 Comment
    pubmed: 30728174 doi: 10.1084/jem.20181765 issn: 1540-9538 issn: 0022-1007

    R. Grant Rowe , Edroaldo Lummertz Da Rocha , Patricia Sousa , Pavlos Missios , Michael Morse , William Marion , Alena Yermalovich , Jessica Barragan , Ronald Mathieu , Deepak Kumar Jha , Mark D. Fleming , Trista E. North , George Q. Daley

    “Would the authors please clarify if a test for outliers in their datasets was performed? In Figure 3, panel D (please see image below), there seems to be a large amount of overlap between the Control and CCl5 groups, except for a single point in Control which is at ~50 (y-axis) which appears to be causing the statistical significance between the groups.
    For convenience I also included the Statistics section from this publication, but cant find indication of an outlier test”

    https://pubpeer.com/publications/D764C2349E16BEB3DE5B0C04A0E720

    Like

  114. More PubPeer comments on Daley iPSC paper (Park, 2008 Cell).

    Disease-Specific Induced Pluripotent Stem Cells
    Cell (2008) – 19 Comments
    pubmed: 18691744 doi: 10.1016/j.cell.2008.07.041 issn: 1097-4172 issn: 0092-8674

    In-Hyun Park , Natasha Arora , Hongguang Huo , Nimet Maherali , Tim Ahfeldt , Akiko Shimamura , M. William Lensch , Chad Cowan , Konrad Hochedlinger , George Q. Daley

    “Reported distinct genotype, but identical dna fingerprint. ”

    https://pubpeer.com/publications/921ADCB7B6A62E2BDB593B9056AA99#19

    Like

  115. PubPeer comments on another paper of Lopez-Otin (Soria-Valles, 2016).

    NovelLMNAmutations cause an aggressive atypical neonatal progeria without progerin accumulation
    Journal of Medical Genetics (2016) – 2 Comments
    doi: 10.1136/jmedgenet-2015-103695 issn: 0022-2593 issn: 1468-6244 pubmed: 27334370

    Clara Soria-Valles , Dido Carrero , Elisabeth Gabau , Gloria Velasco , Víctor Quesada , Clea Bárcena , Marleen Moens , Karen Fieggen , Silvia Möhrcken , Martina Owens , Diana A Puente , Óscar Asensio , Bart Loeys , Ana Pérez , Valerie Benoit , Wim Wuyts , Nicolas Lévy , Raoul C Hennekam , Annachiara De Sandre-Giovannoli , Carlos López-Otín

    “Could the authors pin point which nuclei have irregular shapes? The presented picture is not easy to appreciate the difference claimed by the authors. ”

    https://pubpeer.com/publications/003BE7B1C083EEA3AB412E392FB099#1

    “The same scale bar (50uM) between all three panels in figure 7B? The nuclei of the right panel is smaller than the others, but no description in the text.”

    https://pubpeer.com/publications/003BE7B1C083EEA3AB412E392FB099#2

    Like

  116. PubPeer comment on another paper of Lopez-Otin (Soria-Valles, 2016).

    iPSCs: On the Road to Reprogramming Aging
    Trends in Molecular Medicine (2016) – 2 Comments
    pubmed: 27286740 doi: 10.1016/j.molmed.2016.05.010 issn: 1471-4914 issn: 1471-499x

    Clara Soria-Valles , Carlos López-Otín

    “NF-kB is not a cytokine… (figure 2) ”

    https://pubpeer.com/publications/C2309A425F37BAC231DF7DC791E77E#2

    Like

  117. PubPeer readers commented text overlaps bwtween articles from Lopez-Otin.
    Two papers have significant similarlity over another paper

    Nuclear lamina defects cause ATM-dependent NF-κB activation and link accelerated aging to a systemic inflammatory response. Osorio FG, Bárcena C, Soria-Valles C, Ramsay AJ, de Carlos F, Cobo J, Fueyo A, Freije JM, López-Otín C. Genes Dev. 2012 Oct 15;26(20):2311-24. doi: 10.1101/gad.197954.112. Epub 2012 Sep 26. PMID: 23019125

    The anti-metastatic activity of collagenase-2 in breast cancer cells is mediated by a signaling pathway involving decorin and miR-21
    Oncogene (2014) – 7 Comments
    pubmed: 23851508 doi: 10.1038/onc.2013.267 issn: 1476-5594 issn: 0950-9232

    C Soria-Valles , A Gutiérrez-Fernández , M Guiu , B Mari , A Fueyo , R R Gomis , C López-Otín

    https://pubpeer.com/publications/8D0F4C1D83621DE5F72E92A4C39787#7

    https://imgur.com/a/jlB7KFy

    MMP-25 Metalloprotease Regulates Innate Immune Response through NF-κB Signaling
    The Journal of Immunology (2016) – 2 Comments
    pubmed: 27259858 doi: 10.4049/jimmunol.1600094 issn: 1550-6606 issn: 0022-1767

    Clara Soria-Valles , Ana Gutiérrez-Fernández , Fernando G. Osorio , Dido Carrero , Adolfo A. Ferrando , Enrique Colado , M. Soledad Fernández-García , Elena Bonzon-Kulichenko , Jesús Vázquez , Antonio Fueyo , Carlos López-Otín

    https://pubpeer.com/publications/46D48D7AB88DC28DD57C0CC1BF8DF9#2

    https://imgur.com/a/jlB7KFy

    Like

  118. Now Soria-Valles and her retracted Nature Cell Biology article (2015) are removed from the lab page of HMS Dean George Daley.
    https://daley.med.harvard.edu/people

    Like

  119. PubPeer readers detected more splicings in a former Daley lab member, John Powers.
    https://pubpeer.com/publications/995C961B41FB2660AFE6432D9422A4#2

    It reminds us of Powers’ “unpublished” biorxiv paper with full of splicing and reusing control bands.
    https://pubpeer.com/publications/5D8FDD6767EE6F2424B5D9B0164CF7#1
    https://pubpeer.com/publications/5D8FDD6767EE6F2424B5D9B0164CF7#3
    https://pubpeer.com/publications/5D8FDD6767EE6F2424B5D9B0164CF7#4

    Powers was an alumnus of the Daley lab and is currently a PI at University of Texas at Austin.
    https://dellmed.utexas.edu/directory/john-powers

    Like

  120. The latest publication from the Daley lab (Kinney et al., Nature Biotechnology, 2019) depends on rebutted iPS cell line, which they claimed as the first evidence of human iPS cell reprogramming recently disputed by PubPeer.

    A systems biology pipeline identifies regulatory networks for stem cell engineering
    Nature Biotechnology (2019) – 1 Comment
    doi: 10.1038/s41587-019-0159-2 issn: 1087-0156 issn: 1546-1696

    Melissa A. Kinney , Linda T. Vo , Jenna M. Frame , Jessica Barragan , Ashlee J. Conway , Shuai Li , Kwok-Kin Wong , James J. Collins , Patrick Cahan , Trista E. North , Douglas A. Lauffenburger , George Q. Daley

    https://pubpeer.com/publications/03DAD0E52F64925DA3B4C9B57E68F7#1

    “Experiments in fig. 5c-e used only one cell line, MSC-iPS. According to the original reference (Park et al, 2008, Nature), MSC-iPS line was estalished with six factors. In addition to Yamanaka four factors, the MSC-iPS line has hTERT and SV40 large T. Other posts pointed that MSC-iPS line expresses transgenes OCT4, SOX2, and MYC. The data of hTERT and SV40 large T are not shown. Because silencing resistant pMIG vector was used, one could assume that hTERT and SV40 large T are still expressed. https://pubpeer.com/publications/A600E09BABFB5C7A28B86BBA6F8AD9#2 https://pubpeer.com/publications/A600E09BABFB5C7A28B86BBA6F8AD9#4

    This concerns that
    whether proliferative capacity of MSC-iPS derived cells is due to hTERT and SV40 large T (fig. 5c).
    the validity of ErbB4-Wnt axis in MSC-iPS derived cells (fig. 5d-e). Indeed, the Artandi group has shown that telomerase induces Wnt signaling. https://www.nature.com/articles/nature08137
    The authors could address if they have validated with other iPS lines.”

    Like

  121. Someone should seriously bring these unaddressed concerns in three papers from current and former members of Daley lab to Nature Communications. What power has been silencing the journal for over 6 months – 4 years?

    Alena V. Yermalovich (former member of Daley lab) and Jihan K. Osborne (current member of Daley lab). Image duplication in a paper from Daley lab.
    Unaddressed for 6 months since PubPeer post.
    https://pubpeer.com/publications/730D5F3BC8FD82D483604CEE8442B9#1
    Deepak Kumar Jha. Current member of Daley lab. Image duplication in a paper back to his thesis at Brian Strahl lab.
    Unaddressed for 6 months since PubPeer post.
    https://pubpeer.com/publications/42A80DA0DB5523DEEF61FEE107F982#2
    Pavlos Missios. Current member of Daley lab. Image splicing in a paper back to his thesis at Lenhard Rudolph lab.
    Unaddressed for 4 years since PubPeer post.
    https://pubpeer.com/publications/31B3D6A98C16815ABD9FAAC8364887#1

    Daley lab current members.
    https://daley.med.harvard.edu/people

    Daley lab alumni.
    https://daley.med.harvard.edu/people/alumni

    Like

    • In addition to Nature Communications, some power has been silencing Nature. Refer extensive discussion on PubPeer about image duplication and cell line contamination in Daley’s career-making article.

      In-Hyun Park. Former member of Daley lab. Current PI in Yale. Image duplication in a paper from Daley lab.
      Unaddressed for 3 months since PubPeer post.
      https://pubpeer.com/publications/A600E09BABFB5C7A28B86BBA6F8AD9#19

      Like

  122. Pubpeer has many unresolved cases, since Authors of the papers decide to avoid clear answers. Like here: https://pubpeer.com/publications/2D084E91EDC85D6C23BC63ACF5E6A8#26
    Read comment 25: clearly states the problem. Read comments 22 and 26: talking a lot of nonsense, like loading control can be run on a separate gel with reduced volume of the samples (!). These comments are probably posted by the Authors, actually. Commenter 22 of PubPeer also posted here lengthy explanations some weeks ago about the needless nature of loading controls in Western blot.

    Like

  123. ‘Trust Harvard,’ Said The Controller.
    Shock: top US scientist Dean George Q Daley says it’s time to start editing genes.
    https://www.theamericanconservative.com/dreher/crispr-gene-editing-harvard-daley/

    Like

  124. While Soria-Valles (2015) Nature Cell Biology article had been removed from HMS Dean George Q. Daley Lab website, the same article still remains on HMS Dean Office website as of July 18, 2019.

    Like

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