Research integrity

What Elsa Flores and Tyler Jacks taught each other

"PCR reactions run on agarose gels commonly look similar due to artifacts introduced by the agarose gel and comb." Dr Elsa R Flores, Associate Director, Moffitt Cancer Center

Success in science needs good mentoring. It is not just her amazing creativity which allowed Elsa R. Flores to rise it to the position of Associate Director for Basic Science at the Moffitt Cancer Center in Florida, but also the unwavering support of her postdoctoral mentor, MIT professor, HHMI investigator and a massive heavyweight of cancer research, Tyler Jacks. I like to think that Jacks taught Flores how to rise through academic ranks, and Flores taught Jacks how to, uhm, do science most efficiently.

The Moffitt website informs us:

“Dr. Flores works to accelerate the discovery of cancer mechanisms and to enhance the translation of basic science to the clinic. Dr. Flores’s vision includes recruiting bioengineers to Moffitt to enhance translation of basic science to the clinic through the generation of novel research, biomaterials and medical devices. […] Dr. Flores has published over 85 papers including in high impact factor journals, Nature, Cancer Cell, Molecular Cell, Cell Stem Cell, Cell Metabolism, and Nature Communications.

Dr. Flores is a member of the American Association for Cancer Research (AACR) and American Association for the Advancement of Science (AAAS).  Flores was named an NCI R35 Outstanding Investigator in 2015 and has won numerous prestigious awards throughout her career”

Let’s look at those papers in high impact factor journals then, shall we?

Flores, Jacks, Tsai. You may be forgiven for being confused here who Flores’ partner is in the picture…. Image source: Kenneth Tsai/Twitter

I would like to start with a paper which has most of the key figures on board: Elsa R. Flores, her postdoc mentor Tyler Jacks, and her husband Kenneth Tsai, another mentee of Jacks’ and now vice-chair of pathology at Moffitt. None of them replies to emails, but then again, they are all very important and very busy people, curing cancer and saving lives while you read this.

Elsa R. Flores , Kenneth Y. Tsai, Denise Crowley , Shomit Sengupta , Annie Yang , Frank McKeon , Tyler Jacks p63 and p73 are required for p53-dependent apoptosis in response to DNA damage Nature (2002) doi: 10.1038/416560a 

Fig. S4a
Supplementary figure S4b seems to show a duplicated region that is used to represent the left side of all of the panels. In the case of the mdm2 panel, the region is slightly darker, but shows the same background features at identical locations.
Actinopolyspora biskrensis: “the cyan arrow seems to indicate another differential splice in the PERP panel, and two signals in that band seem unexpectedly similar after horizontal flip. They also seem unexpectedly similar to a signal in the p21 band, after resizing.
Lastly, two of the input signals seem very similar (orange boxes)
.”

Fake gels, what a shame for the great Tyler Jacks. But he is so big, and published so many other papers in Nature, he probably doesn’t care. That two decade old Nature paper did its job, earning millions of dollars for its authors. So what if it’s fraudulent.

But it is not just fake data. Year ago, Nature defended Sam W Lee‘s mouse torture (Raj et al 2011), where poor animals were injected with tumours growing so huge they caused the mice excruciating pain and misery. The reason for the bizarre correction and its mantra that the mice didn’t really suffer and that the “scientific conclusions of the original paper stand” was that Lee was a Harvard professor supported by a bigwig bully, Stuart A. Aaronson. Eventually that Nature paper was retracted, but not for animal abuse of course, but for research fraud findings which “in aggregate undermine the confidence in the integrity of this study“. Read here:

And now, a déjà vu! Again a Nature paper by a research cheater supported by a mighty bigwig, again with mice tortured with huge ulcerating tumours.

Xiaohua Su , Deepavali Chakravarti , Min Soon Cho , Lingzhi Liu , Young Jin Gi , Yu-Li Lin , Marco L. Leung , Adel El-Naggar, Chad J. Creighton, Milind B. Suraokar , Ignacio Wistuba, Elsa R. Flores TAp63 suppresses metastasis through coordinate regulation of Dicer and miRNAs Nature (2010) doi: 10.1038/nature09459

Elisabeth Bik: “Concern about the mouse shown in Supplementary Figure 1a.
The tumor of this mouse looks very big, and it appears the skin is black and burst open. The mouse also looks skinny and in pain. Were these experiments done according to appropriate animal ethics guidelines?

The Nature chief editor announced to me to follow this up. Flores was, at the time of making of that mouse torture study, professor at MD Anderson in Texas. She replied on PubPeer:

We did follow IACUC protocols approved by MD Anderson.

Actually I think Flores is not lying. MD Anderson is a giant research fraud factory where data forgery is not just tolerated but expected, why shouldn’t animal abuse or any other form of misconduct be legal there as well. This huge research hospital in Houston was previously run by the billion-dollar-heavy cheater Ronald DePinho (30 papers on PubPeer), and here by the way is a suspicious paper by he then-MD Anderson president with Flores’ mentor Jacks:

David A Tuveson , Alice T Shaw , Nicholas A Willis , Daniel P Silver , Erica L Jackson , Sandy Chang , Kim L Mercer , Rebecca Grochow , Hanno Hock , Denise Crowley , Sunil R Hingorani , Tal Zaks , Catrina King , Michael A Jacobetz , Lifu Wang , Roderick T Bronson , Stuart H Orkin , Ronald A DePinho , Tyler Jacks Endogenous oncogenic K-rasG12D stimulates proliferation and widespread neoplastic and developmental defects Cancer Cell (2004) doi: 10.1016/s1535-6108(04)00085-6 

And since we talk about MD Anderson: I previously wrote about how whistleblowers get crushed and the worst cheaters like Anil Sood get rewarded and awarded there.

Anil Sood and how much MD Anderson doesn’t care: whistleblowers speak out

My earlier article presented the worrisome research integrity record at the gigantic US cancer research hospital MD Anderson Cancer Center, part of the University of Texas in Houston. Its particular focus was the ovarian cancer researcher Anil Sood, professor of Gynecologic Oncology and Reproductive Medicine and co-director of Center for RNA Interference and Non-Coding RNAs at MD Anderson.…

Anil Sood and other questionable stars of MD Anderson

The MD Anderson Cancer Center, part of the University of Texas and located in Houston, is a giant hub of huge cancer research money, even for US standards. They also do a lot of science there, which only purpose seems to be publishing in big journals in order to generate even more money. If there…

But speaking about Sood… Ta-da, Flores and Sood, plus Sood’s cheating buddy Gabriel Lopez-Berestein, on one fraudulent paper which this journal announced to me to investigate:

Shouyu Wang , Ke Liang , Qingsong Hu , Ping Li , Jian Song , Yuedong Yang , Jun Yao , Lingegowda Selanere Mangala , Chunlai Li , Wenhao Yang , Peter K. Park , David H. Hawke , Jianwei Zhou , Yan Zhou , Weiya Xia , Mien-Chie Hung , Jeffrey R. Marks , Gary E. Gallick , Gabriel Lopez-Berestein , Elsa R. Flores , Anil K. Sood, Suyun Huang, Dihua Yu, Liuqing Yang, Chunru Lin JAK2-binding long noncoding RNA promotes breast cancer brain metastasis Journal of Clinical Investigation (2017) doi: 10.1172/jci91553

Elisabeth Bik: “Orange boxes: The STAT3-CA and ICAM1 panels appear to show an overlap. The green signal is a bit different, however. Some cells appear to be more green in one of the panels, as if exposure changes were not applied over the full photo. The red signal, visible in ICAM1’s panel, appears absent from the STAT3-CA panel.

The Schneider Rule about following one research fraudster in order to meet many others – it always works. In this regard, Flores collaborated with Weizmann Institute professor Varda Rotter in Israel, result is the questionable gels in Bornstein et al 2011:

Chamutal Bornstein , Ran Brosh , Alina Molchadsky , Shalom Madar , Ira Kogan-Sakin , Ido Goldstein , Deepavali Chakravarti , Elsa R. Flores , Naomi Goldfinger , Rachel Sarig , Varda Rotter SPATA18, a spermatogenesis-associated gene, is a novel transcriptional target of p53 and p63 Molecular and Cellular Biology (2011) doi: 10.1128/mcb.01072-10

Rotter posted raw data for Figure 4D, but not for Figure 2A. I previously wrote about Rotter’s research here:

Or how about this PNAS collaboration by Flores with the Cell Death and Depravity team of Gerry Melino and Richard Knight, plus Xin Lu, head of cancer research institute in London (see the two articles below), which had to be corrected in 2014 with:

“The authors note that “Thanks to an alert reader, we noticed that in Fig. 3D, the control ChIP for MDM2 erroneously duplicated a p53-RE-III panel from an earlier paper (1). We thank the reader for bringing this issue to our attention, and we deeply apologize to the scientific community for the error.””

Cell Death and Depravity

Is the journal Cell Death and Disease a disease itself, parasitised by Chinese paper mills? Can it be cured? Not with this team of doctors on editorial board.

The English science supremacy

England leads the world in science, any fule kno. Meet some more of the star jesters: Nick Lemoine, Peter St George-Hyslop and Xin Lu. They are curing cancer and Alzheimer with Photoshop.

With these people, nothing is ever “erroneously” duplicated. Let’s have a look at another beautiful paper by Flores and her mentor Jacks. Its Figure 5 is outrageously fake.

Yu-Li Lin , Shomit Sengupta , Katherine Gurdziel , George W Bell , Tyler Jacks , Elsa R Flores p63 and p73 transcriptionally regulate genes involved in DNA repair PLoS Genetics (2009) doi: 10.1371/journal.pgen.1000680 

“Examining Figure 5 in inverse and adjusting the contrast suggests multiple areas of concern”

Here, Flores explained on PubPeer:

“Agarose gels often look similar due to artifacts introduced by the comb. Image was not flipped as suggested above.”

The requests to share raw data went unanswered. Flores’ coauthor Jacks remained silent. Somehow, these fake gel bands from that evil Figure 5 from the PLOS Genetics study developed a life of their own. Must have been due to that magic comb!

Min Soon Cho , Io Long Chan , Elsa R. Flores ΔNp63 transcriptionally regulatesbrachyury, a gene with diverse roles in limb development, tumorigenesis and metastasis Cell Cycle (2010) doi: 10.4161/cc.9.12.12051 

Actinopolyspora biskrensis: “A panel in Figure 2B seems unexpectedly similar to a panel from an earlier paper, where it is described differently.

Another nice study in Cell Cycle:

Avinashnarayan Venkatanarayan , Payal Raulji , William Norton , Elsa R. Flores Novel therapeutic interventions for p53-altered tumors through manipulation of its family members, p63 and p73 Cell Cycle (2016) doi: 10.1080/15384101.2015.1121333 

Bik: “Of note, this figure is identical to Figure 10 in the PhD thesis of the first author, on page 61.

But this is nothing compared to the Flores masterpiece you will see next. How much money did Jacks, Flores and other coauthors make with this bizarre Photoshop travesty, in grants, personal salaries, cash awards, and don’t forget pharma industry consulting?

Elsa R. Flores , Shomit Sengupta , John B. Miller , Jamie J. Newman , Roderick Bronson , Denise Crowley , Annie Yang , Frank McKeon , Tyler Jacks Tumor predisposition in mice mutant for p63 and p73: Evidence for broader tumor suppressor functions for the p53 family Cancer Cell (2005) doi: 10.1016/j.ccr.2005.02.019 

You probably can guess how Flores retorted on PubPeer when caught:

PCR reactions run on agarose gels commonly look similar due to artifacts introduced by the agarose gel and comb.

Flores then replied to requests for raw data: “I think much of it is gone“.

People like this should be pelted with rotten tomatoes and chased out of science into alternative careers as toilet attendants. But instead, Flores, supported by Jacks, will probably chase you out of whatever job you had for raising the issue of their gels.

Good for them this is Cell Press, hence a retraction is just as unlikely as Flores ever learning to do proper science.

Fousteri affair: Dutch integrity thwarted by academic indecency

Two and a half years after Maria Fousteri was found guilty of scientific misconduct by her former employer, the Leiden University Medical Center (LUMC), exactly nothing at all happened. ERC and Molecular Cell ignored LUMC letters from June 2016, while Fouster’s British co-authors interfered to save own papers. Of 4 scheduled retractions, none took place.

How Emilie Marcus and Cell covered up misconduct at Weizmann

I previously reported about numerous cases of suspected (or even blatantly obvious) data manipulation at the Weizmann Institute of Science in Israel (here, here and here).  Initially I wrongly assumed that the institute does not investigate misconduct evidence on principle. It turned out they do, but these investigations “are not public” as Michal Neeman, Vice…

Here is more, by Flores and her husband Ken, luckily for them in another Cell Press journal:

Xiaohua Su , Young Jin Gi , Deepavali Chakravarti , Io Long Chan , Aijun Zhang , Xuefeng Xia , Kenneth Y. Tsai, Elsa R. Flores TAp63 Is a Master Transcriptional Regulator of Lipid and Glucose Metabolism Cell Metabolism (2012) doi: 10.1016/j.cmet.2012.09.006

Again, Ken and Elsa, the unlikely couple, solving skin cancer:

Deepavali Chakravarti , Xiaohua Su , Min Soon Cho , Ngoc Hoang Bao Bui , Cristian Coarfa , Avinashnarayan Venkatanarayan , Ashley L. Benham , Ramón E. Flores González , Jennifer Alana , Weimin Xiao , Marco L. Leung , Harina Vin , Io Long Chan , Arianexys Aquino , Nicole Müller , Hongran Wang , Austin J. Cooney , Jan Parker-Thornburg , Kenneth Y. Tsai, Preethi H. Gunaratne , Elsa R. Flores Induced multipotency in adult keratinocytes through down-regulation of ΔNp63 or DGCR8 Proceedings of the National Academy of Sciences (2014) doi: 10.1073/pnas.1319743111

Looks like someone cleaned up the first gel lane in these blots
“In Figure 1D, some of the WT-KC panels look very similar

At least Moffitt replied to my emails. Their Senior Member and Research Integrity Officer wrote to me:

We thank you for your note. Moffitt takes these allegations seriously and will review confidentially in accordance with Moffitt’s research misconduct policy.”


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17 comments on “What Elsa Flores and Tyler Jacks taught each other

  1. Earlier trouble at the Moffitt Cancer Center mill.

    https://retractionwatch.com/2016/10/21/cancer-researcher-retracts-19-studies-at-once/

    “A former cancer biologist at the Moffitt Cancer Center in Tampa, Florida has retracted 19 papers from a single journal.”

    https://www.tampabay.com/news/health/research/researcher-left-moffitt-under-a-cloud-from-journal-articles/2300984/

    Like

    • “Daniele Fanelli, a senior research scientist at Stanford University’s Meta-Research Innovation Center who studies scientific misconduct, said the researchers might not have realized they were producing misleading information.”

      Fanelli is really a poisonous gnome and did more damage to research integrity than most of actual research fraudsters.
      No wonder he hangs out with racists, climate change deniers and misogynists.

      Fixing science: with climate denial, misogyny and white supremacism?

      Like

  2. Co-first author of Plos genetics paper and co-authors in two others in Shamit Sengupta, who also had a questionable first-author Nature paper in Sabatini’s lab

    Like

  3. The amount of scientific fraud originating at MD Anderson is staggering at this point.

    Like

  4. NMH, the failed scientist and incel

    I wonder how Patrick Hwu is going to take this story after schilling to NBC news through Flores:

    Like

    • “Dr. Patrick Hwu
      @PatrickHwuMD
      Moffitt Cancer Center President and CEO, @MoffittNews
      . Tumor immunologist. Inspired leader. Girl dad. #DocsWhoRock. Driven to save more lives from #cancer.”

      What is it with these people and their narcissism? Also, what does “Girl dad” mean? Does he like to wear his daughter’s clothes? Does he expect you to applaud him for not forcing his wife to abort a female foetus?

      Like

    • Huh, https://twitter.com/LabElsaFlores is now in private mode.
      Ken still isn’t.

      Proof the couple is unsackable:

      https://en.wikipedia.org/wiki/H._Lee_Moffitt

      Like

      • 27 March Retraction for Elsa Flores and Tyler Jacks.
        https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010699

        Retraction: p63 and p73 Transcriptionally Regulate Genes Involved in DNA Repair
        The PLOS Genetics Editors
        Published: March 27, 2023
        https://doi.org/10.1371/journal.pgen.1010699

        Following the publication of this article [1], concerns were raised regarding Fig 5. Specifically,

        The following data appear more similar than would be expected from experiments representing different conditions:
        ○ RAD51-2&3, lane 6 (WT p73 D) and lane 18 (p63-/- p73 D).
        ○ mre11-3, lane 4 (WT p63 D) and lane 10 (p53-/- p63 D).
        ○ Input, lanes 1–12 and lanes 13–24, flipped horizontally and resized.
        When brightness/contrast levels are adjusted, there appear to be discontinuities suggestive of splice lines in the following locations:
        ○ BRCA2 panel, horizontally near the bottom of the panel from lanes 1 to 16 (WT p53 U to p63-/- p63 D), vertically between lanes 16 & 17 (p63-/- p63 D and p63-/- p73 U), and on the upper edge of the panel between lanes 22 & 23 (p73-/- p63 D and p73-/- p73 U).
        ○ Mre11-3 panel, between lanes 13 & 14 (p63-/- p53 D and p63-/- p63 U) and between lanes 18 & 19 (p63-/- p73 D and p73-/- p53 U).
        The corresponding author stated that the original uncropped images underlying Fig 5 are no longer available. They stated that, to their knowledge, the images were not manipulated.

        In light of the concerns affecting multiple figure panels that question the integrity of these data, the PLOS Genetics Editors retract this article.

        SS, KG, GWB, and TJ agreed with the retraction. ERF did not agree with the retraction. YLL either did not respond directly or could not be reached. SS, KG, and GWB stand by the article’s findings. KG apologizes for the issues with the published article.

        Reference
        1.Lin Y- L, Sengupta S, Gurdziel K, Bell GW, Jacks T, Flores ER (2009) p63 and p73 Transcriptionally Regulate Genes Involved in DNA Repair. PLoS Genet 5(10): e1000680. https://doi.org/10.1371/journal.pgen.1000680 pmid:19816568

        Pupbeer: https://pubpeer.com/publications/C71C74B38AAF69B522C0E82FCF7E87

        Original publicationn.
        PLoS Genet. 2009 Oct;5(10):e1000680. doi: 10.1371/journal.pgen.1000680. Epub 2009 Oct 9.

        p63 and p73 transcriptionally regulate genes involved in DNA repair
        Yu-Li Lin 1, Shomit Sengupta, Katherine Gurdziel, George W Bell, Tyler Jacks, Elsa R Flores

        Affiliation
        1Department of Molecular and Cellular Oncology, Graduate School of Biomedical Sciences, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America.
        PMID: 19816568 PMCID: PMC2752189 DOI: 10.1371/journal.pgen.1000680

        Like

  5. Uncorrupted flowers

    After this retraction and 13 other papers questioned in PubPeer (https://pubpeer.com/search?q=elsa+r+flores), the Moffitt.org website still shows Elsa Flores in the first photo of their front page. She remains Associate Center Director for basic science, as if nothing was happening.

    Like

  6. NMH, the failed scientist and incel

    Whether you get funding or not for your lab comes down to who you know on the committees that review your grant. To get a grant funded, not only do you need have seductive (not necessarily good and reasonable) ideas, you need people that know and like you in places of power. This still happens despite the fact you have several retractions. I bet CR Kahn and Giaccia still say wonderful things about Tanginuchi. Why? Because they have all have retractions to their name. Retractions may be looked upon as the norm for doing research in science.

    Like

  7. Zebedee

    Perhaps it is a p73 thing (p73 is the big brother, or is that sister, of p53)?

    Lots of problematic p73 papers. Something isn’t working. Jumping on the p53 band wagon, but p73 doesn’t hit the spot. Could happen to anybody.

    https://pubpeer.com/search?q=P73

    Like

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