Our First Pre-Registration is Live! Replication of…

After months of efforts, my co-authors and I are absolutely delighted to share this preprint, which is special in many ways:

Said, Maha, Mustafa Gharib, Samia Zrig, and Raphaël Lévy. 2023. “Replication of “Carbon-dot-based Dual-emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for in Vivo Imaging of Cellular Copper Ions”” OSF Preprints. November 29. doi:10.31219/osf.io/kf9qe.

This preprint is special because it does not contain any data*: it is a pre-registration of a study. This means that what you will read is not a selection of results assembled to tell a nice story, but our plans to test experimentally a series of hypothesis. We are submitting these plans for peer review, both formal (through PCI RR) and informal (everyone is invited to comment at PubPeer). This makes so much more sense than the traditional peer review system: by peer reviewing our proposed plans and methodology you can truly help us build a more robust study that will contribute to solve the paradox of intracellular sensing with nanoparticle probes and help establish standards in how to study endosomal escape of nanoparticles. Once the pre-registered report receives “In Principle Acceptance”, after one or more rounds of peer review, we will do the experimental work, following the registered protocol, and the results will be published whatever they are. So, not only does this approach helps achieve a sound methodology before the experiments starts, it also helps to solve the problem of publishing bias where “negative results” don’t get published thus distorting the literature.

This preprint is also special because it is the first public step in the ERC NanoBubbles replication project in which we hope to reproduce several highly cited articles that report intracellular sensing with nanoparticles. We will also use this mechanism of pre-registration of studies for the next replications.

Now, I am sure you are wondering how you can help? The good news is that there are many ways. Read our registered report. Share this post to give visibility to this initiative. Peer review the proposal and give us constructive feedback to improve our plans. Get in touch to help us with the next pre-registration where we want to do a multi-site replication and will therefore need partners (nanoparticle synthesis, characterisation, microscopy, image analysis).

I am incredibly grateful to Maha and Mustafa who have done most of the work preparing this document; to Samia who supervised Mustafa for a little bit of organic synthesis (the only bit that we have done pre-registration; see paper for details). We are also thankful to the European Research Council for funding the project, and to Nicole Hondow (University of Leeds) and Aurélien Deniaud (University of Grenoble) for their suggestions and comments on the manuscript.

Editors and scientific journals are reluctant to correct the scientific record; episode 999

In the context of the post-publication peer review initiative of the NanoBubbles project, we posted a detailed comment at PubPeer on Two-Photon Ratiometric Fluorescent Sensor Based on Specific Biomolecular Recognition for Selective and Sensitive Detection of Copper Ions in Live Cells; Analytical Chemistry (2013).

We also contacted the Editor-in-Chief because some of the findings were suggestive of image manipulation.

Like, for exemple, the same cell twice in the same field of view (pink squares).

The Editor-in-Chief contacted the authors, who argued that there was no image manipulation. I am not authorised to reproduce their argument that, unfortunately, they have not posted at PubPeer. The editor found the explanation reasonable and closed the case.

I responded to the Editor-in-Chief the 17/08. I am yet to hear back.

Dear Jonathan,

Thank you for considering this matter and for contacting the authors. I have to admit that I am rather surprised by the arguments offered in response and the conclusion that was reached.
One could point to the fact that doing different treatments on the actual same cells is neither what is described in the article nor what should be done (because treating with A, then with B, then with C, is obviously not the same as comparing treatments by treating with A or B or C). One could also remark that it is not possible that live cells don’t move at all for more than one hour (A and E).

However, there is no need for those slightly subtle arguments.

The most obvious observation that cannot be explained by anything else than an image manipulation is the presence of the same cell twice in the same image (Fig 4, panel G, pink squares). You will note that the two cells are identical down to the most minute details and that they also have exactly the same orientation. I do not believe that any scientist who has worked with cells would find this plausible.

Then, there is the comparison between E and G. The cells in the green rectangle have been rotated by exactly 90 degrees between the two images… but the cells in the red circle have not been rotated between the two images. So the authors are asking us to believe that some cells have not moved at all nor changed shapes, but some have rotated by 90 degrees while keeping their exact same shapes as well as relative positions to one another (but not to those in the green rectangle, obviously). Some have also mysteriously appeared or disappeared. Obviously washing or microscope movement cannot explain those peculiarities.

This is not serious.

I invite you to reconsider and I am looking forward to hear back from you.

Regards,

Raphaël

82% self-citation and grave misrepresentation in an ACS Nano Focus article

This post is cross-posted at PubPeer.

Mirkin and Petrosko review with enthusiasm and even a certain amount of lyricism the properties and applications of Spherical Nucleic Acids, an expression coined by Mirkin to describe particles prepared in the Mirkin group. Out of the 196 cited references, 160 or 82% have Mirkin as an author. Of the 36 other references, 16 are reviews, books or pre-1920 articles. Of the 20 remaining references, 9 are by Mirkin’s former PhD students or former post-doctoral researchers, and one is the clinical trial of Mirkin’s nanoparticles led by a Northwestern colleague. Thus out of 196 references, 10 or 5% are dedicated to non-Mirkin related original contributions to the topic covered in the Nano Focus (Figure 1). One might wonder whether the Editor-in-Chief (another Mirkin group alumnus) and the editorial board have a view on when an excessive amount of self-citations becomes problematic.

Figure 1: Classifications of the references in the Nano Focus article by Mirkin and Petrosko

My main concern is however not the excessive (?) self-citation but the grave misrepresentation. Table 1 documents the discrepancy between the text in the paragraph “Intracellular Diagnostics and Therapeutics” and what happened in reality. The success story narrated by Mirkin and Petrosko hides a commercialisation disaster (the SmartFlares) and repeated clinical applications failures resulting in hundreds of millions of dollars of public and private investments being wasted as well as false hopes given to patients. Those investments and hopes have been fuelled by scientific articles, which, like this one, hype results and ignore or downplay inconvenient facts, and in particular the fundamental limitation that endosomal escape represents for intracellular applications of nanoparticles. The story even includes research fraud in the Mirkin-founded company Exicure.

Table 1: Misrepresentations in the paragraph “Intracellular Diagnostics and Therapeutics” of Mirkin and Petrosko Nano Focus

Text reproduced from Mirkin and PetroskoComment
In the biomedical space, in 2006, we made the remarkable discovery that, when SNA-gold nanoparticle conjugates were introduced into cell culture (epithelial cells), the cells actively internalized them. (75) Through careful inhibition- and knockdown-studies, it was determined that the SNAs were taken up by scavenger receptor (class A)- and caveolin-mediated endocytosis in high quantities unlike their nanoparticle-free DNA counterparts. (76,77) Later, it was shown that this characteristic is general for SNAs, spanning over 60 different cell types, including stem cells. These nanostructures also resisted enzymatic degradation (78) and did not elicit an adverse immune response. (79) Significantly, we now had a way to use SNAs to measure and manipulate intracellular, not just extracellular, contents. This discovery led to the swift development of DNA-functionalized nanomaterials as gene regulation agents (70,75) and intracellular probes. (80)The paragraph seems to suggest that first they 1) discovered the supposedly special property of active internalisation, 2) then did lots of careful studies, 3) which finally gave them a way to manipulate intracellular concents.   But the big claim in the first article, Ref 75 (Rosi et al, Science, 2006) is notactive internalisation, but, as its title indicates, Intracellular Gene Regulation. Thus, contrarily to what this paragraph seems to suggest, Mirkin claimed intracellular regulation already in the first article and not after “careful inhibition- and knockdown-studies” (Ref 76-79 are between 2009 and 2013). This is important because the most remarkable feature of Rosi et al, the foundational 2006 article that claims intracellular regulation, is that it lacks any discussion of the mechanism of uptake of the particles or of the crucial issue of endosomal localisation and endosomal escape.
Specifically, DNA- and RNA-functionalized nanoparticles were found to be potent agents for gene regulation in antisense and RNAi pathways, respectively. These particles were designed to downregulate the expression of proteins associated with cancer in cells, tissues, animals, and ultimately humans. Because these particles were found to actively cross dermal, blood–brain, and blood–tumor barriers, skin (81) and brain cancers (82) were models for initial demonstrations. Teaming up with Amy Paller and Alex Stegh, we explored their potential in these arenas and later in the context of a variety of other cancers as well. The first-in-human clinical trials of nucleic acid-functionalized nanoparticles of this type, which targeted glioblastoma (83) and inflammatory markers in the skin associated with psoriasis, were run by Northwestern University and start-up companies spun out of it.This paragraph severely misrepresents the status of SNAs clinical trials by omitting critical information, namely the results and eventual follow-up of those clinical trials, and the fate of the Mirkin-founded company Exicure. NU-0129 for the treatment of glioblastoma; the Northwestern-led phase 0 clinical trial mentioned in the paragraph (ref 83) included 8 patients. It ended five years ago in September 2018. I could not find evidence of any follow-up.AST-005 for the treatment of Mild to Moderate Psoriasis; Exicure; phase 1b completed in 2018 as part of a collaboration with Purdue Pharma. The study did not result in any statistically significant indications of efficacy and Purdue Pharma notified Exicure it has declined to exercise its option to develop AST-005 at this time (https://www.sec.gov/Archives/edgar/data/1698530/000169853018000016/a8-k43018exhibit991.htm) AST-008; Exicure; phase 1 (completed) and phase 1b/2 started and then was discontinued for “administrative reasons” ; 57 participants were enrolled, at least 26 patients dosed (https://classic.clinicaltrials.gov/ct2/show/NCT03684785); Press release Dec 10, 2021: Discontinuation of further enrollment and the ethical wind down of the Company’s ongoing Phase 1b/2 cavrotolimod (AST-008) clinical trial in patients with solid tumorsXCUR-FXN for the treatment of neurological disorder Friedreich’s Ataxia; Exicure; A clinical trial had been announced for 2022 but the same Dec 2021 press release tells us that there is an indefinite suspension of further development of the company’s XCUR-FXN program.Exicure, the company founded by Mirkin and others to develop the biomedical applications of SNAs, managed to attract hundreds of millions of dollars in grant funding, stock market financing and partnerships with pharma companies. Its value is currently close to zero after multiple failures to deliver combined with the revelation in November 2021 of a research fraud case within the company.  
Moreover, DNA-functionalized particle-based intracellular detection of mRNA, (40,80,84,85) aptamers, (86) and other moieties in single, living cells was accomplished using “nanoflare” technology; a related system called the sticky-flare was developed for determining both the amount and spatial location of intracellular RNA. (87) Nanoflares were ultimately commercialized by AuraSense along with Merck/Millipore as Smart-Flares, and this platform was later enhanced through the development of FIT-flares. (88,89)Again, this paragraph severely misrepresents the status of SNA-based intracellular detection through omitting critical facts, inconvenient articles, and also through mis-citations: A major shortcoming of the Mirkin studies cited is that they do not report how nanoparticles escape endosomes and which proportion of particles do so. There cannot be intracellular sensing without a large proportion of probes reaching their targets and intracellular RNAs are not in endosomes.
The NanoFlares were indeed commercialised 10 years ago, but they are not available anymore since 2018, more than 5 years ago. In spite of an application potentially relevant to all cell biologist, global advertising and distribution, very few articles reported usage of the SmartFlares and the company eventually gave up. To the contrary, several articles (not cited by Mirkin and Petrosko) report that the SmartFlares are localised in endosomes and do not detect mRNAs, in particular our 2015 article The spherical nucleic acids mRNA detection paradox and Maria Czarnek & Joanna Bereta 2017 article SmartFlares fail to reflect their target transcripts levels.
The Sticky-Flares were reported in a PNAS contributed paper (i.e. Mirkin chose the referees of his own article). Our letter to the Editor re-analysing the data and showing that the signal attributed to mRNA localisation instead comes from vesicular transport is available as a preprint: Sticky-flares: real-time tracking of mRNAs… or of endosomes? David Mason, and Raphaël Lévy (2015); https://doi.org/10.1101/029447
The Fit-Flares are presented as if they are an extension of the commercialised SmartFlares platform when in fact, 1) the SmartFlares are not commercialised anymore, and, 2) the Fit-Flares have nothing to do with SmartFlares. In fact, it is unclear why they are mentioned at all given that the Fit-Flares are not SNAs and not even nanoparticle-based!  

Gold injections – how to use the scientific literature to sell snake oil to patients

To know more about the adventures of Dr Doxey, an unscrupulous charlatan ready to do anything to sell his worthless elixir, read the Lucky Luke Western album by Morris.

To know more about Goldic, a real story that does not happen in Lucky Luke’s imagined Wild West, but in the present time, in the UK, Germany and possibly other places, where doctors will take your money in exchange of a miraculous therapy where they will draw your blood and re-inject it after it has been incubated with gold nanoparticles, read Private Eye’s investigation featuring expert and former colleague Patricia Murray (and a quote from me too):

Khan made even wilder claims to a prospective patient: “It gets your body working as it did in your 20s. You will find yourself having more energy, you’ll be quicker in the way that you think – all those things are going to improve.

All of which is quackery, says Patricia Murray, professor of stem cell biology at Liverpool University. She told the Eye: “I am very concerned that this is being promoted as the next generation of stem cells. There is no evidence to support these claims. It seems patients are, once again, being exploited for financial gain.”

If you are in the UK, go and buy your copy in your local newsagent, or subscribe. For the others, I will, with the Eye’s generous authorisation, update this post and share the full article once the next issue of the Eye is out.

In the meantime, you can read a related PubPeer comment. Dr Doxey claimed the efficacy of his elixir based on “years of tireless research”. Present days charlatans mis-use the peer reviewed scientific literature to prove it.

Need for transparent and robust response when research misconduct is found (another example)

On the 22nd of February, Dorothy Bishop published an open letter to CNRS Need for transparent and robust response when research misconduct is found signed by leaders and activists in the field of scientific integrity, which has now a response from the CEO Antoine Petit. That letter was prompted by a case in which I am the whistleblower and I hope to be able to say more about certain aspects of this story in the future.

It is however important to note, as the letter indeed clearly does, that the need for a more transparent and robust response is hardly limited to CNRS. The experience of Clément Fontana unfortunately illustrates that other research organisms in France have also work to do. Clément Fontana discovered his name on an article which had been published without his agreement a couple of years after he had left a post-doctoral position. He also found serious errors in a second article from the same group, article which turned out to be the basis of a successful grant application. His experience challenging those two problems is less than encouraging as you can see by reading his public letter [French]. It may be that in his case the complexity of the organisation of research with multiple institutions sharing the control and management of a single laboratory, a characteristics of the French research landscape, has made it easier for each of those institutions to evade their responsibilities.

What do scientific prizes celebrate?

Another scientific prize has been awarded to Chad Mirkin for his work on oligonucleotide-modified gold nanoparticles (or Spherical Nucleic Acids, aka SNAs, as Mirkin calls them since 2012)… whilst SNA company Exicure continues on its “death spiral“. The prize is the 2023 King Faisal Prize (KFP) in Medicine and Science.

The KFP and Northwestern press releases show a certain disconnect from reality. They specify that:

SNAs can naturally enter human cells and tissues and cross biological barriers that conventional structures cannot, making it possible to detect or treat disease on the genetic level while leaving healthy cells untouched. They are the basis for more than 1,800 commercial products used in medical diagnostics, therapeutics and life science research.

It is debatable whether there is anything special about the way oligonucleotide-modified gold nanoparticles enter cells, penetrate tissues and cross biological barriers, but what is sure is that this property is not currently used to detect or treat any disease, nor are there any commercial products in therapeutics and life science research based on this supposed crossing of biological barriers.

The 1,800 commercial products is a reference to the SmartFlares, which have been discontinued already 5 years ago because they did not detect mRNAs in live cells. The company that develops the biomedical applications is on the verge of bankruptcy. In 2018, after a clinical trial, Purdue Pharma notified Exicure that “it declined to exercise its option to develop AST-005” [Anti-TNF compound against mild to moderate psoriasis]. In 2021, a research improprieties case in the Friedreich’s ataxia program led to the winding down of that program and also of the immuno-oncology program for cavrotolimod (AST-008, a clinical trial was ongoing and had reported some interim results). At the end of 2022, partnerships with pharmaceutical companies Ipsen and Abbvie were unravelling.

In Northwestern’s press release, Mirkin is quoted as saying that “The prize is extraordinary validation for the strategic bet Northwestern made on nanoscience two decades ago, …”. Indeed, Northwestern University even bought shares in Exicure. Maybe the prize money can be used to compensate that financial loss?

As readers of this blog know, I have been raising questions about SNAs here and elsewhere since 2015. With the risk of being called a scientific terrorist again, I shall continue.

Is it somebody else’s problem to correct the scientific literature?

Last week was rather eventful, starting with 3 days at the French Society for Nanomedicine conference in Strasbourg with several members of the NanoBubbles project (including Nathanne Rost and Maha Said who presented posters on post-publication peer review and replications in bionano) and many interesting discussions. I skipped the Tuesday morning sessions to give a seminar at the Institut Charles Sadron, where, 20 years ago, I defended my PhD. The event was recorded and you can now watch it on YouTube (below). The conference also coincided with the publication (Monday afternoon) in the French Newspaper Le Monde of an investigation of a major integrity case in the laboratory that I had joined two years ago. I am the whistleblower. I am quoted in the article noting that 20 months after reporting this case, most of the articles have not been corrected nor retracted. Indeed, of the 23 articles for which I reported concerns, nine have been “corrected”, one has been retracted and thirteen remain untouched. Remarkably, the retracted article has been republished in a predatory journal. The corrections are problematic both for technical reasons (e.g. this one or this one) and because of the lack of transparency (the editors receiving the correction requests and the readers reading those corrections would have been unaware of the real reason why this correction was necessary in the first place). The question of how and when corrections are appropriate in cases of breaches of research integrity would need to be further explored by journals and research institutions. PLoS One’s conditions to publish a correction includes the requirement that there are no concerns about the integrity or reliability of the reported work. Other publishers have much more ambiguous policies. In any case, given the current lack of appropriate action 20 months after my initial reports to institutions, I have now posted on PubPeer my concerns in full so that everyone can make up their own mind and the authors can respond if they wish to do so.

Spherical Nucleic Acids company Exicure “in survival mode”

In 2011, Mirkin co-founded (with Shad Thaxton) the biotechnology company Exicure to develop the biomedical applications of spherical nucleic acids (SNAs). After an internal research fraud (misreporting of preclinical data) and at least two clinical trials failing to deliver encouraging results, the company seems unlikely to survive 2023. In 2018, Chad Mirkin called me a scientific terrorist for raising questions about the SNA technology.

Is the Lancet complicit in research fraud?

Devastating account of the Lancet complicity in keeping on the record article that they have known for years are fraudulent. And which have caused deaths.

Dr Peter Wilmshurst

This blog was written jointly by Patricia Murray, Professor of Stem Cell Biology and Regenerative Medicine, University of Liverpool, UK and Peter Wilmshurst.

The editor of a medical journal that charges readers for access to articles whilst knowingly keeping fraudulent articles on its website is as guilty of financial fraud as an art dealer who knowingly sells forged artworks, but there is no moral equivalence. The complicity in fraud by the editor of the medical journal may also cause death and harm to patients.

In 2008, the Lancet published “Clinical transplantation of a tissue-engineered airway” in a patient with post tuberculous stenosis of her left main bronchus (Macchiarini P, Jungebluth P, Go T et al.)1. The Lancet also published the five year follow up results of the same patient (Gonfiotti A, Jaus MO, Barale D et al. The first tissue-engineered airway transplantation: 5-year follow-up results.)2.

We…

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Letter from Peter Wilmshurst to UCL President & Provost Prof Spence

Following the publication of our letter in the BMJ “Time to retract Lancet paper on tissue engineered trachea transplants” (doi: https://doi.org/10.1136/bmj.o498, published 02 March 2022), Peter Wilmshurst has written to UCL President & Provost Prof Spence. I reproduce his letter with his authorization. It is (or will shortly) also be cross-posted on Leonid Schneider’s blog.


4 April 2022,

Dear Professor Spence

On 18 May 2021 I wrote to you “to enquire what University College London (UCL) has done and plans to do about the fact that Professor Martin Birchall is a co-author of an article (Macchiarini P, Jungebluth P, Go T, et al. Clinical transplantation of a tissue-engineered airway. Lancet 2008;372:2023-30.) that has not been retracted despite being fraudulent.” At that time I presumed that you had enough integrity to realise that a fraudulent medical research article that was resulting in harm to patients should be retracted and enough common sense to realise that a cover up would harm the reputation of UCL. Since then the BMJ has published a letter from colleagues and I calling for retraction of the paper. The BMJ editors and lawyers checked the supporting evidence before publication. I am attaching a copy of the letter.

On 9 July 2021 UCL informed me that Professor Pillay had been appointed to investigate my allegations under UCL’s Research Misconduct Procedure. On 2 November 2021, UCL informed me that Pillay had decided: “The allegation is to be dismissed on the grounds of the substance of the concerns having been considered previously for the following reasons: As you know UCL has conducted a Special Inquiry into Regenerative Medicine at UCL and the Inquiry report was published in September 2017 which made a number of recommendations. The paper in question has been scrutinised by the Inquiry as well as two internal reviews at UCL, a House of Commons Select Committee as well as reviews by the Lancet itself. After careful consideration, I do not consider that you have submitted any new substantial evidence that alters the substance of the allegations that have already been addressed by all these various reviews.”

The new substantial evidence is the correspondence from Professor Castells in early 2018, in which he said the airway collapsed three weeks after the transplantation and it needed to be stented. That means that the main claim of the paper that the graft “had a normal appearance and mechanical properties at 4 months” was false. In addition, Castells said that the claimed improvement in lung function was also untrue. Therefore Pillay’s claim that I had not submitted any new substantial evidence is spurious, at least as far as UCL is concerned. Before 2018, the integrity of the 2008 Lancet paper had been doubted and the ethical basis had been questioned by distinguished surgeons, who pointed out that it was unethical to subject a patient to high risk experimental surgery without prior research demonstrating efficacy in an animal model, particularly when alternative conventional surgery was eminently feasible. The 2018 correspondence from Castells alters the substance of the allegations because it provides incontrovertible proof that the main claims in the paper are false and, because there is no possibility that this could be the result of inadvertent error, the correspondence is conclusive proof of fraud. UCL confirmed that the House of Commons Select Committee that Pillay referred to is the Science & Technology Committee.

There are a number of things that show that the Science & Technology Committee was very concerned that the 2008 Lancet paper has not been retracted. For example:

1. Sir Norman Lamb, who was then Chair of the Science & Technology Committee, added signposts in the previous Committee Report on Regenerative Medicine (2017) to alert readers to incorrect information about the 2008 Lancet paper. The subsequent Report on Research Integrity (2018) refers to the 2008 paper and some of the subsequent follow up research by Professor Birchall at UCL (i.e. RegenVOX). It says “misconduct processes have revealed that the research on using stem cells to support artificial trachea transplants is not reliable, and is based on exaggerated patient outcomes (see Box 2). The ‘RegenVOX’ clinical trial of stem cell-based tissue-engineered laryngeal implants referred to above is now listed
as ‘withdrawn’ on the Clinicaltrials.gov website. Having explored the issue of correcting the research record with our witnesses, we resolved to find a way of flagging the now contested evidence that the Committee received to readers of its report. We have arranged for a note to be attached at the relevant places in the online report with a forward reference to this inquiry. Our intention is to help readers of that earlier report to find further relevant information, not to alter the formal record of our predecessor’s work.

2. After Sir Norman became aware of the email correspondence from Castells in 2018, he sent letters to the Lancet asking the journal to consider retraction of the 2008 paper. Our BMJ letter quotes from Sir Norman’s letter dated 7 March 2019 and UCL has previously been sent a copy of the letter. Sir Norman clearly believed that the emails from Castells were compelling substantial new evidence.

3. Sir Norman also appeared on BBC Television’s Newsnight programme questioning the Lancet’s failure to retract the paper. The link is https://www.youtube.com/watch?v=CzygeoqvjoM The first part of the clip deals with Shauna Davison who died the day after her discharge from Great Ormond Street Hospital when her trachea collapsed and she suffered asphyxia. The second part shows Sir Norman being interviewed on the Newsnight programme.

4. The Medical Research Council has a timeline of “Leading research for better healthcare”. It originally had two major advances for the year 2008. One was “2008 First stem cell-based windpipe transplant conducted”. In early 2019, Sir Norman criticised the MRC for refusing to remove that entry when the Lancet 2008 paper was known to be false. In May 2019, the MRC removed the 2008 paper from the timeline. Below are links to the current timeline https://www.ukri.org/about-us/mrc/who-we-are/timeline/2000-to-present-day/ and the one that was on the MRC website in early 2019
https://web.archive.org/web/20190527083339/https://mrc.ukri.org/successes/timeline-of-
mrc-research-and-discoveries/accessible-version-of-mrc-timeline/

5. Sir Norman is no longer a Member of Parliament, but he has seen our BMJ letter and amongst his other comments, he said that the failure to retract the paper “beggars belief”.

A question remains whether correspondence from Castell was new substantial evidence as far as UCL was concerned. Pillay maintains that the correspondence from Castells does not add to the scrutiny by the Special Inquiry into Regenerative Medicine at UCL and two internal reviews. The Report of the Special Inquiry was published in September 2017. That was before the date on which the fraud was confirmed by the correspondence in May 2018. So obviously the Report does not mention the correspondence between Castells and the Lancet. However, it does raise other concerns about Birchall. For example, it points out that the cell preparation in Bristol took place in a building not licenced under the Human Tissue (Quality and Safety for Human Application)Regulations 2007. The Regulator made a decision not to prosecute the Bristol team for the breaches of the regulations. In addition there is evidence that the four day incubation of the donor trachea with so-called “stem cells” started in Bristol, because the trachea was transported to Barcelona on 10th June, only two days before the operations. Accordingly the trachea should have been classed as an Investigative Medicinal Product in the UK, requiring regulatory approval from the MHRA, but no approval was obtained. Birchall’s attitude to regulations designed to protect patients is illustrated by his statement about the 2008 Lancet paper in an interview to Vogel (Science, 19 April 2013, volume 340, pages 266-8) “We ran rough-shod over regulations – with permission.” In fact there was no permission. He also said “It wasn’t done to the highest possible standards.”

UCL has refused my Freedom of Information requests for the reports of the two internal reviews that Pillay referred to. The reason given by UCL is “Whilst recognising that there is a strong public interest in this area of research, there is also a need for a safe space away from external influence in which allegations of research misconduct can be reviewed and decisions taken. If there was an expectation that these discussions would be disclosed to the public this would inhibit free and frank discussion and would lead to poorer decision-making. For this particular process, the need to ensure robust decision making is considered significant to maintain the integrity and effectiveness of the process itself.” While the Information Commissioners Office is considering my appeal against UCL’s decision, I made an FOI request for UCL to answer the following questions:

1. Was one of the internal reviews that Professor Pillay referred to titled “Allegation of research misconduct against Professor Martin Birchall, Professor Paolo Macchiarini and Professor Alexander Seifalian. Report of the Screening Panel”, which resulted from allegations made by Professor Pierre Delaere in January 2015?
2. Was one of the internal reviews that Professor Pillay referred to titled “Allegations of research misconduct against Professor Martin Birchall from Professor Patricia Murray. Report of the Screening Panel” with the report dated December 2018?
3. If one or both of the two reports mentioned in questions 1 and 2 were not the reports of the
internal reviews that Professor Pillay was referring to, what were the titles of the reports, when were they completed, who made the complaints that resulted in the internal reviews and when did UCL receive those complaints?

UCL has refused to answer those questions for essentially the same reason that it refused to provide
the reports of the internal reviews. UCL said “Whilst recognising that there is a strong public interest in this area of research, there is also a need for a safe space away from external influence in which allegations of research misconduct can be reviewed and decisions taken. UCL relies on individuals coming forward with complaints of academic misconduct, which they may be less likely to do if they thought the fact they had made a complaint might be made public.”

The reason given by UCL for being unwilling to provide a “yes / no” response to questions 1 and 2 is incomprehensible, because I already know the names of those internal reviews, I have copies of both reports and one of the reports is available on the internet. If these two internal reviews are the ones that Pillay was relying on, it calls into question his judgement and his integrity, because neither considered the evidence from Castells. In addition, subsequent events show that the two internal reviews provided false reassurance about the integrity of UCL employees, which raises additional concerns about the rigor of UCL’s internal review processes. Therefore it is worth considering the findings of the two internal reviews that I believe Pillay was referring to.

In his complaint, Professor Delaere alleged misconduct by Birchall and Professor Seifalian, who were
at the time employed by UCL, and by Macchiarini, who had left his honorary professorship at UCL by
the time the report was produced in late 2015. That was before the proof of fraud from Castells became available in 2018. So the report did not consider that evidence. The three UCL professors had been a co-author of a 2011 Lancet paper (Macchiarini P, et al. Tracheobronchial transplantation with a stem-cell-seeded bioartificial nanocomposite: a proof-of-concept study. Lancet 2011;378(9808):1997-2004). In addition, Birchall was named as senior author and Seifalian was a co-author of a 2012 Lancet paper (Elliot MJ, et al. Stem-cell based, tissue engineered tracheal replacement in a child: a 2-year follow-up study. Lancet 2012;380(9846):994-1000). In paragraph 17 of the report of the 2015 UCL internal review (screening) panel it was “noted that the published report on the 2011 synthetic tracheal transplant case, which had included Professor Seifalian as a co-author, was one of six published articles that had been reviewed by four surgeons at the Karolinska University Hospital and cited by them in their allegation of scientific misconduct against Professor Macchiarini on the grounds that the results published by him as the lead author did not appear to correlate with the patients’ actual clinical outcomes. However, the Panel noted that no reference had been made to Professor Seifalian in this allegation, and it determined that there was no prima facie evidence to suggest that Professor Seifalian could be held to account for any of the major inconsistencies or inconsistent and omitted clinical information that had been highlighted by
the Karolinska surgeons in their report.”

The 2011 Lancet paper has now been retracted because it was fraudulent. Professor Seifalian manufactured at Royal Free Hospital / UCL some of the plastic trachea that were supposedly “seeded with the recipients’ stem cells” before they were implanted by Macchiarini when he was working at the Karolinska Institute – the plastic tracheas were not made to GMP (Good Manufacturing Practice) standards. Professor Seifalian was dismissed from UCL on 15 July 2016 for misconduct during his collaboration with Macchiarini. The 2015 screening panel “determined that there was no prima facie evidence that any research misconduct . . . . had taken place, but that there was nevertheless some substance to (Delaere’s) claim that there was a misleading element within the 2012 Lancet published report which had
included Professor Birchall and Professor Seifalian as co-authors – namely with regard to the two figures within the report . . . . These figures had in the Panel’s view not given sufficient emphasis to the presence and possible contribution of the stent and omentum tissue wrap in the recovery of the child patient. Furthermore, the Panel felt that none of the evidence presented by Professor Birchall in this published report in fact serve to demonstrate that the addition of stem cells to the transplanted tracheal scaffold used in the patient case concerned played any therapeutic role in the functioning of the trachea and that none of the effects that were demonstrated in these published reports could be directly linked to the beneficial effects of stem cells
.”

In addition, the 2015 screening panel “felt that Professor Birchall should be urged to give greater consideration to the need for clearer and more representative presentation of information and evidence in his published reports in order to support his assertions, to allow transparent and complete judgement by the scientific community, and to avoid exposure to further allegations of research misconduct, for example the presentation of misleading information, that might jeopardise his future research efforts and subject both himself and UCL to reputational risk. To this end, the Panel felt that Professor Birchall would be well advised to seek to check some of his assertions and the way that these were presented in his published reports with other senior colleagues and collaborators outside the co-authorship of his publications.

If Macchiarini was solely responsible for the false claims about airway transplantation in the 2008 paper and Birchall, Macchiarini’s co-principal investigator, were blameless, how is it that the 2012 paper made misleading claims about tracheal transplantation when Birchall was its senior author and Macchiarini was not even a co-author? The complaint from Professor Murray raised further concerns about publications by Birchall, but they were unrelated to the 2008 Lancet paper. Murray’s complaint was also before the information from Castell’s was known. Although the internal review screening panel’s report was produced after Castell’s correspondence with the Lancet, the screening panel’s report does not mention either the 2008 Lancet paper or Castell’s correspondence.

Murray alleged use of the same images in two separate publications, which had different methods, and deliberate misuse of research findings to support an application for ethics approval. Birchall admitted six images in one paper should not have been used because they related to animal experiments in a different paper. Birchall blamed this on a mistake by a former UCL PhD student and “the scientist overseeing the publication”. Birchall also admitted inaccuracies in a PhD thesis and errors in a research ethics committee application.

In addition, I understand that UCL refused to investigate more serious allegations and said that University College Hospital and Great Ormond Street Hospital should investigate those. One of the more serious allegations was that Birchall and Professor Lowdell knew from work undertaken by their PhD student that freeze-thawing the trachea significantly weakened the structural integrity, making it more likely to collapse. But this information was omitted from all papers and applications for ethics approval from UCL. Failure to take this into account was the reason that Shauna Davison’s trachea collapsed on the day after she was discharged from Great Ormond Street Hospital and, as a result, this 15 year old child died from asphyxia.

From these documents, I do not gain the impression of an aberrant medical researcher. Rather I see
a departmental culture of dishonesty and poor practice that UCL is trying hard to conceal. Therefore it is difficult to escape the conclusion that the reason UCL will not provide answers to my FOI questions is that those internal reviews did not consider the 2018 correspondence between Castells and the Lancet. If I am correct, disclosure of the information will confirm that Pillay has fabricated a spurious reason to avoid investigating the research fraud involing Birchall. I believe that if all the facts came to light, UCL would have to explain:

1. Why it employed Birchall and gave an honorary contract to Macchiarini on the basis of their fraudulent Lancet paper.

2. How enthusiasm for bogus science was used to justify lethal experimental surgery on young
patients at hospitals associated with UCL.

3. How large amounts of publicly funded grants were taken by UCL for research predicated on
fraud.

I would like to know what UCL is going to do about this scandal and about the apparent attempt at
cover-up by Pillay.

Yours sincerely

Peter Wilmshurst