Evidence of a Prion-Like Transmission of p53 Amyloid in Saccharomyces cerevisiae
Authors: Samir K Maji
Santanu K Ghosh
Shinjinee Sengupta
Journal: Molecular and cellular biology (2017)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: aggregation; amyloid; cancer; p53; protein
Affiliations: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India., Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India .

Abstract:  Loss of p53 function is largely responsible for the occurrence of cancer in humans. Aggregation of mutant p53 has been found in multiple cancer cell types, suggesting a role of aggregation in loss of p53 function and cancer development. The p53 protein has recently been hypothesized to possess a prion-like conformation, although experimental evidence is lacking. Here, we report that human p53 can be inactivated upon exposure to preformed fibrils containing an aggregation-prone sequence-specific peptide, PILTIITL, derived from p53, and the inactive state was found to be stable for many generations. Importantly, we provide evidence of a prion-like transmission of these p53 aggregates. This study has significant implications for understanding cancer progression due to p53 malfunctioning without any loss-of-function mutation or occurrence of transcriptional inactivation. Our data might unlock new possibilities for understanding the disease and will lead to rational design of p53 aggregation inhibitors for the development of drugs against cancer. 

Retracted: Yes

PubPeer comments:
 There are a lot of colony duplications in the figures of this paper. The duplicated and rotated colony in Fig. 1C shown here reappears in subsequent figures too ![image] , 
 There does seem to be a thread of image re-use running through this paper. A closer look reveals several uses of the  white colony with some rotations, as well as a blue one: ![file] There also appears to be re-use of panels showing colony growth assays, and in some cases apparent duplication of individual spots: ![file] This appears to throw serious doubt on the core claims of this paper, which seem to have received limited notice despite their apparent importance. Can the authors clarify these apparent issues? , 
 #2 Thank you *Salsola* for stepping up to the plate. I agree with all of your assessments. You might also take a look at the Fig. 10B top left versus lower right colonies to see if you agree with my assessment that there is duplication? I have not done the full comparison yet but will cross-check the figures once more in case anything obvious is still missing. The Editor in Chief of MCB has now been alerted to the findings we have presented here. Original data in support of the published results for this relatively recent paper should be forthcoming, should they not? , 
 Thank you for critically reviewing my manuscript. Please find the below points: 1.tThe images given in the paper are not COLONIES but PATCHES made from the colonies manually and therefore they have similar appearances. 2.tIn figure 1c the white colonies are looking same. -- It is not the case of image duplication or rotation. They are two same looking patches made on the plates from colonies under same conditions. The patching was done with the use of a bended micro tip and the colonies were all patched in a similar way. For manuscript purpose patches of same appearance and size were selected for figure symmetry. Please see the below figure where you can see marked circles for two same looking patches, if reverted. The same is applied for fig 2 ii and iii). 3.t Regarding the blue color patches, there is a faded outline created on the margin of those patches thus, resulting for them to appear the same. Again, same size patches were selected for manuscript purpose. 4.tFig 1 iii and Fig 2iv, the first panel is same, that is because that panel represents the control type of cells WITHOUT the effect of any 3-aminotriazole (3-AT). Under the conditions of no 3-AT and same dilutions of cells, the frogging assay will show same growth pattern of the cells. 5.t All 3 spots identical except rightmost spot in Fig 1 iii u2013 this happens in frogging assay because it is replica plating of one strain where the cells were spotted with help of a frogger on 4 different plates. The entire image is the representation of a single plate and none of the spots can be individually controlled. The spots look identical since this is a replica plating technique. Hope we have satisfied all the queries. Let us know if you have any other questions. All the above observations will not impact the overall conclusion of the paper. ![file] , 
 #4 Regarding point 2., I can only say that the authorsu2019 ability to duplicate *identical* u201ccoloniesu201d is only matched by their ability to recreate *identical* backgrounds for their images - leaving no doubts in the readersu2019 minds as to the quality of the research presented. *** ![file] *** ![file] , 
 #4 * (A.) Based on many years of experience with the methods being discussed here, I judge that the authors explanations are simply not credible. The suggestion that the similarities already noted are a coincidental result of similar patching and or frogging technique cannot be taken seriously; instead, it is abundantly clear that the spots and patches all have unique  fingerprint features that allow even a casual observer to detect identities and deduce a shared origin. The additional example posted by the author only further reinforces this point -- the circled patches are in fact only mildly similar and have clear differences such that they would never have been flagged as identical by previous commenters. * (B.) Re: the authors response point 4: * Fig 1 iii and Fig 2iv, the first panel is same, that is because that panel represents the control type of cells WITHOUT the effect of any 3-aminotriazole (3-AT). * No, this is incorrect, as the experiments are claimed to be different -- In Fig 1iii, the two rows are claimed to be - + p53, whereas in Fig 2iv, the two rows are both claimed to contain p53 and instead differ in terms of - + the P8 fibril ( seed ). * (C.) There are further problematic issues with additional duplications, as annotated below * * (i.) Fig2Aiv, panels 45 60 mM 3-AT -- there is duplication of some spots but not others: ![file] * * (ii.) Fig5 -- there is duplication of a spot between panels A and B, which are claimed to use different forms of p53 (full-length in A, or  core [= aa 92-312] in B): ![file] * * (iii.) Fig10B -- as described above in #3, there is duplication of rows in two panels (0 mM +seed vs. 60 mM -seed): ![file] , 
 Will further look into these comparing with the raw data. , 
 #4 #5 #6 #7 Thank you Dr. Ghosh for responding. I would expect plating out replicates to be done more or less in the way you indicate. But that does not mean that they should be close to pixel identical in the images placed in the figures. That is why I began by submitting a well-resolved image in my original post, so that the similarities, including the background, would be unambiguous. As has been reiterated in #5. I am in full agreement with both *Actinopolyspora* and *Leucanella* that these images are much too similar to have arisen by chance. And, as visible in #6, the Fig. 10B colonies include line artefacts in the background that would be exactly superposable if one were to be motivated enough to do this. But they are labelled as different experiments: u201c0 mM +seedu201d versus u201c60 mm - seedu201d. , 
 #7 * Will further look into these comparing with the raw data. * That is certainly warranted. Something else to consider when investigating the causes of these irregularities: As mentioned in comment #6, in Fig 2Aiv the two panels contain duplications of several spots (toward left) but not others (toward right). This raises the question of how this could occur. Notably, the two panels share background features throughout, including their right-hand sides. If one examines the places where the growth spots are NOT identical in the two panels, there are hints of smudging or blurring in the right (60 mM) panel, possibly obscuring original growth spots. See below for some illustration. CYAN highlights background features that are shared between the two panels. ORANGE highlights some of the differences. Potential smudged blurred regions can be appreciated by comparing the top vs. bottom images, focusing on regions highlighted in ORANGE in the bottom image. (I did not annotate all relevant feature, only representatives.) ![file] , 
 2020 retraction. https: mcb.asm.org content 40 4 e00627-19 We retract this article because there are multiple image duplications in Fig. 1, 2, 3, 5, and 10 that occurred unintentionally due to inaccurate copying and pasting from the several similar-looking original images. We all agree with this retraction. We apologize for any inconvenience this may have caused. , 
 #10 I would like to thank the several other anonymous commentators who devoted their time to analysing these figures, for their exemplary teamwork in expediting the investigation of this paper. I would also like to thank MCB for their efficient handling of the issues after being contacted and then deciding upon retraction within a 4 month time span. Research institutes (and research funders) in India might want to reflect upon how they can improve scientific rigour in their institutional cultures. It is easy to succumb to the siren voices insisting upon ever more aggressive, hot, scooping outputs. Which then, to widespread mystification, doesnu2019t end well. Because real scientific progress is more often slow, painstaking and incremental and this is unlikely to ever change. Oh, and another thing, as we move into the era of Open Science and the routine deposition of the original data, there will be no hiding place. Science: Do it properly, or donu2019t do it at all. ,