A human torque teno virus encodes a microRNA that inhibits interferon signaling
Authors: James M Burke
Christopher S Sullivan
Jennifer C Cox
Ethel-Michele de Villiers
Rodney P Kincaid
Journal: PLoS Pathogens (2013)
Discipline: MICROBIOLOGY
Keywords: Torque teno viruses; TTVs; miRNA-coding regions; RNA polymerase II; Drosha
Affiliations: The University of Texas at Austin, Molecular Genetics & Microbiology, Austin, Texas, United States of America., Division for the Characterization of Tumorviruses, Deutsches Krebsforschungszentrum, Heidelberg, Germany.

Abstract:  Torque teno viruses (TTVs) are a group of viruses with small, circular DNA genomes. Members of this family are thought to ubiquitously infect humans, although causal disease associations are currently lacking. At present, there is no understanding of how infection with this diverse group of viruses is so prevalent. Using a combined computational and synthetic approach, we predict and identify miRNA-coding regions in diverse human TTVs and provide evidence for TTV miRNA production in vivo. The TTV miRNAs are transcribed by RNA polymerase II, processed by Drosha and Dicer, and are active in RISC. A TTV mutant defective for miRNA production replicates as well as wild type virus genome; demonstrating that the TTV miRNA is dispensable for genome replication in a cell culture model. We demonstrate that a recombinant TTV genome is capable of expressing an exogenous miRNA, indicating the potential utility of TTV as a small RNA vector. Gene expression profiling of host cells identifies N-myc (and STAT) interactor (NMI) as a target of a TTV miRNA. NMI transcripts are directly regulated through a binding site in the 3'UTR. SiRNA knockdown of NMI contributes to a decreased response to interferon signaling. Consistent with this, we show that a TTV miRNA mediates a decreased response to IFN and increased cellular proliferation in the presence of IFN. Thus, we add Annelloviridae to the growing list of virus families that encode miRNAs, and suggest that miRNA-mediated immune evasion can contribute to the pervasiveness associated with some of these viruses. 

Retracted: Yes

PubPeer comments:
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 ![file] This paper does cite the earlier paper (ref 25), but does not state that part of figure 1b had already been published. , 
 Aren t caspase-3 and pro-caspase-3 different proteins? , 
 Following this post, an investigation was instigated by the host institution of the senior author (Barts Cancer Institute) that was then forwarded for further comment and investigation by the host institution where the work was originally performed (Imperial College London), which is also the host institution of the first author. The report is copied in its entirety  Investigation into recent comments made on Pubpeer regarding CANCER GENE THERAPY, Vol: 8, Pages: 308-319, ISSN: 0929-1903 1. Summary Report from Investigating Officer at Barts Cancer Institute (BCI): The BCI has checked the concerns raised by Clare Francis and has made the following assessments on the three points that they are trying to make about the Cancer Gene Therapy paper (McNeish IA, Tenev T, Bell S, Marani M, Vassaux G, Lemoine N, 2001, Herpes simplex virus thymidine kinase ganciclovir-induced cell death is enhanced by co-expression of caspase-3 in ovarian carcinoma cells, CANCER GENE THERAPY, Vol: 8, Pages: 308-319, ISSN: 0929-1903): 1. That the blot in Figure 5 for SKOV3-NRTIS has duplicated 0 24 lanes with 48 72 lanes for p32 and p17, with a cut between them. u2022 The BCI believes that this is true and the lanes have been duplicated. When enlarged 3-fold on screen, you can see the division between lanes 24 48 and there is a small grey sphere embedded in the bands at the same place in both the 0 and 48 lanes. 2. That the blot in Figure 6d for IGROV1-NRTIS for the lower panel has duplicated the mock infected lane and the Ad LM-tk + lane. u2022 The BCI believes that this might also be true. Enlarged, this is not as clear as point 1 above, with only a weak line suggestive of a break between the lanes, although Adobe is picking up the mock infected lane as a separate image from the other 3 lanes. 3. That the blot in Figure 1b was duplicated from another paper (Cell Death Differentiation, 2001; Tenev T, Marani M, McNeish I, Lemoine NR, 2001, Pro-caspase-3 overexpression sensitises ovarian cancer cells to proteasome inhibitors, CELL DEATH AND DIFFERENTIATION, Vol: 8, Pages: 256-264, ISSN: 1350-9047) and is the same as that paperu2019s Figure 5, though it is labelled as Pro-capase 3. u2022 The BCI believes these are duplicates. Perhaps this is just inconsistent labelling with Fig 1b labelled as capase3, though the legend switches between pro-capase3 and capase3, and Fig 5 of the other paper indicating pro-capase3. Although the legend for Figure 1b does not reference the earlier Cell Death Diff paper, which was in press at the time the Cancer Gene Therapy was published, it is referenced in the methods, pg 310, para 2, penultimate sentence ( #25; though again they switch between pro-capase3 and capase3 in the title). When Figure 1b is referred to in the Results, pg 312, para 1, the Cell Death Diff paper is not referenced again. It is unlikely that any of this would have affected the results and is possibly just human error in preparing the plates. 2. Comments on BCI Summary Report by Imperial Investigating Officer. Following discussion with the senior authors of the papers, Profs McNeish and Lemoine, both agree with the Summary Report. They also reported that the original data was no longer available. Imperial College recommends retention of academic research data for 10 years after completion of the project. Since the research was published in 2001, retention of the data is not expected. Contact details are available for two of the co-authors, but they were not contacted. On review of the papers, I agree that there has been apparent duplication of Western blots. For points 1 and 2, these involved vector only control lanes. I also agree that there has been possible duplication of data across papers regarding Figure 1b in the Cancer Gene Therapy paper where the first publication was not references. I note that both papers were being submitted and reviewed at similar times which can lead to reporting confusion on which study takes precedent. Additionally there has been some inaccurate labelling of the figure (for instance Pro-caspase3 is the full-length gene expressed from the vector, while the cleaved caspase 3 protein is what is actually being detected on the Western). None of these issues in my opinion change the conclusions made in the papers. I see no merit in retracting these important publications or publishing an erratum at this late stage, although agree that there have been errors made in producing the figures. Recommendations I recommend that the senior authors make a reply on Pubpeer stating that an internal investigation was carried out at BCI and Imperial, acknowledging the possible duplication of control data on Westerns and minor errors in data reporting. It should also be noted that the original data was no longer available for review. Original data retention following peer-review and publication is advised by Imperial College as 10 years and these papers were published 17 years ago. The investigation stated that the conclusions made from the published studies were valid and important, even accounting for these reporting errors. I recommend that measures are put in place to avoid such issues surrounding research data quality and reporting in future. Since this publication in 2011, Imperial College have made various recommendations on reporting and publishing research data which are now incorporated into research guidelines. It is recommended that the Division of Cancer, Imperial College, reviews current best practice in storing and reporting research data. There is an option of contacting the respective journal editors to highlight this response to Pubpeer. Senior authors may also wish to contact co-authors to share these comments and recommendations. As first author, I accept the findings of this investigation. The Division of Cancer at Imperial College has now established a data integrity committee that will investigates suspected data irregularities and also to review the current practices relating to research data storage and reporting. , 
 #2 Figure 6d. Left p85 panel higher resolution image. High degree of similairy previous noted, but there is also re-sizing. https: imgur.com Dkb0kVT ,