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Interested in XMRV? You MUST read this!

Discussion in 'XMRV Research and Replication Studies' started by alex3619, Jun 23, 2011.

  1. alex3619

    alex3619 Senior Member

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    Tate Mitchell <tatemitchell@GMAIL.COM> sent the following to co-cure on 23 June 2011:

    http://www.hindawi.com/journals/av/aip/341294.pdf

    Phylogeny-directed search for murine leukemia virus - like
    retroviruses in vertebrate genomes, and in patients suffering from
    Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Prostate
    Cancer.

    Jonas Blomberg1*, Ali Sheikholvaezin1, Amal Elfaitouri1, Fredrik
    Blomberg1, Anna Sjsten1, Johan Mattsson Ulfstedt1, Rdiger Pipkorn2, Clas Kllander3, Christina hrmalm1, Gran Sperber4
    1Section of Clinical Microbiology, Department of Medical Sciences,
    Uppsala University 2Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany 3Cavidi tech AB, Uppsala Science Park, 751 83 Uppsala, Sweden. 4Department of Neuroscience, Uppsala University, Box 593, Biomedical Centre, 751 24 Uppsala, Sweden

    *Corresponding author. Address:
    Jonas Blomberg MD PhD, Professor Emeritus, Clinical Microbiology,
    Academic Hospital, 751 85 Uppsala, Sweden. Email:
    jonas.blomberg@medsci.uu.se. fax: +46 18 551012

    Abstract

    Gammaretrovirus-like sequences occur in most vertebrate genomes.
    Murine Leukemia Virus (MLV)-like retroviruses (MLLV) are a subset,
    which may be pathogenic and spread cross species. Retroviruses highly similar to MLLVs (Xenotropic Murine retrovirus Related Virus; XMRV, and Human Mouse Retroviruslike RetroViruses; HMRV) reported from patients suffering from prostate cancer (PC) and myalgic encephalomyelitis/ chronic fatigue syndrome (ME/CFS) raise the possibility that also humans have been infected.

    Structurally intact, potentially infectious, MLLVs occur in the
    genomes of some mammals, especially mouse. Mouse MLLVs contain three major groups. One, MERV G3, contained MLVs and XMRV/HMRV. Its presence in mouse DNA, and the abundance of xenotropic MLVs in biologicals, is a source of false positivity.

    Theoretically, XMRV/HMRV could be one of several MLLV transspecies
    infections. MLLVV pathobiology and diversity indicate optimal
    strategies for investigating XMRV/HMRV in humans, and raise ethical concerns. The alternatives that XMRV/HMRV may give a hard to detect "stealth" infection, or that XMRV/HMRV never reached humans, have to be considered.

    ------------------------------------------------------------------

    Alex: This is an in-depth review article of the science behind MLVs in humans, with a focus on XMRV. Its conclusion is mostly against XMRV association with ME/CFS, but it does review many of the main issues.

    On an anti-association stance, it is pro-contamination, but also said this: "Although false positive PCR results due to contamination in the laboratory is a frequent event, contamination on such a grand scale is beyond previous experience." They also point out the problem with low contamination rates in controls.

    Of particular interest to me is a discussion that looks like it will be deleted from the final document on the similarities between MLVs in animals and ME/CFS. Similarities include immune cell anergy, encephalitis, gastroenteritis etc. In other words, most ME/CFS symptoms match an MLV infection. Mice with MAIDS even have alcohol intolerance.

    Bye
    Alex

    PS I may post more on this later. I am currently writing a summary for my own use, but if it is completed I may post it here. This paper is full of data - like MLLVs (MLV-like viruses) can infect birds (it is found in some turkeys). MLLVs are therefore better thought of as vertebrate viruses.
  2. eric_s

    eric_s Senior Member

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    In this case i will definitely save this document, so the discussion will not be lost...
  3. Jemal

    Jemal Senior Member

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    How did we dig this up?
  4. alex3619

    alex3619 Senior Member

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    Hi Jemal. this information was posted to cocure, an ME/CFS distribution site with about 2000 members (including me). I am currently running an online search for this document to see what else we know about it. Bye, Alex

    PS This journal is open access and has a direct link to the provisional pdf:

    http://www.hindawi.com/journals/av/aip/341294/

    This paper was only accepted for publication on the 22nd.
  5. Jemal

    Jemal Senior Member

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    Thanks Alex. I was wondering, because this document seems to be in editing mode at the moment... if it is still under embargo, it might not be wise to spread it. This isn't the usual negative study, but something else entirely.

    Wasn't there another study leaked or something a while back on cocure?

    edit: I see the study is linked on their website. Looks like they put up the wrong file though, you can see what parts they edited!
  6. alex3619

    alex3619 Senior Member

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    Two things to be aware of when reading this article. The first is that the authors are unaware of the association between ME/CFS and leukemia/lymphoma. The second is they seem unaware of the WPI finding problems in B cells, including a relative lack of mature B cells. Bye, Alex
  7. alex3619

    alex3619 Senior Member

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    Hi jemal, yes there was, and I started that thread too - it is still deleted. This article is accessed from the main web site - there is no indication it is embargoed but that could be because somebody stuffed up. This is however an online journal I think, it publishes almost immediately. I am still looking into it - it would be annoying if this thread has to be deleted. On the other hand, there is nothing new in this paper, it is a review, not original research. Bye, Alex

    PS This article is "In Press":
    http://www.hindawi.com/journals/av/aip/

    Several other XMRV articles are also in press.

    There is only one published article in this special issue, therefore this is unpublished although publically available. I am not sure where PR should stand on this, I will pm several mods and Cort:

    http://www.hindawi.com/journals/av/2011/si.xmlv/

    Just to check, I just went from the parent publisher to the provisional pdf without any warnings, checks or log-in requirements. There is a chain of complete open access. My current view is that because this is an open access journal, the papers are immediately available upon acceptance. However, due to editing the final version may be slightly different. I am not sure there is a problem here. In any case, the original authors own the copyright - I am emailing one of them to be sure.
  8. Jemal

    Jemal Senior Member

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    This paper screams for additional research. It's also pretty sympathetic to us patients, finally...
  9. ukxmrv

    ukxmrv Senior Member

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    Thanks for that Alex!

    I will look forward to reading these

    Review Article
    MoMuLV-ts-1 - a unique mouse model of retrovirus induced lymphoma transmitted by breast milk
    Joana Chakraborty, Henry Okonta, Hussein Bagalb, and Joan Duggan
    Received 31 January 2011; Revised 16 May 2011; Accepted 6 June 2011

    Academic Editor: Paul Jolicoeur

    and

    XMRV Discovery and Prostate Cancer Related Research
    David Kang, Michael Lee, Jaydip Das Gupta, Eric A. Klein, and R. H. Silverman
    Received 28 March 2011; Accepted 25 May 2011

    Academic Editor: Arifa S. Khan

    and

    Research Article
    Sexual transmission of XMRV:a potential infection route
    Prachi Sharma, Kenneth Rogers, Suganthi Suppiah, Ross Ross Molinaro Ross J. Molinaro, Nattawat Onlamoon, J. Hackett Jr., G. Schochetman, Eric A. Klein, Robert Silverman, and F. Villinger
    Received 27 April 2011; Accepted 25 May 2011

    Academic Editor: Arifa S. Khan
  10. ixchelkali

    ixchelkali Senior Member

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    Whew! There's a lot of information in that article; it's going to take a long, careful reading to absorb it. However, a couple of things jumped out at me as interesting (some of which were in the section being rewritten.


  11. alex3619

    alex3619 Senior Member

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    Hi ixchelkali, I noticed those two quotes you used also, they are several of maybe a dozen things I want to discuss at some point about this article. It wont be till after I have some sleep and then some more time to write up my summary and discussion points. The issue about proteins and not whole virus is now important in ME/CFS. At SOK iirc, it was discussed that most of the antibodies to EBV that are being found are not to whole virus but specific protein epitopes. These viruses may only be producing immune damaging proteins, not more virus.

    Bye, Alex
  12. alex3619

    alex3619 Senior Member

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    My review of the paper

    My review of:

    Phylogeny-directed search for murine leukemia virus - like
    retroviruses in vertebrate genomes, and in patients suffering from
    Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Prostate
    Cancer. Jonas Blomberg1*, Ali Sheikholvaezin1, Amal Elfaitouri1, Fredrik Blomberg1, Anna Sjsten1, Johan Mattsson Ulfstedt1, Rdiger Pipkorn2, Clas Kllander3, Christina hrmalm1, Gran Sperber4

    The is a an article in press at Advances In Virology.

    This review is filtered due to my perspective as an ME/CFS advocate. It does not substitute for reading the original paper.

    The initial discussion on gammaretroviruses talks about MLLVs, or "MLV-like retroviruses". These viruses have a wide host range in mammals, but have even been found in turkeys, giving rise to the claim that these are vertebrate viruses, not just mammalian. The XPR1 receptor used by XMRV is found in many vertebrates.

    Gamma retroviruses that incorporate a cancer causing gene into their structure, which is a known issue, frequently lose their capacity to replicate. My implication from this is that gammaretroviruses might have an evolutionary imperative to foster co-infections. Other disease mechanisms include direct insertion near an oncogene, which can then promote that gene, and immunosuppressive envelope proteins from the virus. Gamma retroviruses found in many animals frequently retain their capacity to replicate. In medicine, both pigs and mice are major concerns, as both contain replication capable gamma retroviruses.

    Humans have both antibody and restriction factors that work against gammaretroviruses. Surface sugars on the virus once it adapts to a human host will be less targeted by some antibody responses, even if they are targeted initially. It is implied from the research that an intact RNase L pathway is critical to fighting this kind of virus.

    The authors think that contact with animals which might carry MLLVs should be a part of epidemiological investigation.

    The authors prefer the term HMRV rather than XMRV because a wider range of viruses have been found.

    In animals MLLVs do not appear to cause prostate cancer. It is an open question as to whether or not they do so in people.

    In ME/CFS, they note that patients often have signs of "immunosuppression, neurological symptoms and often an enteritis". MAIDS in mice and FAIDS in cats show similar symptoms. In MAIDS the retroviruses require helper viruses, presumably to enhance replication. However, replication is not necessary for disease, only the production of the envelope proteins is required, and these have immunological impact.

    They state: "Thus, several observations from ME patients could go along with a MAIDS/FAIDS-like pathogenesis (110,111); the low-grade encephalitis with disturbance of cognition and memory, the sometimes low amounts of virus in blood, the inflammatory cytokine pattern, the frequency of irritable bowel syndrome (94), and the occurrence of ME in conjunction with Giardia infection (112,113). It may be a coincidence that MAIDS mice have been reported to react abnormally to ethanol (114-118) and that ME patients often have a reduced tolerance to alcohol (personal communication from drs Oddbjrn Brubakk and Barbara Baumgarten, Oslo, Norway)."

    "Murine and feline diseases where MLLVs are known to play a major role are leukemia, lymphoma and encephalitis (and other neurological diseases) and, as mentioned, immunodeficiency [113-121]. Autoimmune disease has also been linked to MLLVs [122,123]. MLLVs should thus be searched for in these diseases. So far, studies of associations of XMRV/HMRV with such human diseases have not been published."

    My observation is that the association of leukemia and lymphoma has been presented at conferences repeatedly, although they are correct in that no such publication has appeared in high impact journals. The evidence for encephalitis goes back to 1934, but this is Myalgic Encephalomyelitis research, and so probably overlooked in CFS literature surveys. Several studies in the last few years have shown brain damage in ME/CFS though, and I expect we will be hearing a lot more about this over time.

    It is well known that mouse DNA can induce false positives by contaminating test reagents or samples. However, the integration sites have been mapped in prostate cancer, although this is disputed as two such sites were identical to those found in infected cell lines.

    XMRV PCR primers can be selected to not react with mouse DNA. However, a number of endogenous retroviruses in mice might be almost identical to XMRV in part. Care must be taken to assure that these sequences do not give false positives.

    Due to issues with 22Rv1 XMRV contamination, "all cell lines which have been passed in nude or SCID mice should be suspected of retroviral contamination."

    "If contamination explains all positive PCR results in ME/CFS and prostate cancer, why would the frequency in ME/CFS patients be at least tenfold higher than in the controls? The patient samples may have been more frequently opened than the control samples. At least two kinds of contamination, with mouse and XMRV DNA, respectively, have to be invoked. Although false positive PCR results due to contamination in the laboratory is a frequent event, contamination on such a grand scale is beyond previous experience." [My bolding, AY]

    Reverse transcriptase, an enzyme necessary for retrovirus replication, has limited capacity for mutation - change the enzyme, and the virus cannot replicate properly. The authors are looking at assays that look for reverse transcriptase, in the hope it might show retrovirus involvement.

    Virus isolation is a key piece of evidence of XMRV found by the WPI. However, XMRV could not be isolated from some patient samples when tested again. The original virochip used does however produce results with a low chance of issues from contamination - provided the contamination is not due to XMRV escaped from a lab.

    Antigens used to detect XMRV or HMRVs need to meet a number of criteria. Careful selection of the epitopes (amino sequences) they react to needs to be made. These antigens should cover both folded and unfolded epitopes. (Proteins fold up in natural environments, but outside the body frequenty denature or unfold, and they are then just protein strings.) The authors note: "Several of these serological assays are capable of detecting antibody reactivity to other MLVs. Thus, although it may not be intentional, the intense hunt for XMRV antibodies is also a hunt for other MLLVs in humans. The largely negative outcome [84,100,101,105,200] may be taken as evidence against widespread MLLV infection in humans."

    One hypothesis they discuss is that finding HMRVs in humans may become increasingly difficult with duration of infection, and reference the macaque studies as an example. There are two options they mention:

    1. The infection is low grade or "stealthed" so difficult to detect.
    2. The results are false positives due to contamination.

    Whatever the current view, they agree that ME/CFS patients should not be donating blood.

    I have not bothered with summing up or an abstract - you can read those in the original paper, which is a fascinating read. This review is a cut down version of a rough review containing many direct quotes. I have not posted it as the number of quotes may constitute copyright violation.

    Bye
    Alex
  13. Jemal

    Jemal Senior Member

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    Thanks Alex, having read the paper, I think your review contained all the highlights and was easy to follow.
  14. Bob

    Bob

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  15. ukxmrv

    ukxmrv Senior Member

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    Thanks Alex!

    This is what I hoped someone would do

    (quote)
    Reverse transcriptase, an enzyme necessary for retrovirus replication, has limited capacity for mutation - change the enzyme, and the virus cannot replicate properly. The authors are looking at assays that look for reverse transcriptase, in the hope it might show retrovirus involvement.

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