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Negative XMRV CFS study with Ila Singh's name on it (University of Utah)

Discussion in 'XMRV Research and Replication Studies' started by Jemal, May 4, 2011.

  1. Esther12

    Esther12 Senior Member

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    I think that the concerns about contamination have lad a lot of journal to really raise their standards for any positive paper that gets published. If they publish a positive one now, that fails to fully take account of all of the concerns raised by others, then they'll look rather silly if it does turn out to all be contamination. Publishing another negative study is no big reputational risk for them, as if XMRV does turn out ot be related to CFS then it's clearly much harder to show this is the case than most scientists expected.
  2. serg1942

    serg1942 Senior Member

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    Hi, liquid sky. Thanks! In short, some infections like HIV, cancer cells, or even in some autoimmune diseases, there's a released of a substance called Nagalase. This substance inhibits the formation of GcMAF, that is needed to activate macrophages, key cells needed to start the necessary immune response to fight mainly viruses (or other intracellular infections) or cancer cells.

    For instance, in the case of HIV, we could see the release of Nagalase like an evolutionary mechanism for the survival of the virus. When we therefore take GcMAF, we are bypassing this survival mechanism, by activating the proper immune response, that will fight HIV with the proper tools of our own immune system.

    Hi Kurt and ixchelkali, of course, you are very right, I can perfectly be combating infections, other than XMRV, maybe still unknown, or maybe many of the "typical ones" at the same time and with efficacy...What points toward XMRV or a related retrovirus is the high Nagalase found in CFS by Dr. cheney, although this has not been published yet... I have not read that infections other than retroviruses segregate Nagalase... have you?

    And yes, no wonder that lowering pathogens titers improves CFS... The funny thing is that I have been properly tested for all of the typical pathogens in CFS, and I have only been found positive for XMRV and HHV-6... (Again, just an anecdote)

    What I was proposing last night in my post, is the need of thinking in the other direction.

    As far as XMRV, I think there have been 3 solid studies so far: 1 found XMRV, 1 found related XMRV viruses, and the last one found nothing. All of them seem very solid, and for all of them we can find arguments in favor or against... Obviously time will tell, because, as Cort said, one has to be wrong!

    I just thing that it would be more productive if someone would study what we are fighting in order to get better, especially in the case of PWCs undertaken GcMAF treatment, who are improving very much and many of them getting asymptomatic. It can be done by analyzing the immune markers, like cytokines profiles, and many other tests, that would let us to know what to look for.

    Remember that Dr. Mikovits explained that they had found the immunologic-footprint of XMRV. When and if this is published, someone will have to explain what this footprint belogs to, if they don't belong to XMRV...

    Looking forward to Dr. Mikovits's opinion on this ;-)

    Sergio
  3. Daffodil

    Daffodil Senior Member

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    its another retrovirus but when will they find it??
  4. alex3619

    alex3619 Senior Member

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    I have some thoughts on the Shin et. al. study.

    The first is that I concur this is a solid study. We know the reputation of several of the scientists in the study, and Singh especially is acknowledged as an MLV expert. Here are the main discrepances from the study that I can see (I am not doubting the study results, just comparing to Lombardi et. al. and Lo et. al.).

    Shin et. al. have shown, again, that something is very wrong with the studies so far. They have shown that even good testing for XMRV can fail. However, even though they have been very careful, they cannot prove that contamination has occurred - nobody has yet found the contamination source, nor definitively shown how the controls have low levels of positives. They do make one very important point on this though: potential sources of contamination that not usually checked need to be looked at. One that I would like to put forward, again, as a potential contamination source is people - lab workers, researchers, cleaning staff etc.

    Singh is not saying XMRV is not real, and does not infect people - quite the contrary in my view. She is saying that she cannot find an association with XMRV and ME/CFS. The association with cancers, including now breast cancer, is growing however.

    Now further unpublished studies may take a different view on this, I really wish some of them could be made public to help fight the contamination claims, presuming they can do so of course. It has always been possible that XMRV is either not associated or not causal. We just need to know for sure - this is too important to give up on just because the science is getting difficult. The worst case scenario is NOT that XMRV may not be associated with, or causal for ME/CFS, but that it may be causal and we abandoned it too early, perhaps not returning to it for a decade or two.

    I do wonder if XMRV/PMLV contamination is not from people handling the samples or working in the labs. If XMRV is present in even only a couple of percent of people, any lab that employs one of them might be a source of contamination, and so labs with infected employees "find" XMRV, and labs that do not have infected employees don't find XMRV. I am not saying this is the case, but it is a source of contamination that is not always tested, although I do know that at least one lab has done so.

    I agree with those who have been saying that the BWG and Lipkin studies will end the debate on contamination. I am not sure of the timeline on the BWG, but Lipkin is potentially years from completion. Having to wait that long for definitive confirmation of XMRV association is not a pleasing prospect.

    Things that would help enormously include:

    1. Tissue studies - why not run a few simple biopsies? Singh is very good at finding XMRV in tissues. Several people have made this point recently, and many of us have been saying this for many many months. Its kind of obvious. If Singh cannot find any XMRV in a fair number of ME/CFS patient biopsies, that would be very negative for XMRV association, far more negative than a blood study.
    2. Someone commented on going back to tissue positives (prostate cancer patients) and validating their XMRV blood tests on these patients. It is very likely that something like this will be the only way to properly validate tests for some time to come, but I do wonder if there might not be something different between ME/CFS and prostate cancer patients that might make such testing problematic.
    3. Publication of some of the positive studies that are rumoured is important. Several people have commented in recent months, and I concur, that publishing a few of these could really help. Not all of them need to be published, and they do not have to be published in high impact journals - one or two select papers in a very minor journal, just to get the other side of the story out there, could make an enormous difference. One of the possible problems with getting positive papers published is they are trying to get these published in high impact journals, and are finding this difficult.
    4. Nagalase is not the only thing we should be looking at closely. We need a study on finding reverse transcriptase in ME/CFS patients. While there might be viruses or other pathogens that make nagalase, not that I know of any, reverse transciptase is a defining feature of retroviruses. A high prevalence of reverse transcriptase would by definition prove an association between a retrovirus and ME/CFS, though not specific for XMRV or PMLVs. A statistical correlation with nagalase, reverse transcriptase and low NK cell function would be even better. Of course while they are looking at biopsies, why not store some for another study on enteroviruses etc. An ME/CFS gastrointestinal biopsy bank is a good idea.

    I am not committed to XMRV being associated or causal for ME/CFS. I am committed to the view that we need to know for sure. I never ever want to have to read that we found the cause in XMRV and then let it languish for a couple of decades. That would be much harder to take than the news that XMRV is not associated with ME/CFS.

    Bye
    Alex
  5. eric_s

    eric_s Senior Member

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    In this case you will have to give your prostate. No, don't worry, only a bad joke... Thanks for your post.

    Maybe you're right in this point, but i think it would be good to test an assay against a "known positive". So if Ila Singh could correctly determine the XMRV+ prostate cancer cases from her previous study, ideally under blinded conditions, that would prove her assay works in prostate cancer, at least. It could still fail in ME/CFS, who knows.
    And they should also demonstrate it can find the 4% she described finding in healthy controls, if it doesn't do that and so far it hasn't, something's wrong somewhere, don't you think?
    As long as the WPI hasn't correctly identified cases vs controls in blinded samples where somebody other than the WPI only knows the codes, i don't see their samples as "known positives", even though i support the WPI.

    As far as i know, the BWG phase III should be completed by the end of summer, more or less. But there have been delays before.
  6. toddm1960

    toddm1960 Senior Member

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    That's a huge problem also, no one has proved the XMRV in the Science paper was a contamination. This is why Judy goes nuts when the contamination issue is raised. Also under this mind set no new discovery will ever be made, good science looks at all the information available.......not just the safe information.
  7. acer2000

    acer2000 Senior Member

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    Overall this seems like a decently designed study. There are a good number of patients and controls. The patients were supposedly selected by a well known CFS doc and met both the 1994 and CCC criteria. The blood was drawn by a 3rd party. The samples were blinded, etc.. But...

    Dr. Mikovits keeps saying there are specific details of the testing that people aren't following in these studies that make a big difference. From my reading of the paper, the Singh study mainly used 4 PCRs developed in house, an in house ELISA, and an in house Western blot. They used all of these tests on all 300 of the patients and controls.

    They then also tested 14 more people who had been identified by the WPI with their in house methods, and then after also using some of the methods from the WPI/Lo+Alter. But even then, they claim in in the paper that they diverged from the WPI/Lo+Alter testing methods, if even so slightly.

    So while Dr. Singh clearly knows her stuff and appeared to have designed a good study, it wasn't a replication study. Insomuch as those small details of the WPI exact method matter (what Dr. Mikovits keeps saying), this study doesn't directly answer those questions.

    So we still wait for a true exact replication study...

    As a side note, it is interesting that Dr. Singh found that two of the PCR reagent kits had mouse DNA in them (not infectious virus). However, I don't think that can elegantly explain any comprehensive contamination theory.
  8. Parismountain

    Parismountain Senior Member

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    I'm a very very infrequent poster with little to say other than my hope was WPI was right and XMRV was associated with CFS. In my small attempt to communicate with members on the board my repetitive question was on blinding of the original Science paper. I felt all was well with Dr. M as long as samples were treated exactly the same and were blinded. Now I just read this in a summary of the new study:

    Investigators generally not blinded to sample identity

    Ouch I must say that one hurts and deflates. Crud.
  9. Daffodil

    Daffodil Senior Member

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    why cant they just the virochip and find out what we have??? i mean....if it requires taking a slice of our brains to save millions of lives, surely they could do it!?

    i think dr mikovits said the virus lives mostly in brain tissue and isnt even that often found in spinal fluid.
  10. acer2000

    acer2000 Senior Member

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    I saw that reported as well and I can tell you that it clearly states in the Science paper that they were blinded. Not only that, the samples were split and sent to three different labs. I am not sure were that reporter was getting that info.

    I am generally suspect of any media reports on science anymore. They clearly don't read the papers before they write the articles. I have even noticed errors in the so called "science" reporter blogs/reports. Its really unfortunate because the public needs accurate information about ongoing scientific investigations.
  11. CBS

    CBS Senior Member

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    This was not a quick and dirty study that was published in weeks. Blood was drawn from patients and controls at the end of March, 2010. All samples were blinded and the lab began to detect inconsistent results fairly soon after testing commenced. If you read the paper, Dr. Singh describes repeated efforts to reconcile what she was finding with the source of the inconsistent positives. Early efforts were not successful but she eventually found the sources of contamination and once they were removed she could not find any positives, yet her test could still reliably detect very low levels of XMRV in a spiked sample (there is no such thing as an authenticated XMRV positive patient sample at this point in time).

    The authors of this study are of the HIGHEST caliber. I was in the study and was reassured early on that no matter what the authors found, it would be published. Dr. Bateman has devoted her career to ME(CFS). Drs. Alan and Kathy Light authored several genetic expression studies (with more on the way) and they are very hard at work on finding a biomarkers for ME(CFS). Patient selection was meticulous (all met the Carruthers criteria as assessed by a clinician that is as experienced with ME(CFS) as you will ever find). The fact that they took over a year to analyze and publish this research and that it might mean the beginning of the end of Dr. Singh's work on XMRV with prostate cancer speaks volumes to the commitment to their desire to better understand what is going on here rather than a devotion to having an particular answer (whether or not it is the right answer).

    Questions remain. Will Dr. Singh close the door on her XMRV/prostate cancer research? I agree that if that happens it will speak volumes. What of the comments by Dr. Coffin and Dr. Racaniello? Time will tell. I hope that all this research has sparked a greater interest in all things infectious (and not infectious) and that smart people are asking good questions. If that happens, the WPI will deserve a great deal of credit for drawing attention to the seriousness of this disease as well as some of the clear immune and infectious anomalies.

    I strongly suspect that the WPI knows that Drs. Singh, Bateman, Light and Light are not conspiring to close the door on any potentially fruitful avenue of research.

    However, if XMRV is not a factor in ME/CFS, then I want resources directed elsewhere but not before that avenue and related avenues are fully explored. This was a very strong effort to explore XMRV in ME(CFS) and it did address a number of the questions that have weakened other studies (eg. samples from patients and controls collected and handled in an identical manner, replication of some of the original methods that the WPI had used to find XMRV, identification of sources of contamination that accounted for early inconsistent positives in their analysis, etc.).

    I want answers as much as anyone and it might not have been what we were hoping for (a clear direction that can be acted on NOW) but this study took a large measure of character to publish and it provided a great deal of information that will help further our understanding of ME(CFS). What more could we want from those studying this disease?
  12. currer

    currer Senior Member

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    Hi, I have just checked what was written on this forum in November 2010 regarding Dr. Singh's patent applications in prostate and breast cancer.
    The most interesting thing is that she found 7% of her prostate CONTROLS positive for XMRV by semen sample.
    It is right there in Cort's review.
    Why have none of her controls in the ME/CFS study shown any positives? Surely they should have had at least 4-5% positive?

    And just to remind ourselves of the rest of the paper, she found XMRV in 25% of her breast cancer patients, and 27% by imunohistochemistry of her prostate cancer patients. She got agreement with the antibody results too they showed a 30% positive rate.
    According to Cort's front page write up, she found XMRV in immune cells in lymph nodes, bone marrow and peripheral blood, and demonstrated infectious virus.

    This is hard to believe when six months later we have had such a barrage of negative papers.
    How can her breast and prostate research stand up if she finds no xmrv at all in her ME/CFS study. She ought to have found some.
    And check out the latest paper from the CDC.
    They found 1% xmrv and no association with prostate cancer. To me it seems they are suggesting it is not pathogenic. Wheras Dr. Singh said she found the virus most integrated into tumor tissues.

    I cannot make any sense of this. Go back and check the Singh patent report yourselves. Put it into the advanced search and read what we all were reading a few months ago. We have been so affected by the latest spate of negative reports we have forgotten the positive studies and how much impact they had.

    If Dr. Singh's early work was accurate, and I cannot believe it was not, how can we understand this latest 0-0 finding from her? Is XMRV a pathogen or is it not?
    I would also like to say that I too respect Dr Singh as a researcher. I just cannot reconcile these findings. In fact it is impossible to reconcile these findings.
  13. urbantravels

    urbantravels disjecta membra

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    Thank you for that excellent post, CBS.

    I'm saddened to see that so many of us seem to feel that XMRV was "our only hope" and that without it, we will be back in the loony bin. I've been concerned for some time that so many patient advocacy efforts have been so focused on using XMRV as the argument for the seriousness of our disease and why it should be better funded and researched. Too many eggs in one basket.

    I have the utmost respect for Dr. Singh, Dr. Bateman, and the Drs. Light, and I am very grateful for their efforts and their great diligence. It's a shame that some 'patient advocates' seem to have immediately thrown them under the "conspiracy theory" bus because their published results are not what they hoped for. There seems to be a lot of parroting of the same lines, such as "not a true replication study" and "failed to detect known positives" which must all be coming from the same central source....hmmm...

    Many of those quick-and-dirty early negative studies were pretty sloppy work, and we were right to question them and to keep insisting "Do better." But I don't know of anyone out there more meticulous and careful than Dr. Singh, and I *do* believe she has our best interests at heart. To the extent that scientific objectivity matters, it speaks volumes that she's worked so carefully and published work that's in fact detrimental to her own self-interest; to the extent that goodwill matters, I believe Dr. Singh has seen the disease, understands its seriousness, and couldn't have found better, more knowledgeable or more compassionate collaborators than Dr. Bateman and the Lights.
    .
    I know it's hard to focus on at a time when so many must feel so disappointed, but even negative results teach us something. If there has been contamination, then biosafety rules in doing this kind of work need to be upgraded significantly. If we *are* looking at a human-created retrovirus that's capable of infecting humans, boy howdy, that's something we ought to know about ASAP.

    And now we've got a whole new generation of scientists looking at ME/CFS as a fascinating biological puzzle to be solved, not an annoyance created by middle-aged yuppie women who can't cope with life. I saw a lot of interesting conversations going on at the SoK that don't depend at all on XMRV for their continuation. I do have hope, but I also think this is really a moment to keep the pressure on for advocacy, better funding, better understanding, better treatments, better support, all those things we needed pre-XMRV and still need today.

    (And no, I don't think the book is totally closed on XMRV and I think we're due to hear more in the future; but I'd really like to see some dollars channelled toward other lines of research, and patients sending their pennies toward some of those other efforts. Of course, it costs us nothing to contact our elected representatives ourselve, without entirely depending on advocacy groups to do it for us.)
  14. CBS

    CBS Senior Member

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    Hi Jemal,

    Do you have a link for this quote?

    Thanks
  15. eric_s

    eric_s Senior Member

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    CBS and Urbantravels

    Unless XMRV is a regional phenomenon how can both the prostate cancer study (~25% in cases, 4% in healthy controls) and the ME/CFS study (0% in cases, 0% in healthy controls) be correct?

    I don't see it. So i think there are many questions open and the case is not closed at all. Before Dr. Singh and Switzer say their prostate cancer studies were wrong i can't take this study as correct.
  16. Jemal

    Jemal Senior Member

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    That's the big question right now. Does Dr. Singh believe XMRV is all contamination? Her earlier studies could all be contaminated (and at the time she wouldn't have known). Like CBS I want to know if she closes the book on XMRV entirely.

    It's likely either the last study or her earlier work are incorrect. It's unlikely all studies are correct, though not entirely impossible I guess.
  17. CBS

    CBS Senior Member

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    Eric,

    Interesting point about the regional nature of some viruses. If I'm not mistaken, Dr. samples for Dr. Singh's prostate studies could have been collected while she was at Columbia but we know all of her CFS patients were in Utah.

    Dr. Singh also has a very extensive XMRV autopsy study underway. That study has been underway for four years (all of the bodies were obtained through Columbia University).

    I think the answer to your question lies in the biological products (and sources of possible contamination by murine products) used in the evaluation of tissue samples. Switzer's article published yesterday (http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019065#abstract0) is interesting in that he found no XMRV in the blood but "(t)hree of 162 (1.9%) prostate tissue DNA were PCR-positive for XMRV and had undetectable mouse DNA."

    As I said, there are still some questions that ought to be pursued - non-specific antibody responses, negative blood/positive tissue (in light of the macaque studies, I've wondered why we weren't spending more time looking at tissue), etc.

    That said, this was a very good effort that dramatically narrowed the list of issues still on the table with regards to XMRV.
  18. Jemal

    Jemal Senior Member

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  19. liquid sky

    liquid sky Senior Member

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    Thank you for the explanation. So Nagalase is secreted by retroviruses which turns off GcMAF and prevents the immune system from working. Is the only place to get GcMAF overseas in Belgium? What are the overall costs of the treatment? Sounds promising. Hope you continue to get better.
  20. Forebearance

    Forebearance Senior Member

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    I feel really disappointed. Argh.
    Will this study's results have an effect on whether Dr. Singh publishes her autopsy study? I still really want to read the results of that study.
    I hope that this study will become some kind of clue as to what direction the scientists should head next.
    Maybe our illness is caused by a retrovirus that is closely related to XMRV, but not XMRV.
    I don't care what acronym I have. I just know I have a bad case of some acronym!

    Maybe the Nobel prize is still up for grabs, if some other scientist wants to discover another virus that causes CFS.
    I'm not totally giving up on XMRV as the cause. There are so many unexplained questions still. I hope it gets sorted out.

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