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9th Invest in ME International ME Conference, 2014 - Part 2: Pathogens and the Gut
Mark Berry continues his series of articles on the 9th Invest in ME International ME Conference in London, with the emphasis shifting from autoimmunity to pathogens and the gut ...
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Lipkin and Hornig go hunting for ME/CFS pathogens

Discussion in 'Phoenix Rising Articles' started by Phoenix Rising Team, Mar 1, 2013.

  1. Sasha

    Sasha Fine, thank you

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    I just clicked 'like' but that seems hardly adequate for this extremely good point! Just think how Lipkin talked about us at the XMRV press conference. We're in excellent hands.
    vli and snowathlete like this.
  2. Esther12

    Esther12 Senior Member

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    Yes - they do seem aware of the potential problems. And they seem good. Hopefully that's enough! CFS just seems like such a difficult diagnosis to do useful research on (to me anyway).
  3. Gijs

    Gijs Senior Member

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    I do not think they are going to find anything in the blood. The are looking at the wrong place.
  4. anniekim

    anniekim Senior Member

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    Hi Simon, thanks for this. I just read cort johnson's piece on Hornig's talk on the simmaron website. He wrote a lot on how Horning suggests an overgrowth of bad gut bacteria could cause immune, stress and Cns problems.

    I couldn't really connect the dots. Was she saying that one possible cause of the immune dysfunction can be traced back to the bad bacteria in the gut? Is the gut just one avenue she is considering? Was there the implication that the bad gut bacteria could be theroot cause or a consequence of immune dysfunction? Many thanks
  5. Sasha

    Sasha Fine, thank you

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    Xandoff and anniekim like this.
  6. anniekim

    anniekim Senior Member

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    Re cohorts, when studies say they use both Canadian and CDC criteria I never understand how this works. Does this mean the patients have to fulfil both case definitions? Doesn't the Canadian supercede the CDC as there are more symptoms in the Canadian criteria over and above the CDC definition? Am I missing something? Thanks
  7. Simon

    Simon

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    As I'm sure you know, genes encode proteins - but not all genes are 'turned on', many are dormant, and those that are "on" can lead to production of proteins at different levels from very low levels to very high. Gene expression studie looks at the pattern of protein production in healthy patients and controls to see if there are any differences. Eg are some proteins present in CFS patients but not in controls, or vice versa? Or, more likely, are some genes expressed at very different levels between patients and controls? Any differences can give clues as to what;s going wrong in patients. Bit more from Wikipedia.
    CFI will be funding the CFI cohort of 200, for both the pathogen study and proteins studies, I think. Someone else will be funding the rest of the patients, and Mady Hornig is trying to get more funding from elsewhere to increase the study size. I think a lot of scientists' time goes into securing funding rather than doing science.

    And yes, I don't think they will be cheap. I remember watching a Lipkin lecture talking about pathogen discovery (not for CFS) where in the Q&A he was asked about applying these techniques to CFS. "I'd love to" he said, "if someone gave me $1million" - though I think the money was for the science not his fees :). Not long after there was talk that a New York philanthropist was in contact with Lipkin, and not that much later the CFI was formed and Lipkin was lined up for the pathogen study. I don't know if that's a conicidence, but I did wonder if the philanthropist was watching that lecture too.
    justinreilly, Xandoff, ukxmrv and 2 others like this.
  8. Simon

    Simon

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    sorry, struggling a bit to keep up here!
    Interesting point: Mady Hornig did talk about the potential role of the gut. Also, she worked a possible link between the measles virus in the gut and children with autism and gut problems so she's taken that approach before.
    The Canadian Criteria are generally narrower than the CDC ones - CFI specificed that patients had to meet both criteria and my guess is they met Canadian they met CDC anyway - but if they only met Canadian they would not have been included.
    Yes, she was saying that. Cort is ahead of me - I just wrote about her new study, and will write about her other work next week - while Cort got it all into the one article.
    anniekim likes this.
  9. taniaaust1

    taniaaust1 Senior Member

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    If Im understanding this study right... those who are easily found to have things like EBV wont then be going throu the High thoughput PCR senquencing? (and also hence the results of their gene expressions wont be included?). :(

    Its the EBV group I'd like to see very rigoreously studied as that is linked to so many ME/CFS cases... maybe those are even more likely to be carrying other things too then the group which wasnt obviously carrying something. Some stand out things may be missed by not looking deeper at this group in the same way as the other group is being looked at.
  10. acer2000

    acer2000 Senior Member

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    I participated in this study. The "Columbia" studies are in 3 parts. The first was blood samples for the XMRV study. The second phase was looking for all known and novel pathogens. It was several months ago, but my recollection is that they took blood, tears, rectal swab, and I think one more (either nasal or throat swab - my memory is fuzzy so I don't recall at the moment). The third study was/is supposed to use spinal fluid. At the time I gave my samples for part 2, they were still working out the details for part 3. They may well have sorted it out now.
  11. acer2000

    acer2000 Senior Member

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    While I have no idea what they will ultimately find, I know that they were very particular about selection for these studies. I have been a patient with my CFS doctor for over 5 years and it wasn't at all guaranteed that I would be selected when I applied. I know they were very specific about controls as well. I was lucky in that they could find someone around my age/sex/location otherwise I wouldn't have been able to participate despite having qualified due to my illness and labs. My impression is that they are very focused on making sure these studies are done correctly.
  12. Sean

    Sean Senior Member

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    Thanks, acer.

    Good to hear.
  13. vli

    vli

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    This is super interesting, I'd never heard of pathogens being looked for in rectal or throat swabs before. Thx acer.
  14. acer2000

    acer2000 Senior Member

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    Yeah neither had I, but I am glad that they did multiple samples other than just blood. It increases the chance of finding something. Like others have said, I really hope this thing continues to gain momentum and that someone will do another tissue study like Dr. Chia did. That was smart of him.
    vli likes this.
  15. Valentijn

    Valentijn Activity Level: 3

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    You might be right. But we don't know where something will be found - if we did know, it would be because it had already been found, and no one would need to look! They seem to investigating in a very intelligent and reasonable manner, and I'm glad we've got people with the expertise and funding that are willing to do the research.
    SOC and snowathlete like this.
  16. Simon

    Simon

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    Interesting point. I simplified the process slightly and actually 20% of positives from the initial screen will go into high-throughput phase, but most won't. Still, if a lot of people are positive for EBV then they will probably have enough to detect other pathogens, though perhaps not to detect gene expression differences as that tends to need pretty large samples.

    However, these are smart people and if they do find EBV are a substantial group I expect they would want to look at that group in more detail anyway. One of the things that has stood out for me listening to both Lipkin and Hornig is that these are scientists who genuinely want to find out what's going on. They are not looking for ways to show there is no problem. Mady Hornig's work on autism is a good example of this: she looked for and ruled out a link with the measles virus in the gut of children with autism and gut problems - but went on to find a whole load of other abnormalities. More on this in the next blog.
    justinreilly, SOC, Valentijn and 2 others like this.
  17. Simon

    Simon

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    Thanks so much for this acer, it's great to get first hand accounts from patients. Sounds like you are in the NIH/XMRV cohort rather than the CFI one, since you were sampled for XMRV too. I hadn't realised they had collected more than blood to date. Mady is defintitely trying to get funding for the spinal fluid work, but hasn't secured it yet, as far as I know.

    More great info. Having such carefully matched controls will particularly help with the gene expression work as it will reduce the amount of 'noise' since age/sex will be controlled for. Noise is the biggest problem in gene expression, so with matched samples and large cohorts they have a much better chance of finding real differences.
  18. anniekim

    anniekim Senior Member

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    Thanks Simon. So have I understood it correctly that Hornig is researching more than one avenue, looking at pathogens in blood such as you have described in this post, but also thinks it may not be viral pathogens involved but gut pathogens so is looking at that too? I look forward to reading your next post on this. Many thanks
  19. Sasha

    Sasha Fine, thank you

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    Tears, wow - I've never heard of tears being collected in any study. What would show up in tears that doesn't show up in other stuff?

    Nasal swab sounds like a good plan - chronic sinusitis is common in PWME and there's interest in general in chronic sinusitis being associated with disruption of the normal microbiome of the stuff in your sinuses.
  20. redo

    redo Senior Member

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    Thanks for the report, Simon!

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