Planned Lipkin study looking for biomarkers and pathogens in CFS

oceanblue · Jun 30, 2011

Dr Ian Lipkin gave a talk at WPI on 24 June, available as a video.

Talking about his XMRV study, he said:

@71:40
We have some support from a New York Philanthropist interested in looking at biomarkers from well-characterised patients and for doing pathogen searches using the kinds of technologies I've just described. And we have support to do Green chips and we've developed mass-tech(?) PCR panels that will be used to screen these patients, and there is a subset that will have deep sequencing analysis. So assuming that agreement proceeds we will focus on biomarkers associated with acute disease, relapses, remissions - as well as looking at pathogens.

Looks like this study is piggy-backing on the XMRV study, using the same well-characterised patients. Given Lipkin is behind this, it could be interesting.

He was then asked "What would you do to try to find out the cause of CFS?" and he said

Deep sequencing and proteomics on sera from people with well-characterised disease at various time points, before and after stress tests, whatever we could do to increase the expression of the agents

Interesting he brought up stress-testing, which would presumably include exercise challenge, an approach that has brought interesting results elsewhere.

He also said he thought the cause of CFS "smells like a virus to me", though he qualified it by saying

To a guy holding a hammer, everything looks like a nail. I'm a virologist so it looks to me like a virus.

Esther12 · Jun 30, 2011

oceanblue said:
He also said he thought the cause of CFS "smells like a virus to me", though he qualified it by saying: "To a guy holding a hammer, everything looks like a nail. I'm a virologist so it looks to me like a virus."

This XMRV thing has brought in a number of bright researchers who seem genuinely self-aware about their own limitations and biases. This is so rare in CFS!! It's a shame that their interest is in XMRV, not CFS.

It's good news that Lipkin's going to be doing some further work on CFS. I hope it leads on to something, and we don't just get left to the quacks again.

Listening to some of the virologists speaking, both pro and anti XMRV, I get this relieved sense that they're brighter than I am, and are going to be doing a careful, thorough and sensible job with their research. When listening to most 'CFS experts' I get a nervous sense of dread knowing that these are the people I'm relying upon to understand why I'm ill.

Thanks for the news OB.

eric_s · Jun 30, 2011

In my case, not all the virologists give me that sense. Nothing personal, i'm just saying. I think the people we should rely on most are ourselves. Grow and improve our organisations, create more awareness, build up more pressure, if necessary. Become able to give people like Lipkin etc. the cheque he asked for in this video at around 67:20. Then things will go well, i believe.

Dolphin · Jun 30, 2011

Thanks oceanblue (and others)

oceanblue said:
Dr Ian Lipkin gave a talk at WPI on 24 June, available as a video.

That link didn't work for me. Hopefully this one will for others: http://imedia.unr.edu/unsom/whittemore_peterson_institute/dr_ian_lipkin.html .

sensing progress · Jun 30, 2011

This sounds promising. I wonder who the mystery "New York Philanthropist" is?

Dolphin · Jun 30, 2011

sensing progress said:
This sounds promising. I wonder who the mystery "New York Philanthropist" is?

Good for him/her whoever they are.

oceanblue · Jul 1, 2011

I agree with Esther12 that there's been a noticeable increase in class of researcher of late. But such quality is not a rarity in many fields eg molecular biology. I did a biochemistry degree in the 80s and got used to good experimental design and labs routinely replicating other researchers results. When I got ill a decade later I couldn't believe the shite that passed as science in CFS research. Although XMRV researchers often don't agree, the debate seems to be played out at a higher level than we've been used to. And it's worth noting that Lipkin, as well as Singh and Alter have expressed an interest in CFS beyond any XMRV connection.

I agree with eric_s too that trying to raise $1m to give to Lipkin would not be a bad idea.

Thanks for sorting the video link, Dolphin.

Bob · Jul 1, 2011

Snow Leopard · Jul 2, 2011

Thanks Bob.

biophile · Jul 2, 2011

oceanblue wrote: I agree with Esther12 that there's been a noticeable increase in class of researcher of late. But such quality is not a rarity in many fields eg molecular biology. I did a biochemistry degree in the 80s and got used to good experimental design and labs routinely replicating other researchers results. When I got ill a decade later I couldn't believe the shite that passed as science in CFS research.

I don't have a professional science background but one of the first things that occurred to me when I began reading the literature was that the CFS research field is in the intellectual backwaters of the scientific and medical communities. Much of this can be attributed to a lack of resources, and I'm not saying there aren't some good quality researchers in the field (who lack resources).

I can't speak for other patients but I have the impression that many of us are so "used to" poor quality that at this stage a large and decent quality study always sounds a little too good to be true.

oceanblue · Jul 2, 2011

biophile said:
I don't have a professional science background but one of the first things that occurred to me when I began reading the literature was that the CFS research field is in the intellectual backwaters of the scientific and medical communities. Much of this can be attributed to a lack of resources, and I'm not saying there aren't some good quality researchers in the field (who lack resources).

'Backwater' is just right. Molecular biology (in the 80s and now) has 2 things going for it that CFS does not: it's full of 'doable' problems (CFS is phenomenally complex and hard to tackle), and it's very well funded: talent follows the money, and the chance of success. The result is a phenomenally competitive field; people aren't just trying to solve a problem, they are desperately trying to solve it before their competitors do. Imagine that in CFS research.

Bob · Jul 3, 2011

Dr Jamie Deckoff-Jones mentions Ian Lipkin's visit to the WPI, and his XMRV study, in her latest X Rx blog entry:
http://treatingxmrv.blogspot.com/2011/07/treaure-hunt.html?spref=fb&forumid=331851

oceanblue · Jul 4, 2011

Deep sequencing: How the pathogen hunt would work

For those that haven't seen the Lipkin video, here's a brief intro to how the search for pathogens in CFS would work.

He's planning to use deep sequencing, which is a pretty amazing concept. Basically, you take a tissue or blood sample and sequence EVERY scrap of DNA in it. Almost all of it will be human DNA but there will be tiny, tiny amounts of DNA from pathogens: bacteria, viruses, funghi, other parasites. The techniques are phenomenally sensitive, have to be for this to work. Even healthy people will have lots of non-human DNA in their blood - the idea is to find what (if anything) is different between CFS patients and healthy patients.

I don't know how many patients are being deep sequenced but if it's only a few the chances are they won't find anything if there are multiple pathogens causing CFS because there won't be a clear pattern. Similarly, if CFS is caused by an uncommon reaction to a common pathogen (eg EBV) then again this technique won't find it. I've no idea if this technique would be sensitive enough to detect XMRV, given that even those that can find it say it's hard to detect.

eric_s · Jul 4, 2011

oceanblue said:
I don't know how many patients are being deep sequenced but if it's only a few the chances are they won't find anything if there are multiple pathogens causing CFS because there won't be a clear pattern. Similarly, if CFS is caused by an uncommon reaction to a common pathogen (eg EBV) then again this technique won't find it. I've no idea if this technique would be sensitive enough to detect XMRV, given that even those that can find it say it's hard to detect.

But even if it wasn't possible to find a clear pattern, if they found a difference to healthy people that would be reason enough to expand the study, so that there would be enough subjects to be able to find a pattern, i hope.

What about reactivated infections, for example with EBV? Do you think deep sequencing would be able to detect that?

oceanblue · Jul 4, 2011

eric_s said:
But even if it wasn't possible to find a clear pattern, if they found a difference to healthy people that would be reason enough to expand the study, so that there would be enough subjects to be able to find a pattern, i hope.

What about reactivated infections, for example with EBV? Do you think deep sequencing would be able to detect that?

There's a lot of 'noise' in these studies ie substantial differences even between healthy individuals so unless particular pathogens show up they are likely to simpy have an 'inconculsive' result. That said, I'm not very familiar with this field so may be wrong. Similarly, I'm not sure about reactivation: I don't think this technique is suitable for detecting a difference between a latent infection with a low level of, say, EBV, and reactivation with a higher level. I think it tends to givesa there/not there binary result.

Esther12 · Jul 4, 2011

There is a danger that if CFS is caused by a combination of different genetic problems and different viral infections which are less damaging to healthy controls, then a study like this could miss that and end up pointing us in the wrong direction.

oceanblue · Jul 4, 2011

Esther12 said:
There is a danger that if CFS is caused by a combination of different genetic problems and different viral infections which are less damaging to healthy controls, then a study like this could miss that and end up pointing us in the wrong direction.

Certainly it could miss it, but I don't think it's likely to dismiss it. Lipkin strikes me as too smart to say, 'we didn't find anything therefore there isn't a problem'.

Actually, in the video he suggests one possibility is that CFS is caused by an uncommon reaction to a common virus; he seems open to a lot of possibilities. And techniques like deep sequencing are much better for proving there is a pathogen link (positive result) than proving there is none (a negative result is far from conclusive). I'll stop waffling now.

Esther12 · Jul 4, 2011

oceanblue said:
I'll stop waffling now.

Good to be reassured!

I think you're right. And I seem to remember Lipkin mentioning elsewhere that he think it's unlikely that CFS has one single cause... so hopefully any study he does will try to account for the problems that could bring up. Ta.

Dolphin · Jul 4, 2011

I think I heard mention of BLAST by Lipkin. It was used in at least one CFS study: http://www.biomedcentral.com/1471-2180/11/2

Sullivan PF, Allander T, Lysholm F, Goh S, Persson B, Jacks A, Evengrd B, Pedersen NL, Andersson B. An unbiased metagenomic search for infectious agents using monozygotic twins discordant for chronic fatigue. BMC Microbiol. 2011 Jan 2;11:2.
Free full text at: http://www.biomedcentral.com/1471-2180/11/2

Unfortunately, I'm not convinced this was necessarily a "good cohort" e.g. in terms of their severity: http://www.biomedcentral.com/1471-2180/11/2/comments#462684 and they didn't find any differences on gene expression:

Byrnes A, Jacks A, Dahlman-Wright K, Evengard B, Wright FA, Pedersen NL, Sullivan PF. Gene expression in peripheral blood leukocytes in monozygotic twins discordant for chronic fatigue: no evidence of a biomarker. PLoS One. 2009 Jun 5;4(6):e5805. Free full text at: http://dx.plos.org/10.1371/journal.pone.0005805

It reminds me of CDC studies: I think with the Fukuda definition one can pick up mildly affected people who may not be the best people to study, esp. if one is looking for pathogens.

Here's a recent quote on this sort of topic (who to use for biological searches):

The fact that the scores of cases meeting the Canadian criteria were consistently lower than those not meeting the criteria further suggests that diagnosis specificity is related to disease severity, and that diagnostic criteria such as the Canadian may be more appropriate for research studies investigating risk factors and disease biomarkers.

from:

Nacul LC, Lacerda EM, Campion P, Pheby D, Drachler Mde L, Leite JC, Poland F, Howe A, Fayyaz S, Molokhia M. The functional status and well being of people with myalgic encephalomyelitis/chronic fatigue syndrome and their carers. BMC Public Health. 2011 May 27;11:402. Free full text at: http://www.biomedcentral.com/1471-2458/11/402

Rrrr · Jul 4, 2011

what is greenchip? he said he'd do this, too, with the new york philanthropist's donation.

in terms of raising $1 million: we need to start a campaign to get collins to give lipkin this 1 million. it is a tiny drop in the bucket for HHS (which has a $991 billion dollar budget).

Planned Lipkin study looking for biomarkers and pathogens in CFS

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