XMRV Buzz - Take a Deep Breath/the Big XMRV Meeting, Singh On XMRV, Sample prep?

[Cort]

Here's the latest from the XMRV Buzz - some news on the Singh study - guess what? - it's taking longer than expected but it is a big, overlapping study - so maybe that is no surprise.

Some Light on the Singh Study - the Singh study is big (@100 patients) and comprehensive - besides doing culturing Dr. Singh she is using two kinds of PCR and for viral RNA and presumably an antibody test. The blood storage, etc. protocols are the same in both the healthy controls and patientsAND they are all from one area (no geographic sequence variation). Plus Dr. Singh has been studying XMRV and MLV's for years. In short it's quite an important study.

Slippery Beast - I asked Dr. Light, one of the principals in the study, if there was anything he could say about it? He reported they just had a meeting - they think the are, as he put, 'finally getting a handle on it' but are still not sure - and they didn't want to build up hopes one way or the other. He hopes they'll have something definitive to report soon.

XMRV, no surprise, given the ups and downs of the past year, has been a bit slippery. The Singh study began early this year - it's probably somewhere in its 7 or 8th month now. One grace of Dr. Singh's study (and a complicating factor) is its complexity; she will want the results of the different tests (2 PCR's, RNA, culture (and antibody?)) to agree - not an easy task with a relatively new virus. Of course, when the different tests do all agree then you have a really solid result.

XMRV is certainly in good hands; Dr. Singh is pushing the field forward in several ways. She has developed an antibody test and her own XMRV clone and, of course, is a key player in the XMRV prostate cancer hunt.

 

[August59]

Hey Cort - Does some of the XMRV things Dr. Singh working on, just happen to parallel this seminar from Rita's post?

http://www.forums.aboutmecfs.org/showthread.php?8656-Abstracts-from-11th-Symposium-Antiviral-Drug-Resistance

 

[Esther12]

I wish the Singh stuff sounded more positive. Worry, worry, fret, fret.

 

[eric_s]

They could have asked the WPI to identify some CFS patients as XMRV positive, taken independant and blinded samples, and provided them blinded with controls, back to the WPI. If the WPI were able to accurately identify those they'd previously claimed were XMRV positive - that would have moved us on pretty dramatically. It could have been done in a month. I can't believe how long we've been stuck with progressing so little.

Yes, unbelievable they have not done this a long time ago. I think Dr. Enlander suggested it, but it never happened. Would not take very long, not be expensive and everybody could stop all that contamination talk.

 

[Cort]

I wish the Singh stuff sounded more positive. Worry, worry, fret, fret.

Things clearly are not clear yet unfortunately....

 

[eric_s]

I just don't get how things can not be clear after 8 months or so... Either you're finding something or not. And if you're finding something and you have unblinded the samples or done it with positive and negative controls you know wheter it means something or not. Of course this is much too simplistic, but i just can't believe the "we are not sure". Neither the "XMRV is it" nor the "it's all contamination" people took so long to come to a conclusion. Of course it's a good sign they are so thorough and want to really be sure, but i find it very hard to imagine an explanation for this. But this is true for the entire situation since last year...

 

[Navid]

I wish the Singh stuff sounded more positive. Worry, worry, fret, fret.

dr singh has my blood, which tested poz w/wpi...one of dr singh's lab asst's wrote me yesterday: that testing and research is taking longer than they had anticipated...it is more complicated than they first thought....i don't interpret that as meaning they are finding nothing but perhaps variations???? but that's my optimistic side speaking again : )

 

[Esther12]

dr singh has my blood, which tested poz w/wpi...one of dr singh's lab asst's wrote me yesterday: that testing and research is taking longer than they had anticipated...it is more complicated than they first thought....i don't interpret that as meaning they are finding nothing but perhaps variations???? but that's my optimistic side speaking again : )

I think that with CFS research I always interpret an absence of good news as being probably bad news.

Interesting to know that they're testing your blood when you've tested positive with the WPI. Did they know that when they selected you?

I can't believe how long I've been desperate for news on this. I'm amazed that I've maintained this rapt attention for over a year now!

 

[Navid]

I think that with CFS research I always interpret an absence of good news as being probably bad news.

Interesting to know that they're testing your blood when you've tested positive with the WPI. Did they know that when they selected you?

I can't believe how long I've been desperate for news on this. I'm amazed that I've maintained this rapt attention for over a year now!

it is a blinded study...but they are testing 100 known poz from across the US who have also been dx'd by a recognized cfids expert....so all poz really do have me/cfs...i guess the blinded part is that my name is not attached to the blood sample....dr singh nor the lab knows which samples are poz and which are neg....the negs are from healthies from the same regions of the country as us sickies.

hope i explained this correctly but that is how i understand it.


a number was assigned to my sample....when the testing all done they will coordinate the names and numbers and let us know our status thru her testing.

 

[Cort]

I just don't get how things can not be clear after 8 months or so... Either you're finding something or not. And if you're finding something and you have unblinded the samples or done it with positive and negative controls you know wheter it means something or not. Of course this is much too simplistic, but i just can't believe the "we are not sure". Neither the "XMRV is it" nor the "it's all contamination" people took so long to come to a conclusion. Of course it's a good sign they are so thorough and want to really be sure, but i find it very hard to imagine an explanation for this. But this is true for the entire situation since last year...

I really have no idea. One idea I had was that they did unblind the samples and that not all the results correlated as much as Dr Singh wanted - that is the PCR results didn't quite fit with the antibody results...or with each other - maybe they were close but not close enough - which might not be that surprising since this is a new virus. In the original WPI study about half of the 15 samples, I think it was, tested postive for XMRV. I don't know what Dr. Singhs criteria are - maybe she wants a higher percentage. Just a guess.

 

[Cort]

dr singh has my blood, which tested poz w/wpi...one of dr singh's lab asst's wrote me yesterday: that testing and research is taking longer than they had anticipated...it is more complicated than they first thought....i don't interpret that as meaning they are finding nothing but perhaps variations???? but that's my optimistic side speaking again : )

Did the lab asst write you because you asked her or are they just catching everybody up with what's going on?

The fact that our Utah XMRV/MLV expert has found that it's more complicated than she thought it would be - means its pretty complicated...but what else is new?

Maybe we shouldn't be surprised that this too is taking a bit longer than expected - that's the way its been from the beginning, really.

 

[Navid]

Did the lab asst write you because you asked her or are they just catching everybody up with what's going on?

The fact that our Utah XMRV/MLV expert has found that it's more complicated than she thought it would be - means it's pretty darn complicated.

Maybe we shouldn't be surprised that this too is taking a bit longer than expected - that's the way its been from the beginning, really.

hi:

i wrote her first because i was originally told i shld hear result by mid Nov...and we me/cfs'ers are calendar watchers : )....so it was not an unsolicitated note.

 

[Cort]

hi:

i wrote her first because i was originally told i shld hear result by mid Nov...and we me/cfs'ers are calendar watchers : )....so it was not an unsolicitated note.

Well, that's not so bad....

 

[Otis]

Damn, Otis - could you do my website next??????

My guess is that they don't have anything definitive to release and that -based on what Jenny said- Ian Lipkin doesn't have their protocols yet. That's just a guess.

I think they should be more forthcoming about what's going on and what the timeline is - that's not a state secret! - and hopefully this will help with that and with their apparent reluctance to keep us informed. At least they'll know we are out here.

I'll put it up on the Buzz page.

(I'd love to see what you can do when you actually have some time...... Nice site! )

Thanks Cort, but I'm no webmaster. The Google 'sites' tools make it pretty easy.

 

[akrasia]

Did the lab asst write you because you asked her or are they just catching everybody up with what's going on?

The fact that our Utah XMRV/MLV expert has found that it's more complicated than she thought it would be - means its pretty complicated...but what else is new?

Maybe we shouldn't be surprised that this too is taking a bit longer than expected - that's the way its been from the beginning, really.

I think whatever is going on here should be read in the light of Singh's recent meditation on methodology. It sounds as though she may end up with an explanation, accompanied by concrete examples, of why it's so difficult to find, even when you are in unimpeachably good faith.

Simply put, I suppose she wants to nail down proof that positives are real, not a lab artifact, and show how false negatives happen. If she is proceeding this way, and who knows if she is, then her research would beat Lipkin to the punch on its claim for greatest explanatory value. That might be interesting and would be extremely satisfying on all kinds of different levels...

 

[Cort]

I think whatever is going on here should be read in the light of Singh's recent meditation on methodology. It sounds as though she may end up with an explanation, accompanied by concrete examples, of why it's so difficult to find, even when you are in unimpeachably good faith.

Simply put, I suppose she wants to nail down proof that positives are real, not a lab artifact, and show how false negatives happen. If she is proceeding this way, and who knows if she is, then her research would beat Lipkin to the punch on its claim for greatest explanatory value. That might be interesting and would be extremely satisfying on all kinds of different levels...

I agree! (Akrasia and I agree again ) I think she's trying to vault the field forward and her study may very well be a definitive one, and, of course it will be published long before Lipkin's is. Put it this way - if she can find XMRV using all her tests - I imagine her paper will be like the Science paper #2 - a landmark paper that helps to reorient the field. Whatever she finds will have a big impact on XMRV because she's looking at it from so many different angles.

I almost think - how could it not take longer than expected?....There are some definite twists with XMRV otherwise it would have been found by now. Even the WPI readjusted their methods in midstream - they put out an altered methodology section five months or so into the process - so she's working and adjusting as she goes along as well.

 

[pictureofhealth]

And if Singh comes up with results sooner than Lipkin, that is great news for patients. So far, she has been really good at communicating findings and results as she goes along. She was very happy to answer questions in her TWIV interview with Raccaniello too.

Maybe this is simply the difference between the approach to public communications by privately funded, University conducted research bodies versus the approach taken by Government funded Federal research agencies.

The bigger government bodies appear to operate in a disconnected and rarified sphere of their own. Consideration of the effects and results of their findings on patients like us further downstream seem to rarely enter into their picture.

 

[akrasia]

And if Singh comes up with results sooner than Lipkin, that is great news for patients. So far, she has been really good at communicating findings and results as she goes along. She was very happy to answer questions in her TWIV interview with Raccaniello too.

Maybe this is simply the difference between the approach to public communications by privately funded, University conducted research bodies versus the approach taken by Government funded Federal research agencies.

The bigger government bodies appear to operate in a disconnected and rarified sphere of their own. Consideration of the effects and results of their findings on patients like us further downstream seem to rarely enter into their picture.

There is a very precious freedom embodied in the academic world, as long as it can remain free of the tentacles of "policy" and commercial interests.

You are right, the world of the BWG has other considerations besides mere truth, although I'm sure they'd be apoplectic if I said this to them.

Public perception, accountability, and the actual effects of research on civic and political life all come into play with research by government entities. At its best, academic work can be relatively free, as long, of course, as the participants have tenure and independent spirits, both of which I think Singh possesses.

If there is a "problem" with academic research it's the problem that haunts much intellectual work in the sciences, unexamined assumptions and the inertia of received ideas. These cripple a lot of work and attitudes. Consider how badly people with M.E. have been treated in places like Harvard and Yale.

But the distinction you are drawing is interesting and deserves more attention than I can give it at the moment.

 

[Cort]

And if Singh comes up with results sooner than Lipkin, that is great news for patients. So far, she has been really good at communicating findings and results as she goes along. She was very happy to answer questions in her TWIV interview with Raccaniello too.

Maybe this is simply the difference between the approach to public communications by privately funded, University conducted research bodies versus the approach taken by Government funded Federal research agencies.

The bigger government bodies appear to operate in a disconnected and rarified sphere of their own. Consideration of the effects and results of their findings on patients like us further downstream seem to rarely enter into their picture.

At the Reno Conference in 2009 - so long ago! - Dr. Mikovits told me she would have never, ever considered talking to the press when she was at the National Cancer Institute. It's just not done there - it sounded almost like a career killer. Obviously she feels much freer at the WPI and Dr. Singh does at the Univ of Utah to speak to the 'media'.

 

[Cort]

From the latest XMRV Buzz page

No Surprise - news that even our Utah XMRV/MLV expert was finding XMRV more complicated than expected probably should have come as no surprise...broken timelines have been maybe the most consistent thing we've been able to observe with XMRV. Consider these

(*)WPI, with Glaxo Smith Kline reportedly on board, was reported to expect treatment trials to begin within six months of the Science publication.
(*)At the CFSAC meeting late last year Dr. Coffin thought we'd have the answer 'within six months'
(*)The antibody tests were promised and promised....but eventually they did arrive (so there's hope )
(*)The WPI started with one set of methods in the Science paper and then brought forth an improved set about five months later
(*)Dr. Singh's study is taking a bit longer than expected because - a PR Forum member was just told -it's more complicated than expected
(*)Dr LeGrice and Dr. Glynnis just a month ago thought Phase II would wrap up about 10 days ago....

Who wants to bet on Phase III being wrapped by New Years? XMRV is clearly complicated. It's definitely past time to stop expecting anything to happen on a timeline. All we know for sure is that the results won't be done until they are done - and not a second before.

International Conference Rita on the PR Forums somehow found some interesting XMRV abstracts in the 11 Symposium on Antiviral Drug Resistance - demonstrating again that XMRV is getting in anywhere it can.

XMRV in Immune Cells - One from the National Cancer Institute sought to explain an interesting dilemma - research done after the WPI's Science paper indicates that XMRV is basically knocked down and rendered non-infectious by the APOBEC3 enzyme in the immune cells in the blood the WPI found it in. (The amino acids the enzyme replaces in XMRV makes it impossible for XMRV to replicate.) Yet after digging XMRV out of these immune cells the WPI was able to grow the virus and replicate it! If that enzyme had rendered XMRV inert, so to speak, how was the WPI able to get it to replicate again? These researchers found that XMRV could replicate in PBMC's only if the APOBEC enzyme was inactivated. However, if they cultured the cells with 'canine indicator cells' they could recover infectious virus. This suggests to me, a laymen, way in over his head, that there are substances that can help XMRV bypass the APOBEC3 enzyme.

However, these researchers suggested that this does not happen in the blood in the body, and that at least as regards replication, the immune cells tested thus far are essentially a dead end for XMRV. (Hence the search for a different viral reservoir)

One of the most interesting part of this study was the ease with which they did it. They simply infected cells with XMRV and monitored virus production using quantitative PCR. It's clearly much easier to purposefully infect cells and then detect the virus again than it is to find it in the blood.

Dr Coffin Gets Down to Work! - Dr. Coffin's at Tufts and the National Cancer Institute (again) have been taking on one of thorniest problems - how to distinguish XMRV from mouse DNA or from an endogenous retrovirus.

An endogenous retrovirus is a retrovirus that, sometime in the distant past, inserted parts of itself into the genome of an organism. The genomes of inbred mice in labs, in particular, are swarming with degraded non-infectious MLV gene sequences. The right bit of mouse DNA contaminating a sample could,therefore, look like XMRV. The WPI was able to isolate the whole virus - indicating they did not discover an endogenous retrovirus - but no one else has.

A very specific PCR assay Dr Coffin developed for XMRV has not found it all in inbred or wild mice - suggesting, as Dr. Mikovits reported, that it is unique to humans. They developed another assay that distinguishes between XMRV and endogenous MLV retroviruses - thus enabling them to quickly tell if a gene sequence belongs to XMRV, an endogenous retrovirus or from mouse DNA. Plus they've developed another PCR assay that focuses on mouse 'DAN' contamination.

It appears that researchers are becoming ever more effective at determining when an XMRV result is real and when it actually reflects something else. These tests will be be very helpful (a) to researchers such as Dr. Alter and Dr. Hansen who have found gene sequences that are XMRV-like but have pMLV characteristics and (b) to clearing up the contamination question. Basically it appears Dr. Coffin now knows XMRV when he finds it.