Maldarelli XMRV Study Underway

[Cort]

I admit I don't understand all the science. This is at the end of the Supplemental Sciences section - First they show that three CFS XMRV strains were very similar to the reference strain (VP62). They also show where the strains differ - which, would I think be important.

Figure S1. Gag sequences of XMRV in CFS patients. Partial sequences (nt 6491017) from CFS XMRV strains WPI-1130, WPI-1138 and WPI-1169 in comparison to XMRV strains VP35, VP42 and VP62 derived from prostate cancer patients. The yellow highlighting denotes the differences from the reference strain (VP62).

Maybe all the other strains after that were different - they were unlucky with those first strains..

This next part is difficult but it appears to me to state that they could detect the VP 62 clone in their XMRV infected samples. They used lysates prepared using Raj(VP62), the LnCap cells they were using and another. If you'll look on the figure you'll see that XMRV shows up in all three of them..in fact in B it shows up better in the VP62 line than the LNCap line which could mean, I suppose, that VP62 does not show up well when you are using LNCap to grow the cells at least in some cases.

I don't know what all this means - and I grant that the VP62 clone is not the best - but it was in there, in some fashion, in the first study...Maybe you explain more about this.

Figure S3. Detection of cloned XMRV-VP62 using a rat mAb to SFFV Env and a goat antiserum to mouse NZB xenotropic MLV .

A. Lysates were prepared from XMRV-VP62-infected Raji (lane1), LNCaP (lane 2) or Sup-T1 (lane 3). Positive controls used were HCD-57 cells, a mouse erythroleukemia cell line expressing polytropic MLV gp70 Env (lane 4), and HCD-57 cells infected with SFFV, which also express SFFV gp55 Env (lane 5). WB analysis was carried out using rat anti-SFFV Env mAb 7C10. Molecular weight markers in kD are shown on the left.

B. Lysates were prepared from XMRV-VP62-infected Raji (lane 1), LNCaP (lane 2) or Sup-T1 (lane 3). Lysates from SFFV-infected mouse HCD-57 cells (lane 4) and from uninfected Raji, LNCaP and Sup-T1 are shown in lanes 5-7, respectively.

 

[Cort]

I'm behind on this thread, but this is yet another example of subtly distorting the facts. You casually slip the phrase "using the same techniques the WPI did" in there, when there is absolutely no indication that his study would use the WPI's methods.

I didn't casually slip in anything. Dr. Miller said in a comment to Gerwyn's blog that was posted on the ME/CFS Forums that he would do that.

http://niceguidelines.blogspot.com/2011/01/must-read-if-you-are-xmrv-positive.html

A basic tenet of science is that results obtained in one lab should be reproducible in other labs. We plan to use many of the same techniques used in the Lombardi et al. study from the WPI, and some additional techniques we have developed, to detect XMRV. One of the criteria for inclusion in our study is that subjects must have tested positive for XMRV by another lab.

You are so suspicious... I'm not trying to distort anything or subtly get anything over on anyone..
No one was out to get XMRV or the WPI. The intent was to find XMRV...why would we not want to find XMRV? What would anyone with CFS get out of that? What would our motive or Dusty Miller's motive be in doing that? We would love to find it. Can you imagine how happy people would be if a gamma retroviriologist of Dusty Miller's ilk said "yes, XMRV is there." Do you know how much that would mean for everyone???

But what about this asleep?

Why, then, has the CAA not helped coordinate/fund a true replication of the WPI's findings?

The CAA collaborated with GSK to use a cohort that looked very like the original WPI cohort. I don't know what the methods were but I think we can agree that it's in the best interests of a major producer of antiretroviral drugs to prove that XMRV is present in CFS? If we can agree on that then maybe we can agree that they are going to use the techniques they think can best find it....I assume that that includes those techniques in the original study.....Maybe Jennie knows more particular.

I will grant that the CAA has not given the WPI money and maybe they should have. Can you grant, though, that they are helping produce a study that is trying to find XMRV?

 

[garcia]

I will grant that the CAA has not given the WPI money and maybe they should have. Can you grant, though, that they are helping produce a study that is trying to find XMRV?

Cort, they could start by donating $180,000 to the WPI instead of donating the same amount annually to Kim McCleary's personal bank account. Right now $180,000 would go a heck of a long way at the WPI. I only wish I had that money to give them myself.

 

[asleep]

I admit I don't understand all the science. This is at the end of the Supplemental Sciences section - First they show that three CFS XMRV strains were very similar to the reference strain (VP62). They also show where the strains differ - which, would I think be important.

I am not a virologist either, but I'm pretty sure that the reference you provide here is to serology methods, not stand-alone PCR as you originally implied. So your original quote is still unsubstantiated.

I didn't casually slip in anything. Dr. Miller said in a comment to Gerwyn's blog that was posted on the ME/CFS Forums that he would do that.

http://niceguidelines.blogspot.com/2011/01/must-read-if-you-are-xmrv-positive.html

You are so suspicious... I'm not trying to distort anything or subtly get anything over on anyone..
No one was out to get XMRV or the WPI. The intent was to find XMRV...why would we not want to find XMRV? What would anyone with CFS get out of that? What would our motive or Dusty Miller's motive be in doing that? We would love to find it. Can you imagine how happy people would be if a gamma retroviriologist of Dusty Miller's ilk said "yes, XMRV is there." Do you know how much that would mean for everyone???

But what about this asleep?

I don't know why you are talking about Miller here. The context of your original quote about using WPI methods was clearly referring to Maldarelli:

Dr. Malderilli;s inability to only look for XMRV in severely, severely ill patients is not a reason, in my book, to not support his study. He has still loaded the deck, so to speak, by looking at patients who already tested positive....and while I would be surprised if he could validate all the patients - since the WPI is obviously the most adept at find XMRV - he should be able, using the same techniques the WPI did, to find it in some of them - and that is what the field needs at this point.

As such, it is still completely unjustifiable and an insidious undermining of fact.

But even if I grant that you were talking about Miller (which you weren't), let's take another look at the quote you supply from Miller:

A basic tenet of science is that results obtained in one lab should be reproducible in other labs. We plan to use many of the same techniques used in the Lombardi et al. study from the WPI, and some additional techniques we have developed, to detect XMRV. One of the criteria for inclusion in our study is that subjects must have tested positive for XMRV by another lab.

The phrase "many of the same techniques" is spectacularly vague. If his common techniques include "some use of" PCR and WB, then he will likely not find XMRV. Methodology encompasses far more than just "techniques." Moreover, the abundance of failed attempts to find XMRV using the same tired methods makes it clear that we need scientists who will use all of the Lombardi methods down to the most seemingly insignificant detail.

The CAA collaborated with GSK to use a cohort that looked very like the original WPI cohort. I don't know what the methods were but I think we can agree that it's in the best interests of a major producer of antiretroviral drugs to prove that XMRV is present in CFS? If we can agree on that then maybe we can agree that they are going to use the techniques they think can best find it....I assume that that includes those techniques in the original study.....Maybe Jennie knows more particular.

I will grant that the CAA has not given the WPI money and maybe they should have. Can you grant, though, that they are helping produce a study that is trying to find XMRV?

This is not a negotiation of truth. There is no "granting" that the CAA hasn't funded the WPI. They haven't, end of story.

As for the GSK study, it's hard to find much information (perhaps because the CAA announced it using their famous Inside Voices?). Here is your description from your ongoing studies page

CFIDS Association of America will collaborate with Glaxo-Smith Kline to test for XMRV in a cohort similar to that found in the Science study. The CAA will provide samples from its BioBank and GSK will do the testing. Importantly they will include people who have tested positive for XMRV by VIP Dx/WPI in the study.

Firstly, what evidence is there that this is a true replication study? In other words, what reason is there to believe this study is not using methods that have pre-programmed it for failure? (Hint: the answer is not a generic claim that everyone wants to find XMRV)

Secondly, this study contains the same political dynamite that sparked this whole debate: the use of XMRV+ samples. This is becoming something of a theme for the CAA...they really want those XRMV+ samples retested. Given the potential danger this poses, this theme reflects very poorly on them.

 

[jspotila]

Why, then, has the CAA not funded a single penny to the WPI for XMRV research?

Why, then, has the CAA not helped coordinate/fund a true replication of the WPI's findings?

From the Association's FAQ - http://cfids.org/cfidslink/2010/010607.asp#2r "Like most grantmaking organizations, our research policies preclude us from disclosing details about studies that were not approved for funding. This preserves the applicants ability to submit the study to another institution or to revise and resubmit on another round. It is possible to state that at the time of the Associations most recent Request for Applications (March 2008) there were no applications on the topic of XMRV and CFS." I can't say anything more than that.

Also from the FAQ "The Association is also collaborating with several groups studying XMRV and attempting replication studies. These collaborations have taken various forms, from providing consultation on CFS (since many of the researchers engaged in these studies are new to CFS research), to linking bench researchers with sources of clinical samples."

I can't comment on the specifics of the GSK study because of confidentiality agreements. However, the Association requires BioBank collaborators to publish their data, regardless of the results. I do not have a timeline, but the GSK study will be published.

 

[Roy S]

Gerwyn posted this at ME/CFS Forums. Judy Mikovits wanted it to be known about the Malderalli study:

Quote

"She informed me that neither the WPI or the others mentioned [Drs Ruscetti and Lo/Atler] are involved in any way.

She also informed me that the retesting of XMRV positive people is set to take place in John Coffin' s laboratory and that Dr. Malderalli works for John Coffin.

She asked me to make the contents of our communication known and she is willing to answer individual e-mails from people who are still in doubt about the above."

 

[eric_s]

Very interesting, thank you. We should not let go until we know the reason for what has happened. Time for people to show where they stand and what their motives are.

 

[Kelly]

Paranoia, half truths and misinformation

....Paranoia is a thought process heavily influenced by anxiety or fear, often to the point of irrationality and delusion. Paranoid thinking typically includes persecutory beliefs concerning a perceived threat towards oneself.

There is so much, pardon my French, crap, floating around on patient forums it is frightening.

How to sort it out - post only original material from original sources - stop trying to read scientists minds unless you can provide official scientific evidence of having ESP personally - stop rumors by refusing to repeat them.

These people are scientists not people with a gun on a grassy knoll - patients need to get a grip.

 

[floydguy]

....Paranoia is a thought process heavily influenced by anxiety or fear, often to the point of irrationality and delusion. Paranoid thinking typically includes persecutory beliefs concerning a perceived threat towards oneself.

There is so much, pardon my French, crap, floating around on patient forums it is frightening.

How to sort it out - post only original material from original sources - stop trying to read scientists minds unless you can provide official scientific evidence of having ESP personally - stop rumors by refusing to repeat them.

These people are scientists not people with a gun on a grassy knoll - patients need to get a grip.

Yes, and you are adding to it. Please specifically state the basis for your alleged conspiracy theories.

 

[ukxmrv]

We do have a grip, Kelly. Are you qualified to diagnose paranoia?

That's why we are dissecting and discussing all of the information that we can find. I've been through the political hell of this for around 27 years and I've seen very little paranoid behaviour from patients. I have seen very savvy judgements and warnings.

If you are so sure of this paranoia diagnosis why not furnish some proof?

 

[Esther12]

I understand what Kelly means.

I think that some people are extending the more justified paranoia we have about the psychosocial approaches to CFS to virolgy. Virology is much more of a hard science, and at this point in the search for XMRV, almost impossible to permanently distort through prejudices and prior presumptions. If the WPI are able to sort blinded blood samples from CFS patients and healthy controls, then their work will not be covered up or discarded.

 

[Mark]

In general, you make a fair point Kelly, though like ukxmrv I'm not sure who or what precisely you're referring to here: it frustrates me too when good and legitimate questioning is accompanied by speculation about people's motives and attempts to look inside other people's heads and to infer sinister motives to anyone with a different opinion, or to get angry with people over such differences of opinion: that's a sure way to freeze yourself out of the debate and ensure your valid points aren't taken as seriously as they deserve to be. It's true that there is some of that sort of thing that goes on, though not usually very much of it at all on Phoenix Rising I would say, and whether that goes as far as to be called 'paranoia' might be stretching it a bit as well I think.

In this case though, there's a legitimate question to be answered: why the contradiction in the public statements about the WPI's involvement in this study? It's a waste of time and energy to speculate about the answer to that: the situation could be very different to what we are assuming, so the only way forward is to pursue an answer to the question: set out the contradictory statements clearly, and write and ask for an explanation from the people involved. Just that - that's all that's needed, the rest is just hot air really. So please let's all just set out the facts in a straightforward way, pursue an explanation, and try to avoid making any assumptions until we have some more information. In and amongst the angry allegations, there's a genuine apparent contradiction here, and really I think people just want to get to the bottom of that.

 

[eric_s]

I am not into conspiracy theories and have always tried to avoid them. Also at this moment, i am not making any theories. But do you think it's normal to look for patients for a study and tell them about a number of labs that are involved and then to hear from those labs that they are not involved at all?
I realize that most of the knowledge presented here is second hand, so i don't say i know the truth, but in such a situation i want to know what the truth is. I don't speculate, i just say there is a blank spot and i'd like to know what's there.
Or can you make sense of this? Or don't you think this matters at all?

 

[Esther12]

I realize that most of the knowledge presented here is second hand,

That does make it hard to know what's going on. It just takes a small degree of chinese whispers to confuse matters.

edit: looking back at my post the use of crude imperialist era stereotyping rather stands out. Not sure what to replace it with though...

 

[eric_s]

That's absolutely true... unfortunately it's almost imossible to get everything firsthand. Just imagine how many emails Judy Mikovits would have to write for example. I realize this is a problem.

 

[acer2000]

It would be better if anyone, regardless of the source of the information or topic, requested permission from the source and then posted the actual full email instead of just paraphrasing it. A screenshot would be ideal. That way everyone could judge for themselves and we'd have less room for mis-interpretation.

 

[Roy S]

I'm not sure if I was being accused of paranoia there, but no matter.

FWIW, before posting that I confirmed the facts with someone who I trust that is also in communication with Judy Mikovits. I didn't want to bother her because she's got more important things to do than answer a bunch of e-mails from patients.

 

[Esther12]

I didn't want to bother her because she's got more important things to do than answer a bunch of e-mails from patients.

Yeah... I feel like I'd rather live in ignorance and have more work being done on getting papers published at the moment.

 

[eric_s]

But what if the ignorance hurts your chance of reaching the goal? I'm not saying it is like that, but if we are ignorant we can't know. Of course we have to live with some uncertainty...

But seriously now. If you were the boss of an organisation and someone working for you tries to find participants for a study and tells them that other labs from your organisation plus yet others will participate and that is not true, would you not care?
I don't think this is a bagatelle, no matter why it happened. So someone should find out what happened.

 

[Roy S]

Cort, "Who shall remain nameless"? I read what you posted over there; so did others. I thought maybe that was why you got banned, or maybe because you registered under MEman last June 31.

I've been reviewing this thread and I think Asleep made some very good points about how damaging a flawed study can be. This is very serious stuff and I don't think amateurs should get involved.

Here's the letter that got me banned. She asked me not to post it but then when someone, who will remain nameless, posted the first part of it - she asked that the whole thing be posted.

from Judy Mikovits <judym@wpinstitute.org>
to Cort Johnson <phoenixcfs@gmail.com>
date Tue, Jan 11, 2011 at 7:29 AM
subject Re: Dusty Miller's Pilot XMRV Study
hide details Jan 11
Hi Cort
Please post the entire comment. this taken out of context is misleading. It implies I endorse the study and I do not!
Dear Cort
I can only say positive things about Dusty Miller. He is an excellent scientist with more than 30 years experience in gamma retrovirus study. I met him at the NCI closed meeting on XMRV in July 09 when we first presented these data prior their publication in Science. I don't know him well because our paths did not cross until that meeting. He is a long time colleague of Sandy Ruscetti (I would encourage you to contact Sandy or Frank) if you would like support from co-authors of the science paper. Our work could not have been done without the expertise of Sandy Ruscetti and I have no doubt that Dr Miller's lab is fully competent and can add significant insight into the potential mechanisms of neuropathogenesis as Sandy's lab has done.

As for the IAP assay, I strongly advise not to use the IAP assay as a measure of mouse contamination. Dr Evans showed that the mobilization of endogenous retroviruses in mice after infection with an exogenous retrovirus (J Virol 83:2429, 2009, attached). This occurs with great frequency even after one day of infection. Dr. Evans recently presented at a meeting that IAPS can be packaged and mobilized. This says that a human infected with XMRV might also be infected with co-transferred mouse IAP sequences or polytropic sequences. Moreover, infectious retroviruses can continue to package these sequences at a high level. My concern is that the finding of IAP sequences may not be evidence of contamination but of real infection (or unrelated).Since the mitochondrial DNA in the Lo et al. publication is every bit as sensitive as the IAP assay, and has been used for all studies at the WPI as well, why not use it?

Given my scientific concerns about mouse based viral sequences, which can easily be packaged and moved by XMRV/MRVs being used in any study as an assay for contamination, I cannot advise any patients in good conscience to participate in such a study. I would be happy to discuss anything in this email with Dr Miller at any time but would politely ask that you not post this email. It would be better for Dr MIller, the Ruscettis and I to talk directly and in that way we can all present a unified front to the entire patient community. It is so important that the patients concerns be heard given how politicized this complex problem has unfortunately become. I have cc'd Dr Miller.

Kind regards
Judy




I was later told that the problems had been worked out. I was not told that from Dr. Miller or Dr. Mikovits. I do not believe the Miller study is continuing at this point, however. He is still investigating XMRV in some fashion, I believe.