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Hanson study was positive, others out there too scared to publish

RustyJ

Contaminated Cell Line 'RustyJ'
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Denise S. O'Keefe University of Pittsburgh) [says the Hanson study is a positive study (because they could not prove it was contamination) and that there are others out there too scared to publish.

Novel MLV-GAG sequences detected in blood samples of ME/CFS patients
From the Hanson lab, this paper published today in PLoS ONE describes a study carried out with meticulous attention to detail and proper use of controls while analyzing ME/CFS patient samples for murine-leukemia related viruses. Although novel MLV-like GAG sequences were isolated and sequenced from the patient samples (as opposed to controls collected from the same sites) Lee et al. concludes that it is not possible to determine the origin of these sequences, although the samples were not contaminated with mouse DNA at a detectable level. First, bravo! to the Hanson group for being able to get anything published that might go against the current dogma regarding MLV-like viruses in human samples published -- I guarantee you that there are people with similar data whom don't want to torture themselves by attempting to publish.

http://okeefe-lab.blogspot.com.au/
 

currer

Senior Member
Messages
1,409
Hmmmm.....so we're not the only conspiracy theorists over here then! Our paranoia has a basis!

Maybe you cant get published if your paper concludes that the contamination might actually be in the patients! This COULD be as close as they can get if they want to get published.
 

currer

Senior Member
Messages
1,409
Incidentally I got a security warning on my computer saying it was risky to access the O'Keefe website. I was using Eco's link from another thread. So I did not go there and could not read what she wrote.
 

RustyJ

Contaminated Cell Line 'RustyJ'
Messages
1,200
Location
Mackay, Aust
Yes, er, no, we are not the only conspirators out there.

Her statements do show that the line being put forward by some posters on this forum that researchers are reluctant to get into XMRV because of pressure from patients is baloney. It is the contamination researchers themselves that are applying all the pressure and some posters on this forum are part of that push. If that is the case I find it difficult to believe these posters are helping me/cfs patients and must assume they are actively working against us.
 

RustyJ

Contaminated Cell Line 'RustyJ'
Messages
1,200
Location
Mackay, Aust
Incidentally I got a security warning on my computer saying it was risky to access the O'Keefe website. So I did not go there and could not read what she wrote. That makes me suspicious too!
Odd, I have trendmicro running, there is no warning when I access it.
 

currer

Senior Member
Messages
1,409
Its Ok managed to get there safely!
"From the Hanson lab, this paper published today in PLoS ONE describes a study carried out with meticulous attention to detail and proper use of controls while analyzing ME/CFS patient samples for murine-leukemia related viruses. Although novel MLV-like GAG sequences were isolated and sequenced from the patient samples (as opposed to controls collected from the same sites) Lee et al. concludes that it is not possible to determine the origin of these sequences, although the samples were not contaminated with mouse DNA at a detectable level. First, bravo! to the Hanson group for being able to get anything published that might go against the current dogma regarding MLV-like viruses in human samples published -- I guarantee you that there are people with similar data whom don't want to torture themselves by attempting to publish. The fact is, that it seems somehow MLV-like nucleic acids somehow end up in patient samples quite a bit, albeit at exceedingly low levels. Theoretically, even if there was an MLV-type infection in a human, it would be rapidly eliminated (unless of course we don't know everything about the immune system yet). I wonder if it is possible that such viruses could hide somewhere in the body, not replicating much - perhaps killing host cells occasionally resulting in a release of (potentially degraded) viral nucleic acid that is ultimately detected in the blood stream. I haven't analyzed these sequences yet compared to those we have detected in tissue samples from BPH patients, but seeing as our sequences were recently published on the USPTO website, someone else will probably try that."
 

VillageLife

Senior Member
Messages
674
Location
United Kingdom
HERE IS THE FULL POST....

Novel MLV-GAG sequences detected in blood samples of ME/CFS patients

From the Hanson lab, this paper published today in PLoS ONE describes a study carried out with meticulous attention to detail and proper use of controls while analyzing ME/CFS patient samples for murine-leukemia related viruses. Although novel MLV-like GAG sequences were isolated and sequenced from the patient samples (as opposed to controls collected from the same sites) Lee et al. concludes that it is not possible to determine the origin of these sequences, although the samples were not contaminated with mouse DNA at a detectable level. First, bravo! to the Hanson group for being able to get anything published that might go against the current dogma regarding MLV-like viruses in human samples published -- I guarantee you that there are people with similar data whom don't want to torture themselves by attempting to publish. The fact is, that it seems somehow MLV-like nucleic acids somehow end up in patient samples quite a bit, albeit at exceedingly low levels. Theoretically, even if there was an MLV-type infection in a human, it would be rapidly eliminated (unless of course we don't know everything about the immune system yet). I wonder if it is possible that such viruses could hide somewhere in the body, not replicating much - perhaps killing host cells occasionally resulting in a release of (potentially degraded) viral nucleic acid that is ultimately detected in the blood stream. I haven't analyzed these sequences yet compared to those we have detected in tissue samples from BPH patients, but seeing as our sequences were recently published on the USPTO website, someone else will probably try that. The link to the Hanson paper is here --
 

natasa778

Senior Member
Messages
1,774
Denise S. O'Keefe (University of Pittsburgh) says the Hanson study is a positive study (because they could not prove it was contamination) and that there are others out there too scared to publish.
http://okeefe-lab.blogspot.com.au/


I am aware of one such study that was done under the umbrella of NIH - it found positives in autism samples, but later decided that "it must be contamination" (because CDC/Willams study said so!) and never published. Since they never published and didn't share details with me I don't know if they found positives in controls etc.

This was written to me by one of the authors involved in the study, in November 2010:


Dr Mike Iadarola is now ready to run the XMRV assays on samples from our children with autism (approx 100), typical development (60) and developmental delay (30). We did send him a batch of approximately 100 samples last summer (from the three groups), almost immediately after the initial report of the positive results in autism (ref. Mikovits unpublished results). However, that assay proved to be quite unreliable, yielding positive results in individuals who were known to be negative by more extensive testing. So, we elected to wait for the assays to be better standardized before running our children's sample. Meanwhile, we finished enrolling subjects in the phenotyping study and Dr Iadorola can now run the assays on the whole cohort.

This will allow direct comparison of the rates of + Abs in autism with those in children without any autism symptoms. Those results should be quite helpful in interpreting the meaning of a positive XMRV result. The Nevada group has assumed that positive results are equivalent to the pathology of the individual providing that specimen. However, the wide variety of disorders in which they've found "increased" rates of XMRV suggests that a third factor may be involved and the 3rd factor is the one of true interest in autism. At present, XMRV-positivity appears to be much more common that the small initial study suggested. XMRV may be the equivalent of a positive Epstein-Barr viral titer - in the vast majority of cases, the positive titer merely represents a past exposure to the virus. For the few in whom the EBV infection produced long-lasting sequelae, other markers are better determinants of the pathology. Dr Iadarola's assays will tell us if XMRV positivity is more frequent among children with autism than among children without autistic symptoms. If so, it would be a strong hint that XMRV may play a role in autism (but won't know whether it is a primary or secondary player).”

(so she is saying that XMRV is widespread in humans but basically harmless, whereas her colleague later took the “it is all contamination, there is no XMRV in humans” approach)

In later correspondence, when I asked about how they decided that their assay “was unreliable” and what they meant by “yielding positive results in individuals who were known to be negative by more extensive testing” --- Dr Iadorola only mumbled something about CDC/Satterfield study (see quote below) and never gave me a straight answer.

My repeated question as to why they refused to publish their initial results was also NEVER answered. It would be very interesting to know what “extensive testing” was carried out and by whom/how, what was the ratio of patients to controls with initial positive results etc…


This is the reply from Mike Iadorola on my question as to why they didn’t publish their positive findings:

“ …. Please look at this recent paper from Molecular Autism (attached). They used PCR to look for XMRV DNA and did an antibody test. The results were uniformly negative: no XMRV in autism samples (and they had plenty, some from USA, some from abroad. Thus, my projection is that we likely will corroborate their study. We will examine the serum for the presence of antibodies to couple of XMRV proteins. The assay we developed is called Luciferas Immunoprecipitation systems..."

So totally avoiding explanation of his own POSITIVE results, no explanation on why not publish them...

Not sure what happened to this second study – the one he expected will “likely corroborate” the negative studies - I suspect if they did find positives they would be very reluctant to publish, wouldn't they? But I suspect if they DID found all their samples negative they would be very keen to publish, no?



Btw Dr Collins, head of NIH, was copied in all of the correspondence…

 

RustyJ

Contaminated Cell Line 'RustyJ'
Messages
1,200
Location
Mackay, Aust
Btw Dr Collins, head of NIH, was copied in all of the correspondence…

Huh.

I notice they couldn't even get their stories straight. Where they found evidence of XMRV, they dismiss it as non benign? They way they talk about XMRV as a virus in the same terms of behavior a EBV, rather than as a retrovirus, indicates dissembling.
 

asleep

Senior Member
Messages
184
Her statements do show that the line being put forward by some posters on this forum that researchers are reluctant to get into XMRV because of pressure from patients is baloney. It is the contamination researchers themselves that are applying all the pressure and some posters on this forum are part of that push. If that is the case I find it difficult to believe these posters are helping me/cfs patients and must assume they are actively working against us.

Completely agree. The idea that patients saying "mean things" about researchers was driving them away was always baloney. In fact it was and is laughable. Nothing anyone has said could hold a candle to what Act Up actually did, and despite that HIV research is probably one of the most lucrative and fruitful (from a funding and career perspective) academic fields of all time. "XMRV" research was always going to be contentious from the outset and any researchers who are whining about "mean words" are like someone who would charge into a street brawl and erupt into an epic hissy-fit when someone bumps into them. Such researchers probably should take their brittle egos to safer pastures and make room for the numerous others with the personal fortitude to withstand controversy.
 

currer

Senior Member
Messages
1,409
http://www.upmc.com/Services/Urology/Experts/ResearchFaculty/Pages/Denise-S-OKeefe.aspx
(courtesy of another forum)
Has anyone put this link up on PR yet?
It gives more details of a novel retrovirus O'Keefe found in benign prostatic hyperplasia.
Not XMRV, comes in two variants.

"Given the recent findings of a novel virus, XMRV, found in some prostate tumors, we analyzed the BPH affected tissue for viral infection. We found that the majority of tissue from symptomatic BPH patients contained low levels of a virus not previously found in humans. Sequencing confirmed that the virus consists of 2 variants, is not XMRV, and likely produces a protein that has been related to inflammation in other species. Interestingly, the exact virus sequence differs among patients, suggesting that upon infection of the tissue, the virus undergoes replication. Furthermore, sequencing revealed that the virus is likely transcriptionally regulated by androgens, which is consistent with the fact that cell growth in BPH is androgen-dependent and the classic non surgical treatment for BPH is inhibition of DHT (an androgen) production. Both variants of the virus have submitted to the USPTO as a provisional patent, as they may be a therapeutic target for this disease.
 

VillageLife

Senior Member
Messages
674
Location
United Kingdom
The Patent:

http://www.freshpatents.com/-dt20120503ptan20120107338.php

The PDF File (Full Patent:) http://images3.freshpatents.com/pdf/US20120107338A1.pdf

Agent: University Of Pittsburgh - Of The Commonwealth System Of Higher Education - ,
Inventor: Denise S. O'Keefe
USPTO Applicaton #: #20120107338 - Class: 4241871 (USPTO)

Identification of a novel retrovirus in patients with benign prostatic hyperplasia

A quote from the patent......
The BPH viruses disclosed herein are related to previously identified gammaretroviruses such as murine leukemia virus and xenotropic murine leukemia virus-related virus (XMRV), but are distinct from these viruses based on nucleic acid and amino acid sequences.
 

currer

Senior Member
Messages
1,409
Good post by anciendaze on the O'keefe sequences on the other forum
(Hope you dont mind me quoting you here, anciendaze)

"What strikes me about this patent is the result of a BLAST alignment with known sequences, including the putative pre-XMRV2, as discussed here:
http://peoplewithme.com/thread-1178.html

While it is very close, it is no more identical to the putative ancestor than many recognized exogenous viruses. Furthermore, it seems to have G to A changes characteristic of hypermutation. These take place in the reverse transcription of RNA to DNA, which points to active viral infection. No such result from the XMRV contaminating cell lines shows up here. The origin of the corresponding XMRV envelope sequence is becoming a serious question.

This tissue was never passaged through mice, nude or hairy. This researcher has also done extensive testing for contaminating sequences, even discovering a novel form of cross contamination which can mask the presence of up to 80 ng. of target DNA.

I think this lays to rest the idea that XMRV was formed by recombination of two passive ERV sequences in a single mouse. At least one of the sequences had to be the result of an active viral infection. How it showed up in human prostate tissues without bringing along either mouse mitochondrial DNA sequences or mouse IAP sequences, which far outnumber the proposed ERVs, is a real problem for recombination arguments