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Negative study: XMRV in prostate cancer cells likely represents a laboratory artifac

Jemal

Senior Member
Messages
1,031
I don't think this study brings anything new to the table, but I am posting it here for the record.

Jiawen Yang 1,2*, Partho Battacharya 1,2*, Ruchi Singhal 1*, Eugene S. Kandel1

1Roswell Park Cancre Institute, Department of Cell Stress Biology, Elm & Carlton St., Buffalo, NY, 142263, USA

2City Honors School, 186 East North Street, Buffalo, NY, 14204, USA

*These authors contributed equally to this work

Keywords: XMRV, prostate cancer, CWR22, 22Rv1

Received: April 27, 2011; Accepted: May 29, 2011; Published: June 2, 2011;

The prevalence of xenotropic murine leukemia virus-related virus (XMRV) in human population and its involvement in prostate cancer are subjects of ongoing research and debate. 22Rv1, which is a human cell line that serves as a common model of androgen-independent prostate cancer, was recently reported to carry infectious copies of XMRV. 22Rv1 was derived from a prostate cancer xenograft CWR22 that was serially passaged in immunodeficient mice. Based on the analysis of the DNA from CWR22 and 22Rv1, we present evidence against the presence of XMRV in CWR22 and, by inference, the tumor, from which CWR22 and 22Rv1 were established. While the presence of XMRV in 22Rv1 is likely to be an artifact, it may be a significant factor in determining the biological properties of this cell line. This consideration warrants additional caution for the interpretation of the relevance of the studies, which utilize this popular cell line as a model. It also invites a closer look at the sources of viral contamination in xenografts and cultured cells, as well as in the experiments that allege the presence of this virus in human cells and populations.

http://www.impactjournals.com/oncot...et&page=article&op=view&path[]=287&path[]=438

The fight is definitely on though, XMRV prostate cancer research is a target for the contaminists. This could be a good thing, as one can hope it forces researchers like Silverman, Klein, Singh, etc to take a stand. Silverman is out there defending his work, let's see Singh do the same.
 

alex3619

Senior Member
Messages
13,810
Location
Logan, Queensland, Australia
Hi Jemal I tried to post this in another thread but the link was broken by PR, I had to manually format it. While this paper clearly says 22Rv1 XMRV is probably an artifact, it leaves the door open as to what it means in my opinion. This is a lot more balanced than Coffin's statements, although the science is similar. It also leaves open the possibility that the cell line was contaminated by XMRV, just as I have been wondering. In other words, yes, it appeared suddenly in the developing cell line, but that does not nail down why.

I still think XMRV is way too adapted to these cells. I think it is pre-adapted - it has a long history of infecting this type of cell. If so, this might be an old virus, just unusually capable of contaminating everything. Which raises the question: how many in the public are at risk of infection just from random virus particles? I hope Levy is right that we can stomp it before it takes hold, but I doubt it - mucous membranes, particularly the lungs, are viable targets. This could be an airborne retrovirus, but I do think that there is evidence that the transimission rate is very low, regardless of the mode of transmission.

So even in the prostate cancer and ME/CFS links are a bust, which I dont think will be the case, this virus is still a threat.

It is fine to argue that XMRV is problematic because we can't be sure we are finding it and not contamination. That is a two way argument though - it could imply we are not capable of effectively detecting a new retroviral epidemic that has been left unchecked for an unknown number of years. If the WPI cannot reliably find it, if nobody else can reliably find it, and it is really out there, then there are major problems on the horizon if this virus is pathogenic. Thats a lot of ifs, but the downside is very worrying.

Bye, Alex
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
Hi Jemal I tried to post this in another thread but the link was broken by PR, I had to manually format it. While this paper clearly says 22Rv1 XMRV is probably an artifact, it leaves the door open as to what it means in my opinion. This is a lot more balanced than Coffin's statements, although the science is similar. It also leaves open the possibility that the cell line was contaminated by XMRV, just as I have been wondering. In other words, yes, it appeared suddenly in the developing cell line, but that does not nail down why.

I still think XMRV is way too adapted to these cells. I think it is pre-adapted - it has a long history of infecting this type of cell. If so, this might be an old virus, just unusually capable of contaminating everything. Which raises the question: how many in the public are at risk of infection just from random virus particles? I hope Levy is right that we can stomp it before it takes hold, but I doubt it - mucous membranes, particularly the lungs, are viable targets. This could be an airborne retrovirus, but I do think that there is evidence that the transimission rate is very low, regardless of the mode of transmission.

So even in the prostate cancer and ME/CFS links are a bust, which I dont think will be the case, this virus is still a threat.

It is fine to argue that XMRV is problematic because we can't be sure we are finding it and not contamination. That is a two way argument though - it could imply we are not capable of effectively detecting a new retroviral epidemic that has been left unchecked for an unknown number of years. If the WPI cannot reliably find it, if nobody else can reliably find it, and it is really out there, then there are major problems on the horizon if this virus is pathogenic. Thats a lot of ifs, but the downside is very worrying.

Bye, Alex

I totally agree with you Alex.

The paper is far more balanced that Coffin's paper, and the authors raise some issues relating to why Coffin's study might have come to the wrong conclusions.


There's a number of reasons why Coffin's conclusions are premature:

1. A wider variety of XMRV sequences have now been detected and published in genbank.

2. The original prostate cancer sample, which initiated the cell line, may have harboured undetectable minuscule quantities of XMRV, which then flourished as the cell line was propagated, making it detectable in later samples of the cell line.

3. Switzer's recent abstract challenges Coffin's conclusions, because Switzer has worked out many other possible recombinations.

4. Apparently, not all mice have yet been tested for XMRV, so it is possible that some mice, somewhere, harbour XMRV.

5. Coffin might have only detected contamination in his own study, in which case all of his results and conclusions are invalid.


That's all I can think of right now... There may be other reasons.
 

Jemal

Senior Member
Messages
1,031
4. Apparently, not all mice have yet been tested for XMRV, so it is possible that some mice, somewhere, harbour XMRV.

Can they even find XMRV in mice? I mean, they are detecting 0/0 in patients, could they be detecting 0/0 in mice too? They all say they can find XMRV, yet I remain suspicious of their assays and tests.

Also, maybe they should not be looking in mice only?
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
Can they even find XMRV in mice? I mean, they are detecting 0/0 in patients, could they be detecting 0/0 in mice too? They all say they can find XMRV, yet I remain suspicious of their assays and tests.

Good point!

If it's an endogenous mouse virus, then it would be more straightforwards to detect than an exogenous mouse virus.

Do you know if it could it theoretically be an exogenous mouse virus, based on current knowledge?

Also, maybe they should not be looking in mice only?

Another good point!
 

Jemal

Senior Member
Messages
1,031
Good point!

If it's an endogenous mouse virus, then it would be more straightforwards to detect than an exogenous mouse virus.

Do you know if it could it theoretically be an exogenous mouse virus, based on current knowledge?

I have no idea, though I do think some mouse viruses can be both exogenous and endogenous. Mouse mammary tumor virus (MMTV) is such an example. It's not a gammaretrovirus.
 

Cort

Phoenix Rising Founder
I totally agree with you Alex.

The paper is far more balanced that Coffin's paper, and the authors raise some issues relating to why Coffin's study might have come to the wrong conclusions.


There's a number of reasons why Coffin's conclusions are premature:

1. A wider variety of XMRV sequences have now been detected and published in genbank.

2. The original prostate cancer sample, which initiated the cell line, may have harboured undetectable minuscule quantities of XMRV, which then flourished as the cell line was propagated, making it detectable in later samples of the cell line.

3. Switzer's recent abstract challenges Coffin's conclusions, because Switzer has worked out many other possible recombinations.

4. Apparently, not all mice have yet been tested for XMRV, so it is possible that some mice, somewhere, harbour XMRV.

5. Coffin might have only detected contamination in his own study, in which case all of his results and conclusions are invalid.


That's all I can think of right now... There may be other reasons.

I think you have some good reason but I think they're more based on hope :)

yes new sequences were posted to GenBank but the CAA reported that they are much the same as the other sequences.....and nobody other the WPI seems to feel otherwise - not a good sign.

Yes, there could have been miniscule amounts of XMRV present but they looked very hard for it with very sensitive tests....so while that could be true - my guess is that it probably isn't.....

It is true that not all mice have been tested but a heck of alot of mice have..probably most that are available - so again - you're kind of hoping for something unusual to happen...that one strain of mice that has XMRV has been missed.

Switzer - the Paprotka paper suggested that there was a 1 in a trillion chance that some other recombination event could have caused this strain of XMRV to show up.

These are all longshots, in my opinion.....unfortunately.
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
I think you have some good reason but I think they're more based on hope :)

yes new sequences were posted to GenBank but the CAA reported that they are much the same as the other sequences.....and nobody other the WPI seems to feel otherwise - not a good sign.

Yes, there could have been miniscule amounts of XMRV present but they looked very hard for it with very sensitive tests....so while that could be true - my guess is that it probably isn't.....

It is true that not all mice have been tested but a heck of alot of mice have..probably most that are available - so again - you're kind of hoping for something unusual to happen...that one strain of mice that has XMRV has been missed.

Switzer - the Paprotka paper suggested that there was a 1 in a trillion chance that some other recombination event could have caused this strain of XMRV to show up.

These are all longshots, in my opinion.....unfortunately.

Cort, I was just pointing out why the Coffin paper is not conclusive. And there are a number of reasons.
Some of my points were 'longshots' (but not invalid), but some were strong points.

Switzer's new study challenges the Paprotka study, and basically says that the info re recombinations is nonsense.
Have you read it? It's a brand new publication.

There's been no professional or peer reviewed analysis of the new sequences in genbank, as far as I'm aware, so it is premature to make any firm conclusions about them either way. The analysis that I've seen does suggest increased variation. And the WPI say that they have a whole load of viruses that they can't afford to sequence.

But even if there is no significant variation, this does not confirm that it is contamination, for a couple of reasons:
1. A possible different route of infection, such as via vaccines.
2. A possible virus mutation pattern similar to HTLV.
 

jace

Off the fence
Messages
856
Location
England
They will never find xenotropic murine leukaemia-related viruses in mice. Polytropic, yes, xeno, no, by definition a xeno cannot infect the originating species. However, the polytropic HGRV's such as those being found now in various labs are near enough to XMRV to be called the same species, just as there is only 85% homology in the various strains of HIV and HTLV varies too.

Beware of the nomenclature trap. When something new is named for the first time, it is named with the best of knowledge and belief at that time by the discoverer. It does not mean that the name is real. The thing is real, but imperfectly understood. The name may well prove later to be inaccurate, with greater knowledge. We would do better to talk about HGRVs, which fits the understanding of the retrovirus we are discussing better now that the name that was given it in 2006.

Does anyone here have knowledge of the sequences recently published in Genbank by the WPI? Can someone provide a link, so I can see for myself? I'm not interested in hearsay or the CAA's assessment, I want to compare for myself.
 

Bob

Senior Member
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16,455
Location
England (south coast)
Does anyone here have knowledge of the sequences recently published in Genbank by the WPI? Can someone provide a link, so I can see for myself? I'm not interested in hearsay or the CAA's assessment, I want to compare for myself.

http://phoenixrising.me/forums/showthread.php?11714-New-WPI-and-CDC-XMRV-sequences-in-genbank

Keep in mind that it has been said that there is usually more variability in the unpublished sections of the genome, so that the amount of variability in the published section might not indicate the total variability.

So it seems to be more complex than it first appears, and I think that we need a proper scientific, peer reviewed analysis before we make any conclusions.
 

Jemal

Senior Member
Messages
1,031
They will never find xenotropic murine leukaemia-related viruses in mice. Polytropic, yes, xeno, no, by definition a xeno cannot infect the originating species. However, the polytropic HGRV's such as those being found now in various labs are near enough to XMRV to be called the same species, just as there is only 85% homology in the various strains of HIV and HTLV varies too.

Beware of the nomenclature trap. When something new is named for the first time, it is named with the best of knowledge and belief at that time by the discoverer. It does not mean that the name is real. The thing is real, but imperfectly understood. The name may well prove later to be inaccurate, with greater knowledge. We would do better to talk about HGRVs, which fits the understanding of the retrovirus we are discussing better now that the name that was given it in 2006.

Does anyone here have knowledge of the sequences recently published in Genbank by the WPI? Can someone provide a link, so I can see for myself? I'm not interested in hearsay or the CAA's assessment, I want to compare for myself.

Yes, the name... it might not have been the best.

Although xenotropic murine leukemia viruses cannot productively infect cells of laboratory mice, cells from various wild-derived mice can support replication of these viruses.

http://www.ncbi.nlm.nih.gov/pubmed/2991590

This is a really old publication from 1985, but I think I remember seeing a more recent paper that said the same.

edit: ah yes, from the same author in 2010: http://jvi.asm.org/cgi/reprint/JVI.01863-10v1
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
Beware of the nomenclature trap. When something new is named for the first time, it is named with the best of knowledge and belief at that time by the discoverer. It does not mean that the name is real. The thing is real, but imperfectly understood. The name may well prove later to be inaccurate, with greater knowledge. We would do better to talk about HGRVs, which fits the understanding of the retrovirus we are discussing better now that the name that was given it in 2006.

Well it seems that you may have fallen into your own trap, jace! :D :

They will never find xenotropic murine leukaemia-related viruses in mice. Polytropic, yes, xeno, no, by definition a xeno cannot infect the originating species. However, the polytropic HGRV's such as those being found now in various labs are near enough to XMRV to be called the same species, just as there is only 85% homology in the various strains of HIV and HTLV varies too.

The 'xenotropic' label is a 'nomenclature trap' because it does not apply to all mouse species. I can't remember the exact details now, but some mice have now been discovered that can be infected by X-MLV's. So X-MLV's do behave like P-MLV's in some strains of mice.

ETA: Ah, I see that Jemal has given you more info.
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
yes new sequences were posted to GenBank but the CAA reported that they are much the same as the other sequences.....and nobody other the WPI seems to feel otherwise - not a good sign.

I had forgotten about this, but in one of his recent studies, Switzer specifically says that the XMRV sequence variation that he has detected is "consistent with virus evolution during spread and persistence." Switzers's evidence and conclusions directly contradicts the conclusions that Coffin and his co-authors have come to in relation to there being no variety in any XMRV sequences. Switzer indicates there is evidence of virus evolution expected during normal human infection in the wild.

Switzer study:

Sequence analysis showed that patients 5935, 5956 and 6203 are infected with variant XMRV strains. The 168-bp pol sequences from all three patients showed 90.5100% nucleotide identity to each other, 94100% to XMRV, 91.798.8% to XMLV, 94100% to PMLV, and 91100% to ecotropic MLV (EMLV) in this short region.
164-bp env sequences from persons 5956 and 6203 were identical to each other and shared the highest nucleotide identity (94.9100%) to XMRV and other xenotropic MLV strains, respectively, [25].
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Nearly identical phylogenetic tree topologies for each gene region were obtained with both the NJ and ML methods. The XMRV sequences from both prostate cancer patients were also distinct from the PMLV sequences amplified from the murine cell line (RAW) used for preparing WB antigens demonstrating further that these are not laboratory contaminants (Fig. 2). These results confirm the presence of XMRV in both patients and demonstrate that XMRV diversity is greater than currently appreciated.
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Sequence analysis of the PCR-positive specimens was highly informative because it confirmed that all three specimens were XMRV-related. Also, the finding of a viral strain in three prostate cancer patients that is distinct from the XMRV seen in previous studies is significant and demonstrates a broader viral diversity. This would be an expected result consistent with virus evolution during spread and persistence.

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019065#abstract0