Restricted Replication of XMRV in Pigtailed Macaques

[Firestormm]

You are highlighting the bits that suit the agenda of 'no need to worry folks lets look the other way' brigade (which imo is highly driven by wanting to avoid the issue of contaminated biologicals, avoiding the V word).

Again they don't account for very real and documented possibility of this suposed hypermutation by human APOBEC being very much dependent on you APOBEC polymorphism. In other words not everyone's APOBEC acts in the same way or has the same effect etc. Do I need to repost those papers once again? Have you even read them?

What if there is a tiny minority of humans (say 1%) whose APOBEC is no match for your average gammaretrovirus. It is a no-brainer that medical science should err on the side of caution, and these attempts to write of MulVs as harmless to humans are scientists simply trying to cover their behinds. Or not doing their job properly. Ignorance or willful spin?

Natasa - you are of course correct. Perhaps I should not have bolded certain parts but that was my decision and rather than post just those sections, I did post a lot more to give greater context.

I do not understand the minutiae of science papers - I tend to rely on scientists to interpret them for me if I feel a need to understand more - and indeed I do refer to scientists when I feel a need for more general interpretation of a paper including the authors themselves (though not in this case I should add).

I certainly don't feel I was 'cherry picking'. I mean that is a fairly extensive couple of posts there and most of it is from the 'Discussion' part of the paper. Meaning simply that - it was a discussion by the authors about their results in the greater context of previous and future studies.

There was an awful lot that is I think relevant but was not bolded so I think your comment is unfair. This paper also refers back to the original paper on Macaques that appeared to raise a number of 'concerns' not least the 'fear' that XMRV 'disappeared' from blood and 'hid' in tissue - most recently Lymph Nodes if I remember correctly.

It also provides greater information about XMRV replication in general I felt. Again though, this thread was about this paper and of course - as even the authors would and have pointed out - it does leave questions unanswered.

But science is a process towards greater understanding and the focus - if you like - is now on trying to understand more about this novel gammaretrovirus.

XMRV has not been found in humans and the next best thing in terms of trying to understand how this retrovirus works is apparently to inject MASSIVE amounts of the virus into primates.

The exact reasons for doing so in this study are laid out above. It will I am sure lead to further research but it will take another paper like (but better than) Lombardi et al. for anyone to look again at XMRV and human infection and especially XMRV and CFS patients.

Nobody has ever said XMRV was not a retrovirus. Nobody. It will continue to be studied and this paper implies that in the absence of confirmed human infection - primates are the next best thing.

What did you make of this out of interest - I thought it important (then I am not a scientist of course):

'Because gammaretroviruses lack the accessory genes possessed by other retroviruses, such as HIV and SIV, they are ill-equipped to counteract intrinsic host restriction factors like the APOBEC3 proteins.'

I hadn't seen this mentioned before - at least not on the forums - though I confess I may well have missed it, but it does seem to get to the nub of the matter perhaps, no?

 

[RustyJ]

Natasa - you are of course correct. Perhaps I should not have bolded certain parts but that was my decision and rather than post just those sections, I did post a lot more to give greater context.

I do not understand the minutiae of science papers - I tend to rely on scientists to interpret them for me if I feel a need to understand more - and indeed I do refer to scientists when I feel a need for more general interpretation of a paper including the authors themselves (though not in this case I should add).

I certainly don't feel I was 'cherry picking'. I mean that is a fairly extensive couple of posts there and most of it is from the 'Discussion' part of the paper. Meaning simply that - it was a discussion by the authors about their results in the greater context of previous and future studies.

There was an awful lot that is I think relevant but was not bolded so I think your comment is unfair. This paper also refers back to the original paper on Macaques that appeared to raise a number of 'concerns' not least the 'fear' that XMRV 'disappeared' from blood and 'hid' in tissue - most recently Lymph Nodes if I remember correctly.

It also provides greater information about XMRV replication in general I felt. Again though, this thread was about this paper and of course - as even the authors would and have pointed out - it does leave questions unanswered.

But science is a process towards greater understanding and the focus - if you like - is now on trying to understand more about this novel gammaretrovirus.

XMRV has not been found in humans and the next best thing in terms of trying to understand how this retrovirus works is apparently to inject MASSIVE amounts of the virus into primates.

The exact reasons for doing so in this study are laid out above. It will I am sure lead to further research but it will take another paper like (but better than) Lombardi et al. for anyone to look again at XMRV and human infection and especially XMRV and CFS patients.

Nobody has ever said XMRV was not a retrovirus. Nobody. It will continue to be studied and this paper implies that in the absence of confirmed human infection - primates are the next best thing.

What did you make of this out of interest - I thought it important (then I am not a scientist of course):

'Because gammaretroviruses lack the accessory genes possessed by other retroviruses, such as HIV and SIV, they are ill-equipped to counteract intrinsic host restriction factors like the APOBEC3 proteins.'

I hadn't seen this mentioned before - at least not on the forums - though I confess I may well have missed it, but it does seem to get to the nub of the matter perhaps, no?

As stated previously, A3G is at lower levels in some tissue. So irrespective of how effective it is (and it is not), it is not in high levels in all tissue. Please note, the referenced study is more recent than others being referenced by the Coffin macaque study.

We propose that XMRV replicates efficiently in prostate epithelial cells by downregulating A3G expression. Given that XMRV lacks accessory proteins such as HIV-1 Vif that are known to counteract A3G function in human cells, our data suggest a novel mechanism by which retroviruses can counteract the antiviral effects of A3G proteins.

Interestingly, XMRV infects and replicates efficiently in prostate cancer cells of epithelial origin.

We believe the discrepancy in A3G detection is due to selection and sensitivity of A3G antibodies employed in the prior studies.

http://www.virologyj.com/content/8/1/531/abstract


And lest you say that's just one paper (Paprotka et al, no less):

We found that expression of A3G, A3F, or murine A3 in virus-producing cells resulted in their virion incorporation, inhibition of XMRV replication, and G-to-A hypermutation of the viral DNA with all three APOBEC3 proteins. Quantitation of A3G and A3F mRNAs indicated that, compared to the human T-cell lines CEM and H9, prostate cell lines LNCaP and DU145 exhibited 50% lower A3F mRNA levels, whereas A3G expression in 22Rv1, LNCaP, and DU145 cells was nearly undetectable. XMRV proviral genomes in LNCaP and DU145 cells were hypermutated at low frequency with mutation patterns consistent with A3F activity. XMRV proviral genomes were extensively hypermutated upon replication in A3G/A3F-positive T cells (CEM and H9), but not in A3G/A3F-negative cells (CEM-SS). We also observed that XMRV replication was susceptible to the nucleoside reverse transcriptase (RT) inhibitors zidovudine (AZT) and tenofovir and the integrase inhibitor raltegravir. In summary, the establishment of XMRV infection in patients may be dependent on infection of A3G/A3F-deficient cells, and cells expressing low levels of A3G/A3F, such as prostate cancer cells, may be ideal producers of infectious XMRV.

http://www.ncbi.nlm.nih.gov/pubmed/20335265


There are others, of course, but I'll leave some work for you

 

[Firestormm]

Thanks Rusty.

Perhaps then subsequent studies will take this further. The paper I was reading (above) did indeed look at prostate and lymph nodes with a more sensitive device than Omnimoon I believe. Did you see their findings and what would you say about their interpretations?

My interest in XMRV was obviously as a result of the Lombardi paper. Prior to that I didn't have any inkling about XMRV being discovered or the associations with human prostate cells.

Until such time as (and I hope it never happens) XMRV can be 'found' in humans then the study of XMRV is confined to primates, extracted human blood and cell work I suppose.

We never have gotten as far as research linking XMRV or indeed any gammaretrovirus to disease, but had Lombardi been upheld, and the association replicated, that would presumably have been the next step.

So in the meantime so to speak they will continue to study this retrovirus but no research has indicated yet that there is a disease causation association and certainly not in humans - until that happens we are talking about XMRV for what it is - a novel gammaretrovirus.

Science hasn't closed the door on XMRV - far from it. However, the paper from Lombardi and the associations it claimed - along with those papers that also purported to 'find' XMRV in human blood - has not been upheld.

I also don't think Science has closed the door on the possibility of a retrovirus being associated per se with my condition or any other. If they can find something then it will be published - assuming the paper is worth publication.

But it was interesting to read this paper (above) and to continue to follow XMRV as a subject. I am still though rather bemused by the repeated claims that MLVs are somehow associated with my condition and so will continue to follow it all I suppose (but perhaps will less enthusiasm).

Lipkin should prove interesting. Not because of the results so much but to see how they put it all together and what will come after this effort.

Thanks again.

 

[RustyJ]

Thanks Rusty.

Perhaps then subsequent studies will take this further. The paper I was reading (above) did indeed look at prostate and lymph nodes with a more sensitive device than Omnimoon I believe. Did you see their findings and what would you say about their interpretations?

Firestormm, thanks for that. For someone who says they aren't on top of the science and need help getting it explained, you seem to have a good grasp of the technical details of the research, well above my pay grade I'm afraid. I could never have read the above paper in such a short time and made a qualified criticism as you have, especially with me/cfs.

Not sure why you keep hammering away at Lombardi. Maybe ease off there, makes you sound like you are doing PR for the HGRV denialists.

 

[natasa778]

I also don't think Science has closed the door on the possibility of a retrovirus being associated per se with my condition or any other. If they can find something then it will be published - assuming the paper is worth publication.

That to me sounds like you are spinning it. Something may well be turned down for political reasons - one of the MulV researchers has recently commented on that on her blog. They ARE finding something and that something sounds very interesting but are thinking twice about even submitting or talking about it in this climate. Nothing whatsoever to do with Science, everything to do with Politics.

 

[natasa778]

re means by which MuLVs evade the action of APOBEC3, in the absence of Vif

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950561/?tool=pubmed

Firestormm, if you have so many scientist friends to tell you how to interpret papers and what to think, why are you on here discussing with laics? What are you hoping to learn from patients here that you cannot learn from scientists directly?

 

[natasa778]

Interestingly, in a CEM-derived cell line CEM-T4, which expresses high levels of A3G/A3F proteins, the vif-deficient virus replicated as equally well as the wild-type virus, suggesting that these endogenous antiretroviral genes lost anti-HIV activities . It was confirmed that these A3G/A3F genes do not contain any mutation and are functionally normal. Consistently, overexpression of exogenous A3G/A3F in CEM-T4 cells still failed to restore their anti-HIV activities. However, this activity could be restored if CEM-T4 cells were fused to 293T cells to form heterokaryons. These results demonstrate that CEM-T4 cells lack a cellular cofactor, which is critical for A3G/A3F anti-HIV activity.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435275/?tool=pubmed

 

[barbc56]

Not sure why you keep hammering away at Lombardi. Maybe ease off there, makes you sound like you are doing PR for the HGRV denialists.

Maybe I have misinterpreted what you are saying and if I have I apologize, but what's wrong with someone saying that they don't believe HGRVs are connected with me/cfs, especially when someone is backing up their statements with science and asking appropriate questions related to the discussion. Aren't we allowed to have different opinions?

Firestormm, if you have so many scientist friends to tell you how to interpret papers and what to think, why are you on here discussing with laics? What are you hoping to learn from patients here that you cannot learn from scientists directly?

I can only speak for myself but I'm trying to learn as much as I can with my limited expertise and appreciate people, whatever their take, not only citing their work but also explaining how they come up with conclusions.

If there is misinformation, it needs to be countered.

Different opinions are not inherently negative but name calling and put downs are.

I do think on the whole we are seeing more appropriate debate and that's great. I don't want to sound entirely negative here.

 

[barbc56]

re means by which MuLVs evade the action of APOBEC3, in the absence of Vif

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950561/?tool=pubmed


Dang, I keep losing information but I do have a question about the above study.

 

[Mya Symons]

I could be wrong, but aren't these the same people who, after XMRV was discovered, wanted to use it for Gene Therapy? So, are they doing these experiments so they can try to prove it is harmless in order to get the go ahead to use XMRV in gene therapy or is there some other reason? Are they worried that there may be a slight chance that Lipkin could find the virus so they are already moving on to the next step-attempting to prove it does not make people sick? Why even do this?

Doesn't HTLV, for example, sometimes take 20 to 30 years to make a person sick? I guess am not understanding how this short study proves much of anything.

 

[currer]

I object to the dogmatism of some of the negative posters.

Little is known about MLVs as a human pathogen. We need much more research before any assumptions can be made about their susceptibility to APOBEC in HUMAN infection.

Given the importance of this research to not only people with ME but people with some cancers which also could be connected to these viruses, I am shocked at the willingness of some people to jump in with a facile negative and try to close the debate.

There are good reasons for thinking that there could be links between MLVs, lymphoma, (rate doubled in thirty years) breast cancer (up by 50%) prostate cancer (tripled in all age groups).
Health agencies are concerned about this rise in cancer rates, for which no explanation exists.

And autism. A new disease. Unknown before the 1940s.
Boys (not girls) have a hormone surge in the womb and in the first six months of life - if there is a link between androgens and the activation of MLVs via an immune challenge, there could be the reason for the link between boys and autism. (boys have a ten to one chance of getting autism vs. girls)
You do not want to switch on an MLV in the early stages of the growth of the brain as it will be developmentally much more vulnerable.

MLVs and human disease - the implications are very worrying. I doubt the theory will be welcomed but it must be investigated. Quick and easy negative reactions do not do the matter justice.

 

[Firestormm]

Firestormm, thanks for that. For someone who says they aren't on top of the science and need help getting it explained, you seem to have a good grasp of the technical details of the research, well above my pay grade I'm afraid. I could never have read the above paper in such a short time and made a qualified criticism as you have, especially with me/cfs.

Not sure why you keep hammering away at Lombardi. Maybe ease off there, makes you sound like you are doing PR for the HGRV denialists.

You are most welcome. Of course I don't consider myself a 'denialist' though I have been called that often enough. And it does take a lot of effort to read such papers which is why my 'in-tray' is overflowing and I have to pick and choose to some extent and this study - following up on Onlamoon was I felt important. It also provided a (what I considered) useful resume of XMRV to date.

In my own little world I think there are three parts to this if you like:

1. The main one having been established by Lombardi and that related directly to my condition. It was about XMRV being found in the blood of patients to a startlingly high amount. And so as I see it this whole 2 year tale thus far has been about Lombardi and trying to replicate that association.

And then from that we had the whole 'commentary' from scientists and those associated with that study, all the conferences, the interviews, the media-storm, etc. and all the analysis and interpretation and 'spin' of what was said as well as the paper itself and those that resulted from it.

I mean it has been a mammoth undertaking and for a patient especially one hell of a lot to even try to keep on top of and I think too much has been speculated upon by those key players that has led to frustration and hurt among patients even to 'fallings out'. But this was for me the most important part about XMRV/MLVs and now (as in at this moment) that association has not been upheld.

When it comes to the 'Lipkin Study' those that have been quoted as calling it definitive are I believe referring to the associations proposed by Lombardi (and Lo) to my condition. As this is the only fully funded (and pretty much now spent) research looking at XMRV/MLVs and my condition - then I also regard it as being the 'final' word on Lombardi (and Lo) and indeed all those other papers that appeared to support that association.

However, and as I have said, I am very much interested in learning about how this study was put together and what will happen as a result - probably more so that what if anything it 'finds' in relation to XMRV/MLVs to be honest - because I don't think it will find anything significant.

2. XMRV in it's own right as a novel gammaretrovirus. Novel meaning 'new' obviously but also not understood. And so that gets my interest too. But to a lesser extent and unless future research again attempts to link it to my condition - my own interest will wane. I understand that in science the research is only as good as the last and that science marches on and so am perfectly aware that someone could demonstrate that XMRV does indeed play a role in the causation of human disease and who knows? It could one day be linked to my condition but until that happens I don't think I will be all that interested.

3. MLVs in general. I do 'get' people's interest in this broader topic really I do (or maybe I think I do?). However, we are again talking about the subject in isolation of my condition and so for me I can't get into it until and unless it does get linked.

I do trust science and I know it might sound lame to some but there we go. There are some things - especially now - I acknowledge I haven't a hope of understanding or indeed learning about. But what bugs me is spurous links to my condition. So I'll leave it to science I think and when a paper is published whose conclusions appear to link in with ME in a more readily identifiable way - then I will push aside other things and take a closer look.

That to me sounds like you are spinning it. Something may well be turned down for political reasons - one of the MulV researchers has recently commented on that on her blog. They ARE finding something and that something sounds very interesting but are thinking twice about even submitting or talking about it in this climate. Nothing whatsoever to do with Science, everything to do with Politics.

Hi Natasa,

Whatever. If a paper links MLVs to my condition I will take a look. That scientists are experiencing difficulty with funding - well what's new?

re means by which MuLVs evade the action of APOBEC3, in the absence of Vif

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950561/?tool=pubmed

Firestormm, if you have so many scientist friends to tell you how to interpret papers and what to think, why are you on here discussing with laics? What are you hoping to learn from patients here that you cannot learn from scientists directly?

Do you know how many papers are quoted from on forums like this and blogs? How many patients cherry pick and seem to think 'so and so' is majorly important to the study of my condition? If I asked my 'scientist friends' to help me understand all of them - I wouldn't have any friends left.

They help with the complex stuff - you know that gets posted as 'evidence' - or if they themselves have posted a paper and I don't understand a part of it (not always relating to 'CFS') then they will help me also.

In the main though I plod. I am a plodder. I select a paper that seems interesting after a read of the extract and I try to obtain the full version (and yes this does sometimes come from those 'friends').

Then I plod. I have an 'in-tray' full of such papers - that appear 'interesting' but those that are more interesting that others I read and try to understand.

Then I start a thread to see if others think they are interesting - or join an already established thread - and posit opinion in an attempt to understand more.

It is 'interesting'. It helps break the monotony of my existence. It stimulates my addled brain. I hope for a debate on the subject of the thread.

Remember what a debate is?

 

[Firestormm]

The extracts posted by Rusty are being debated on the thread to which that paper relates Natasa where Miller has provided further information in the Journal to which it was published.

As I keep saying, until I am able to read a paper I don't really tend to comment upon it except in general terms. I did find 'his' comments 'interesting' as I said.

My opinion about XMRV's involvement in my condition is not altered by that paper and the one this thread is all about reinforces my opinion.

Prove XMRV is in humans and not a contaminant and then this further research into XMRV that we are discussing will provide a greater understanding.

Here's the thread discussing how APOBEC MIGHT be side-stepped by some part of XMRV and the observations from Miller: http://forums.phoenixrising.me/show...-of-APOBEC3G-by-XMRV-in-Prostate-Cancer-Cells

 

[Undisclosed]

Moderator -- Could we please stop the personal attacks (which have now been removed) and go back to debating the topic at hand.

Kina.

 

[barbc56]

The extracts posted by Rusty are being debated on the thread to which that paper relates Natasa where Miller has provided further information in the Journal to which it was published.

As I keep saying, until I am able to read a paper I don't really tend to comment upon it except in general terms. I did find 'his' comments 'interesting' as I said.

My opinion about XMRV's involvement in my condition is not altered by that paper and the one this thread is all about reinforces my opinion.

Prove XMRV is in humans and not a contaminant and then this further research into XMRV that we are discussing will provide a greater understanding.

Here's the thread discussing how APOBEC MIGHT be side-stepped by some part of XMRV and the observations from Miller: http://forums.phoenixrising.me/show...-of-APOBEC3G-by-XMRV-in-Prostate-Cancer-Cells

Thanks, firestorm. It looks like my question belongs on the other thread.