Author Topic: In vivo hypermutation of XMRV DNA... 10/6/2011  (Read 19181 times)

Patricia

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In vivo hypermutation of XMRV DNA... 10/6/2011
« on: October 13, 2011, 03:38:17 AM »
http://www.sciencedirect.com/science/article/pii/S0042682211004375

In vivo hypermutation of xenotropic murine leukemia virus-related virus DNA in peripheral blood mononuclear cells of rhesus macaque by APOBEC3 proteins

[size=-1]A Zhang, H Bogerd, F Villinger, JD Gupta, B Dong… - Virology, 2011[/size]


[size=-1]... Results. XMRV proviral sequences isolated from infected rhesus macaques contain extensive
 G→A mutations typical of A3 activity. ... 962–965, TGGC, TGAC, A3DE, RIl-10: 11/18. RYh-10:
 0/18. Full-size table. View Within Article. XMRV is susceptible to rhA3 isoforms in cultured cells ... [/size]


Received 13 July 2011; revised 26 July 2011; Accepted 17 August 2011. Available online 6 October 2011. AbstractThe gammaretrovirus, xenotropic murine leukemia virus-related virus (XMRV), replicates to high titers in some human cell lines and is able to infect non-human primates. To determine whether APOBEC3 (A3) proteins restrict XMRV infections in a non-human primate model, we sequenced proviral DNA from peripheral blood mononuclear cells of XMRV-infected rhesus macaques. Hypermutation characteristic of A3DE, A3F and A3G activities was observed in the XMRV proviral sequences in vivo. Furthermore, expression of rhesus A3DE, A3F, or A3G in human cells inhibited XMRV infection and caused hypermutation of XMRV DNA. These studies show that some rhesus A3 isoforms are highly effective against XMRV in the blood of a non-human primate model of infection and in cultured human cells.Keywords: XMRV; APOBEC3; Hypermutation; Retrovirus; Host restriction; Innate immunity

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bullybeef

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #1 on: October 13, 2011, 08:24:49 AM »
I find it fascinating that Silverman continues to churn out XMRV papers at will. It is interesting that the Cleveland Clinic doesn't seem to suffer the wrath of government, yet the WPI and Mikovits are hounded.
BB

Tango

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #2 on: October 13, 2011, 08:45:06 AM »
Gammaretroviruses can evade APOBEC. 
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

Billy

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #3 on: October 13, 2011, 12:20:34 PM »
http://www.sciencedirect.com/science/article/pii/S0042682211004375

In vivo hypermutation of xenotropic murine leukemia virus-related virus DNA in peripheral blood mononuclear cells of rhesus macaque by APOBEC3 proteins

[size=-1]A Zhang, H Bogerd, F Villinger, JD Gupta, B Dong… - Virology, 2011[/size]


... Results. XMRV proviral sequences isolated from infected rhesus macaques contain extensive
 G→A mutations typical of A3 activity. ... 962–965, TGGC, TGAC, A3DE, RIl-10: 11/18. RYh-10:
 0/18. Full-size table. View Within Article. XMRV is susceptible to rhA3 isoforms in cultured cells ...


There's another paper that you may be interested in reading that's related to this, dealing with primate APOBEC3s and restriction of gammaretroviruses (and friends).  It's an open journal so no paywall.

http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000181

Title: Evidence for Restriction of Ancient Primate Gammaretroviruses by APOBEC3 but Not TRIM5α Proteins

And http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1963317/ restriction of another gammaretrovirus (from pigs this time) by Human APOBEC3G.

Title: The Restriction of Zoonotic PERV Transmission by Human APOBEC3G

« Last Edit: October 13, 2011, 12:31:03 PM by Billy »

Karin

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #4 on: October 13, 2011, 01:00:00 PM »
I find it fascinating that Silverman continues to churn out XMRV papers at will. It is interesting that the Cleveland Clinic doesn't seem to suffer the wrath of government, yet the WPI and Mikovits are hounded.

As long as they produce litterature showing how XMRV is defeated by the immune system, confirming that XMRV is unlikely to cause disease, they are more than welcome to publish and receive grants.

Tango

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #5 on: October 13, 2011, 01:19:24 PM »
HGRVs don't need reverse transcriptase, they can increase their titre by using T and B cells via clonal expansion.  That evades APOBEC, which has no effect on none dividing cells. 

The gag region of HGRVs also protects against APOBEC, reducing hypermutation.

So variation is limited, except from what the APOBEC or oxidative stress causes. 

MuLV glycogag also protects against APOBEC and APOBEC is inactivated in mitotic cells and MuLVs integrate into B cells to evade APOBEC.

"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

B8b_E

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #6 on: October 13, 2011, 01:33:15 PM »
Silverman is the new McClure.

subtr4ct

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #7 on: October 13, 2011, 01:33:36 PM »
Disclaimer: I am not a medical doctor.  This post is not medical advice.  Consult your physician before taking any action.

JT1024

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #8 on: October 13, 2011, 03:03:44 PM »
IMHO, XMRV is still significant since it can infect humans and obviously, rhesus monkeys.

One of the authors listed (in addition to Silverman) is John Hackett of Abbott Labs. Substantial research will continue - especially since the stakes are higher.

Has anyone really figured out where XMRV came from yet? There have been theories (?? published by Coffin??).

This was published in the Journal of Virology back in June:

The left half of XMRV is present in an endogenous retrovirus of NIH/3T3 Swiss mouse cells
Ramon Mendoza, Andrew E. Vaughan, and A. Dusty Miller
Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
J. Virol. doi:10.1128/JVI.05137-11
« Last Edit: October 13, 2011, 03:09:08 PM by JT1024 »
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Tango

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #9 on: October 13, 2011, 03:10:05 PM »
I think 293T cells

There is a study and I will have to really dig for it, but only in the last few years, that showed xenotropic MLVs cannot infect 3T3 cells.
« Last Edit: October 13, 2011, 03:13:49 PM by V99 »
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

JT1024

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #10 on: October 13, 2011, 03:29:08 PM »
I had just been reading something about that, but not sure where.

Do you use www.scirus.com and www.mednar.com for searches? Those two work really well.
First they Ignore you , then they Laugh at you , then they Attack you , then you WIN!!!

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Tango

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #11 on: October 13, 2011, 04:05:03 PM »
Quote
The NIH 3T3 cells were resistant to xenotropic vector transduction even when treated with tunicamycin (vector titer <1 cfu/ml), a glycosylation inhibitor known to abrogate resistance of CHO cells to MLV infection at the receptor level (35, 36).

http://www.pnas.org/content/96/4/1385.full

This wasn't it, but it is somewhere.
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

Billy

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #12 on: October 14, 2011, 01:41:53 AM »
IMHO, XMRV is still significant since it can infect humans and obviously, rhesus monkeys.

One of the authors listed (in addition to Silverman) is John Hackett of Abbott Labs. Substantial research will continue - especially since the stakes are higher.

Has anyone really figured out where XMRV came from yet? There have been theories (?? published by Coffin??).

This was published in the Journal of Virology back in June:

The left half of XMRV is present in an endogenous retrovirus of NIH/3T3 Swiss mouse cells
Ramon Mendoza, Andrew E. Vaughan, and A. Dusty Miller
Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
J. Virol. doi:10.1128/JVI.05137-11

The short of it is that it appears to be a contamination that began when a prostate tumor was passaged through different mice as a xenograft.  The sequence is basically half of one mouse virus recombined with half of another from a separate mouse virus.  There is a short blog post about it that will probably explain it better here: http://www.virology.ws/2011/05/31/xmrv-is-a-recombinant-virus-from-mice/

Tango

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #13 on: October 14, 2011, 07:31:41 AM »
Oh silly Billy Bob

The short of it is that Coffin used a different PCR assay to scan the early and later xenografts.  The second assay was not measured in the paper.  Is this scientific misfeasance?

Coffin and Miller defined XMRV as VP-62, which is a synthetic clone not found in nature.


Tropism is a measure of host range and nothing more.

This sequence has nothing to do with the human MLV-related gammaretrovirus or viruses detected in the blood of ME.

There are several different xenotropic MRV related gammaretroviruses in the human population.

In short there are a number of different XMRVs.
« Last Edit: October 15, 2011, 01:12:16 AM by V99 »
"I suspect there have been a number of conspiracies that never were described or leaked out. But I suspect none of the magnitude and sweep of Watergate." Woodward

"I would favor any name that does not impose (or give the appearance of imposing) taxonomic preconceptions on the nomenclature." Coffin

anciendaze

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Re: In vivo hypermutation of XMRV DNA... 10/6/2011
« Reply #14 on: October 14, 2011, 12:42:23 PM »
The short of it is that it appears to be a contamination that began when a prostate tumor was passaged through different mice as a xenograft.  The sequence is basically half of one mouse virus recombined with half of another from a separate mouse virus.  There is a short blog post about it that will probably explain it better here: http://www.virology.ws/2011/05/31/xmrv-is-a-recombinant-virus-from-mice/
I like the way you can tell this is a mouse virus because it refuses to infect mouse cells, preferring human cells.  If it infected mouse cells, I am sure that would also increase your confidence.  The way you are certain the second fragment must be present, even when it is not detected, also hints at special insight.  Failure to detect the complete sequence in early passages is given deep significance;  failure to detect the second sequence is unimportant. 

The sequence feature generally taken as essential by deniers is a deletion.  Why not assume the occurrence of a deletion event leads to a detectable sequence with rapid replication?  Do you need examples from the extensive literature on mouse viruses?  Have you ever heard of RNA pseudoknots? 

Phylogenetic analysis should give you some idea of the date of common origin of this sequence and other MuERVs.  Are you certain this was before the creation of a strain of laboratory mice peculiarly susceptible to human viral infections, since they lack T-4 and T-8 cells? 

Finally, by arguing that this kind of recombination event only takes place in laboratories, it might appear you were trying to restrict laboratory research to high-level containment facilities.  This sounds like a strategic blunder which could set back biomedical research for an indefinite period.  If similar recombination events generating human pathogens are randomly distributed outside laboratories you would appear to be fanning the flames of public panic.  Your logic seems to be aimed at disposing of an immediate problem without reasoning further.  Such reasoning is characteristic of a muddle.