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Two Unique Events?

Blog entry posted by anciendaze, Jun 25, 2011.

Gerwyn (he who must not be named) has turned up an early paper on virus which appeared when tissue samples were 'passaged' through nude mice. Type C virions include retroviruses; some sizes can hardly be anything else. I've selected some sentences from the abstract which practically jumped off the page at me.

> In another instance type C virus particles were seen replicating in the chondroblastic human cells of a xenografted osteosarcoma. The type C virus produced in the human cells failed to transform NIH/3T3 cells, the C-127 rat cell line, or mink cells. Nucleic acid hybridization studies in which a human endogenous retroviral probe and a xenotropic murine leukemia virus envelope probe were used suggested that the retrovirus present in the human osteosarcoma cells is related to murine leukemia viruses. Intracisternal A-particles (IAP) were also detected in the human osteosarcoma cells. Their presence in the human cells was demonstrated by simultaneous visualization of IAP and human HLA determinants at the cell surface

Several points are worth emphasizing:

1) the particles were definitely associated with human cells;
2) the virus failed to infect offered mouse, rat or mink cells;
3) DNA hybridization showed it resembled X-MLV;
4) human cells showed both IAP and HLA epitopes on their surfaces;
5) the strain of nude mice, NIH/3T3 is the same one in which sequences called pre-XMRV1 and pre-XMRV2 were found.

There is even a relation to prostate cancer, where XMRV was originally discovered. Osteosarcomas are primary cancers of bone, but when prostate cancer metastasizes it frequently spreads to bone. The PC-3 cell line was derived from such tissue.

More germane to the current controversy, this took place at least 9 years prior to the alleged recombination event claimed to create XMRV. Were there two such unique events? How many more should we assume? Is this a more parsimonious assumption than one assuming a common human source?

(A side issue here is that the human cells were producing IAPs, expressed on their surfaces. This says tests for contamination by mouse DNA relying on IAP sequences may also exclude infected human cells, a point I had previously made w.r.t. the Shin/Singh paper.)

If this was, in fact, the origin of XMRV, and we reject the idea that such a highly-specific event could happen twice, we have evidence the resulting virus could escape detection at a later date, (a key point in current debate.) If this early event was not the origin, we must ask where a virus capable of infecting human cells most likely originated in mice carrying human xenografts. My answer would be that it was passed from humans with the disease under study.

What distresses me most here is that deniers (of a human retrovirus) often seem to be intelligent, energetic and knowledgeable, but impervious to perception of circularity in their own reasoning. One aspect has to do with the possibility that the virus in nude mice, where the virus in the 22Rv1 cell line was first detected, actually came from the human xenograft, yet remained undetected until testosterone used to stimulate tumor growth activated latent provirus which had previously escaped detection.

The current definition of XMRV used by deniers says it is identical to the retrovirus contaminating the 22Rv1 cell line derived from human xenografts in the strain of nude mice above. The original XMRV virus was described as 94% homologous to X-MLV (mentioned in the reference above,) and 95% homologous to a HERV soon after discovery. This would leave only a tiny gap for a distinct virus. Defining anything in this gap as a contaminant neatly plugs the hole. This argument was possible the day the original paper in Science was published, without any laboratory work.

The problem with defining the virus as a contaminant is that the hypothesis of a previously undetected human retrovirus associated with prostate cancer would also produce contamination of cell lines derived from human prostate cancer xenografts in mice made prior to assays to detect that virus. All this furor does nothing to distinguish competing hypotheses.

(To escape a flame war, let me say I'm aware the assumption of an undetected retrovirus in humans may also lead to circular reasoning. I am trying hard to find an argument which allows people to come out of debate by a different door than the one through which they entered.)

The recombination-origin hypothesis simply takes the circularity into a larger circle. Let me explain.

There are good reasons to believe the endogenous pre-XMRV sequences are of recent origin, in evolutionary terms. They have only been found in one strain of nude laboratory mice. They have only been seen as two fragments. The retrovirus which inserted them would have left a larger set of overlapping sequences allowing its full genome to be reconstructed if it had been around very long. The nude mice in question have not been around too long, they would not survive in the wild.

The peculiar characteristic of nude mice is a defective immune system. They have no thymus. They do not produce either CD4+ or CD8+ T cells, making them exceptionally vulnerable to viral infection. The purpose is to allow xenografts of human tissue. They are isolated from most sources of infection, except humans. Humans control every aspect of their environment. If you had to select a strain of mice most vulnerable to viral infection from humans this would be it. If they were any more vulnerable, they might be kept in bubbles.

One other point, we don't find any complete copies of the virus inserting the pre-XMRV sequences in the NIH/3T3 strain. Had nude mice carrying the gene shown signs of active viral infection they would have been culled.

The contamination/recombination argument is not falsifiable. In seeking to attack a new finding, deniers have gone outside of science entirely. Every possibility has been neatly covered, even for viruses not yet discovered.

Anyone want to place a bet on never finding a previously undiscovered human retrovirus resembling a mouse virus?
anciendaze

About the Author

As the name suggests, I am old and dazed. The avatar illustrates my rule of thumb: "Hang on! This ride isn't over."
  1. anciendaze
    Had I seen the full text of that paper before I posted I might have used the title "Forty Unique Events?". In addition to the one case that took place in their laboratory, the authors surveyed existing literature for similar events. They found 38. The assumption all along was that the virus had to have come from the mice, because it resembled a virus known in mice, but not in humans. We next need to look for a pattern in the xenografts.

    All were from cancers. By my count, 13 were from leukemia/lymphoma. There was one from an adenocarcinoma of the prostate, which now has special significance. We also find two carcinomas in transitional cells of the bladder, a number of nasopharyngeal carcinomas, an ethmoid carcinoma and another from the lungs. There was an oat-cell carcinoma (now called small-cell carcinoma) likely from the lungs. A few rhabdomyosarcomas and one odd neuroblastoma complete the picture.

    Even if the virus is coming from the mouse, something in these particular tissues is activating it. We also note that the viruses appear well-adapted to infect human cells, not mouse cells. If the viruses are all mouse viruses, these are anomalies.

    The pattern in the above would not have jumped out at me a year ago. Today it suggests we might be dealing with a virus very similar to X-MLV which is found on mucous membranes and in bone marrow. However, no one followed up because they 'knew' this was a contaminant originating in mice.

    The start of this trail goes back before the beginning of the "War on Cancer". This issue is not a minor problem affecting people with a chronic non-lethal illness.
  2. alex3619
    Hi ancientdaze, I have been considering the possibility of the contamination being from humans for some time. Whether it is from the grafts or from lab workers is not really relevant, as either leads to similar issues.

    Then argument that XMRV is highly adapted to humans is very interesting. There is a claim we have a high capacity to destroy them, therefore we can't be infected. If we have adapted so much, it is far more likely that the virus has adapted even more, and bypasses our defences. If you think about what it would need to do to be effective, you get a list of properties. (Please add to this list, or start a contrary list that has properties we should not find.)

    On the presumption that MLVs infect people (still not proven) what could they look like to evade the immune system? First, they would target immune privileged sites - ovaries, testes, brain, eyes. I don't think MLVs target eyes, but the others are likely. Second, they could have low copy number - if the immune system can't see them they can't be attacked. Third, they would disrupt the immune response. This can be through toxins or other effects. Fourth, they could promote other immune issues, decoy targets that make the immune system fight other things. Mimicry and induction of co-pathogens fit this case, with mimicry leading to autoimmune issues. Fourth, the could find a way to remain long term - every retrovirus can do this through DNA integration.

    If XMRV is indeed highly adapted to humans, or other MLVs are, then we have a long history of co-evolution. We would have highly evolved defences against these viruses - defences that would prevent them infecting us most of the time, but not all of the time. It is a property of highly adapted viruses that while they make the host ill, they do not kill or at least not quickly.

    These are some of the reasons I think HGRVs are still our best candidate.

    These lists do not mean we are proven to be infected, nor that it is a MLLV, but they show the possibility. We need more data, and better studies, and therefore more funding. It always comes back to funding.

    Take any disease of similar impact to society as ME or CFS. Find a yearly research budget. Compare that to the entire ME or CFS research budget, ever. I suspect we would still get less.

    Bye
    Alex

    PS There are other viral strategies. HIV is different, and produces large number of infective virus. MLVs appear more stealth.
  3. anciendaze
    I'm still trying to get that paper. It takes me a little longer than others. Even so, I don't expect anything I read to settle the question in my mind, how close is that virus to XMRV? We need samples of the virus or cell line.

    In case anyone remains confused by my prose, let me state my belief that the simple explanation for the result above and the virus in 22Rv1 is a common human source.
  4. anciendaze
    Anciendaze, as I am a member of the "unwashed masses" and obviously need to be "enlightened" -- (some of us do read the other forum), could you please explain how you came to the conclusion about the recombination events. Your irony detector may need recalibration. As for recombination origin, I don't place much credence in that taking place where we just happen to observe it. I am pleased that, finally, we do have someone trying to think about the problem. The authors stated that their results "suggested" that the retrovirus present in the human osteosarcoma cells is related to murine leukemia viruses. Nude mice carry many endogenous proviruses related to XMRV -- were these authors referring to these -- I just don't get the leap you made into describing an earlier unique recombination event from this abstract. I can't find anything but the abstract online so really one can't really know what they found. Nude mice do carry many endogenous proviruses, but only two fragments fit together like pieces of a puzzle to make XMRV. I want to know where those two came from. If they came from a single virus, it would have to be very similar to XMRV. Following that line of reasoning, I would look for reports of such a virus in that strain of mice.

    When such a report turns up, I agree that it does not meet current criteria as proof, at that date this would be unlikely. (Notice, however, that nearly all arguments on this question are about probabilities.) What we do find is a report of a virus that clearly acts like a retrovirus infecting human cells. There are several possible origins, but we must consider its clear preference for human cells.

    If it came from a mouse, this is some kind of fluke. If it came from a human, this is natural. If you deny a possible human origin, a recombination event turning a mouse pathogen or ERV into a human pathogen is one alternative to consider. The question mark in the title indicates how little weight I place on this. I'm asking deniers if they want to try the same argument in this case.

    If they feel the virus obviously originated in mice, we have to wonder where it came from. The non-human contacts of these mice are severely restricted. Intimate connection with human tissue is central to their raison d'etre.
  5. Kina
    Anciendaze, as I am a member of the "unwashed masses" and obviously need to be "enlightened" -- (some of us do read the other forum), could you please explain how you came to the conclusion about the recombination events.

    The authors stated that their results "suggested" that the retrovirus present in the human osteosarcoma cells is related to murine leukemia viruses. Nude mice carry many endogenous proviruses related to XMRV -- were these authors referring to these -- I just don't get the leap you made into describing an earlier unique recombination event from this abstract. I can't find anything but the abstract online so really one can't really know what they found.

    Please enlighten me regarding how you came to your conclusions regarding this abstract and present research.

    Thanks.
  6. Enid
    Difficult for me to follow through anciendaze (non scientist) but much appreciate your thoughts/reasoning in the reading. ME/CFS always was viral/retroviral for me - confirmed by my Neurologist by a process of elimination but could not identify.
  7. Carrigon
    Everyone has a tree, but no one has a forest when it comes to this disease. In other words, there are a thousand theories on the actual cause. And we could spend a thousand years discussing XMRV and a thousand other viruses and other causes at this point.

    I was already half CFIDS/ME in the 80's from aspartame poisoning and Lyme disease. But I caught something in January of 91 that felt like a retrovirus. And I've been saying it for twenty years. I caught something. And it nearly killed me. XMRV? Who knows. Could be. I don't know when we will ever have real answers.