Review: 'Through the Shadowlands’ describes Julie Rehmeyer's ME/CFS Odyssey
I should note at the outset that this review is based on an audio version of the galleys and the epilogue from the finished work. Julie Rehmeyer sent me the final version as a PDF, but for some reason my text to voice software (Kurzweil) had issues with it. I understand that it is...
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Human Endogenous Retrovirus K and W Activity in other Diseases.

Discussion in 'Other Health News and Research' started by Ecoclimber, Oct 5, 2014.

  1. Ecoclimber

    Ecoclimber Senior Member

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    Human Endogenous Retrovirus W Activity in Cartilage of Osteoarthritis Patients
    Signy Bendiksen, 1 Inigo Martinez-Zubiavrra, 2 Conny Tümmler, 3 Gunnar Knutsen, 4 Jan Elvenes, 4 Elisabeth Olsen, 3 Randi Olsen, 5 and Ugo Moens 6 ,*

    Abstract
    The etiology of viruses in osteoarthritis remains controversial because the prevalence of viral nucleic acid sequences in peripheral blood or synovial fluid from osteoarthritis patients and that in healthy control subjects are similar.

    Until now the presence of virus has not been analyzed in cartilage. We screened cartilage and chondrocytes from advanced and non-/early osteoarthritis patients for parvovirus B19, herpes simplex virus-1, Epstein Barr virus, cytomegalovirus, human herpes virus-6, hepatitis C virus, and human endogenous retroviruses transcripts.

    Endogenous retroviruses transcripts, but none of the other viruses, were detected in 15 out the 17 patients. Sequencing identified the virus as HERV-WE1 and E2. HERV-W activity was confirmed by high expression levels of syncytin, dsRNA, virus budding, and the presence of virus-like particles in all advanced osteoarthritis cartilages examined. Low levels of HERV-WE1, but not E2 envelope RNA, were observed in 3 out of 8 non-/early osteoarthritis patients, while only 3 out of 7 chondrocytes cultures displayed low levels of syncytin, and just one was positive for virus-like particles.

    This study demonstrates for the first time activation of HERV-W in cartilage of osteoarthritis patients; however, a causative role for HERV-W in development or deterioration of the disease remains to be proven.
    5. Conclusions

    We have shown higher prevalence of ERVWE1 and ERVWE2 activity in chondrocytes and cartilage of OA patients compared to non-/early OA patients. However, we cannot conclude whether these viruses are innocent bystanders that are activated by pathological processes occurring during the development of OA or whether they are involved in the onset or the progression/deterioration of the disease. The high prevalence of activated ERVWEs, especially ERVWE2, may be an indicator of OA, making the detection of ERVWE transcripts a putative diagnostic marker.


    J Virol. 2014 Oct 1;88(19):11108-20. doi: 10.1128/JVI.01623-14. Epub 2014 Jul 23.
    HIV-1 Infection Leads to Increased Transcription of Human Endogenous Retrovirus HERV-K (HML-2) Proviruses In Vivo but Not to Increased Virion Production.
    Bhardwaj N1, Maldarelli F2, Mellors J3, Coffin JM4.
    Author information
    Abstract

    Recent studies suggest that human endogenous retrovirus group K (HERV-K) provirus expression plays a role in the pathogenesis of HIV-1 infection. In particular, RNA from the HML-2 subgroup of HERV-K proviruses has been reported to be highly expressed at the cellular level and detectable in the plasma of HIV-1-infected patients, suggestive of virion production and, perhaps, replication.

    In this study, we developed an HML-2-specific quantitative-PCR assay that detects 51 of the 89 known HML-2 proviruses in the human genome. Plasma and peripheral blood mononuclear cells (PBMCs) from HIV-negative controls and HIV-1-infected patients were collected for analysis of HML-2 RNA expression. Contrary to previous reports, we did not detect high levels of HML-2 RNA in the plasma of HIV-1-infected patients, but we did observe a significant increase of HML-2 RNA in total PBMCs compared to HIV-negative controls.

    The level of HML-2 expression in PBMCs does not appear to be related to patient use of antiretrovirals or to HIV-1 plasma RNA, cellular RNA, or cellular DNA levels. To investigate the source of HML-2 RNA expression, patient PBMCs were sorted into CD3(+) CD4(+), CD3(+) CD8(+), CD3(-) CD14(+), and CD3(-) CD20(+) cell subsets and then analyzed for HML-2 RNA levels. No single cell subset was enriched for HML-2 RNA expression in HIV-1-infected patients, but there appears to be substantial variability in the level of HML-2 expression depending on the cell type.

    IMPORTANCE:
    Here, we report that human endogenous retrovirus group K (HERV-K) (HML-2) proviruses are expressed at significantly higher levels in peripheral blood mononuclear cells (PBMCs) from patients with HIV-1 infection than in those from uninfected individuals. However, contrary to previous reports, this expression did not lead to detectable virions in the plasma of these patients. In addition, we found that HML-2 proviruses were expressed in multiple blood cell types from HIV-1-infected individuals, and the magnitude of HML-2 expression was not related to HIV-1 disease markers in this patient cohort. These findings may have implications for HML-2-based therapies targeting HIV-1 infection.


    J Gen Virol. 2014 Sep 12. pii: vir.0.070631-0. doi: 10.1099/vir.0.070631-0. [Epub ahead of print]
    Recent developments linking retroviruses to human breast cancer: infectious agent, enemy within or both?
    Salmons B1, Lawson JS2, Gunzburg WH3.
    Author information
    Abstract

    Evidence is accumulating that one or more beta-retrovirus is associated with human breast cancer. Retroviruses can exist as an infectious (exogenous) virus or as a part of the genetic information of cells due to germline integration (endogenous). An exogenous virus with a genome that is highly homologous to mouse mammary tumor virus (MMTV) is gaining acceptance as possibly being associated with human breast cancer and recently furnished evidence is discussed in this article, as is the evidence for involvement of an endogenous human beta-retrovirus, HERV-K. Modes of interaction are also reviewed and linkage to APOBEC3 suggested.

    Copyright © 2014, the Society for General Microbiology.

    Eco
    ERV activation aboard but why? Over active immune system? Is it causing a wide-spread disregulation and expression of ERV RNA/DNA/proteins?
     
    Last edited: Oct 5, 2014
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  2. NK17

    NK17 Senior Member

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    Thanks @Ecoclimber, always extremely interesting what you post and upload here on PR.
    Just by the title of the new thread I can guess that it's you.
    Your line/s of research are very sharp, too bad most of this studies will not be replicated, so we are always left with the big ? of wether HERVs are just innocent bystanders or active players in many chronic diseases.
    IMHO the future of research has to seriously take into account HERVs and their role in the pathogenesis of many so called autoimmune diseases, ME included.
    Hervé Perron research on MS and HERVs and Andrew Mason on PBC are two examples to follow.
     
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  3. anciendaze

    anciendaze Senior Member

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    We have had a number of indications that HERVs are far more active than often supposed. What they generally do not do is form replication-competent virions which conform to requirements of the social construct of infectious diseases specialization. You can easily estimate replication rates which patients with chronic diseases would be able to survive, and these will all be too low to be detected in laboratory experiments possible in a short time. (This does not rule out an infectious cause, and the disease called "shingles" is a prime example of such a long-term infectious disease which leaves episomes in major ganglia for many years until *something* causes the virus to break free from latency. If shingles did not produce prominent clinical signs, and show up on laboratory tests for VZV, I'm sure the pain would be considered psychological.)

    We also hear repeatedly that all HERVs are seriously defective, despite having some, like HERV Fc1, in which known defects are quite small. The next question should be "what is the chance that a helper virus can act in place of a defective gene?" This is well known in laboratory animals, and one beta retrovirus which causes mammary tumors in mice, MMTV, has at least two defects which slow replication. (If this were not so, rapid replication would kill the host before the virus was passed on to a new generation.) This is both endogenous and exogenous, and nobody has found a clear line of demarcation between the two forms. It really looks like common exogenous forms can serve as helper viruses for ERVs in this example.

    If all the genes are not in a single unique package, and the host has large numbers of similar sequences, how do you tell if the host is infected with a slow infection causing chronic disease? You don't. We can't even say that common laboratory animals are free from replication-competent retroviruses which are being held latent until experimental changes cause them to become active. A detected infection might have come from the outside, or it might have come from ERVs and infected host cells where virus was held latent. When researchers make definitive statements on this subject political considerations likely play a role.

    As an example of just how confusing the problem is, we know that HERV-W's pol gene is active under a variety of circumstances, including pregnancy. It happens that both known defects in HERV-Fc1 are in the pol gene. Can a pol gene for one gamma retrovirus serve as a helper for another gamma retrovirus? Aren't the resulting proteins highly sequence-specific? Sometimes yes, sometimes no.

    Here's a paper on a notorious gamma retrovirus known to infect human cells in vitro which concludes the integrase it produces is not very sequence-specific.! We should have long been expecting to find similar lack of the sequence specificity which makes life so much simpler for researchers. In addition to viral sequences from retroviruses and DNA viruses found in considerable numbers throughout the human genome, there are also some strange viral sequences which do not correspond to either, but do resemble the results of reverse transcription of RNA viruses (like influenza or polio) which are not retroviruses. Even in the case of DNA viruses, where the answer would seem to be simple, we have questions about how complete DNA sequences for HHV6 turn up in the telomeres at the end of chromosomes of about 1% of humans.

    There were earlier proclamations that retroviruses do not integrate their genomes in the repetitive sequences of telomeres and centromeres. This hypothesis is in bad shape after the discovery of over 100 copies on HERV K111 in centromeres, where nobody had looked.

    I'd say that interaction between exogenous retroviruses, HERVs and herpes-group viruses is extremely plausible.
     
  4. Marco

    Marco Grrrrrrr!

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    Near Cognac, France
    @Jonathan Edwards

    I know it"s not your field as such but any thoughts?
     
  5. Jonathan Edwards

    Jonathan Edwards Senior Member

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    A bit beyond me I fear.
     
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  6. anciendaze

    anciendaze Senior Member

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    More on interactions between herpes-group viruses and retroviruses.

    I don't have to engage in wild speculation to talk about the entire genome of a gamma retrovirus being inserted into the genome of a herpes virus. This has already happened, though not in humans. Avian reticuloendotheliosis virus (REV) was spread to many fowl, both domesticated and wild, through such an unlikely event. The herpes virus was Marek's Disease Virus (MDV) which has significant similarities to VZV, which causes chickenpox and shingles in humans. Please note that shingles results from a very long-lasting infection of the nervous system. In particular, we know the virus remains in dorsal root ganglia, which have also been suggested as locations of problems in ME/CFS. Damage to afferent nerves like these is less likely to produce clear clinical signs, even though the patient perceives quite a bit of evidence of damage which the doctor does not see.

    Now, as an ordinary rule of thumb, you do not expect viruses to jump between animals in such different phylogenetic classes. The general idea is that these rare events may happen on evolutionary time scales, but are unlikely to take place on human timescales. The exceptions are exceptionally important in epidemiology, as various epidemics of influenza illustrate. (The H1N1 epidemic misleadingly called the "Spanish flu" may have killed as many as 100 million people. We simply do not have records from many affected regions. We don't even have reliable figures for actual populations prior to the epidemic, for example, in the Congo. If you read "King Leopold's Ghost" you will see why. There were other major causes of mortality it did not serve colonial interests to discuss. Added: that book was written before the recent news that the most important strain of HIV-1 originated in Kinshasa around 1920, when it was called Leopoldville.)

    The problem of REV was further complicated by a very unlikely jump from echidna or rare mongoose hosts to the Borneo fire-backed pheasant, plus transmission via a parasite, plasmodium lophurae, to other fowl. While there seems no doubt that plasmodium lophurae is a real wild-type parasite (similar to plasmodium falciparum, a cause of malaria,) it has never been independently isolated a second time. That part of the science is non-reproducible.

    While examples of retroviral insertions have been found in vaccines for fowl, it has been hard to find complete retroviral genomes there. These are more easily found in wild-type infections of fowl which have never been vaccinated.

    REV also turned up inside fowlpox genomes. This considerably complicated the problem of detection since virions produced by pox viruses or herpes viruses are morphologically quite different from gamma retrovirus virions. Add to this the fact that many species with ERVs derived from gamma retroviruses do produce virions of the characteristic type, which are either not replication-competent or extremely hard to culture, and you have an explanation for how researchers could ignore evidence of actual virions seen in electron micrographs.

    When you go looking for possible human gamma retroviruses you can't depend on evidence from electron micrographs or similar DNA sequences. We already know these are present in humans without identified diseases. If you are using criteria developed to deal with acute infectious diseases you can't find the cause of a chronic infectious disease which clearly violates Koch's postulates. What can you depend on? (Note: an acceptable answer is not "officially-approved expert opinion". Entire books have been devoted to situations where this was tragically wrong.)

    While the bizarre sequence of events behind the spread of REV in fowl is unlikely to be repeated, it is anything but reassuring w.r.t. human infectious diseases. If there is one species which can be found everywhere on Earth it is homo sapiens. This species also travels rapidly between very different biogeographic regions. Many members of this species are currently subject to infections by parasites resembling plasmodium lophurae which can carry infected blood from one host species to another.

    Recent events have shown just how hard it is to deal with even the most virulent acute infectious diseases. Work on chronic infectious diseases is still in its infancy.
     
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  7. anciendaze

    anciendaze Senior Member

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    An afterthought: I must make clear that I am not refighting the war over XMRV. I accepted years ago the idea that there had been a recombination event. The paper I linked above is one of several indicating unusual properties of the virus isolated in laboratories. I have long been interested in the origin of various components of that genome.

    The immunosuppressive domain in the envelope was the first feature which interested me. This shows evidence of functioning in human hosts, via experiments on transgenic mice with approximately human immune systems. I would really like to know how such domains arise. I do know they can be disabled quite easily by random mutations.

    The integrase now reveals still more interesting properties suitable for a kind of retroviral toolbox for creating novel pathogens. The question of how common such elements are, and how improbable their appearance in a recombinant retrovirus may be remains open. The ERVs chosen as likely precursors for XMRV are so thoroughly defective as to require a replication-competent retrovirus to start the process of recombination. No such virus was ever identified. Were the laboratory animals infected with a hidden retrovirus? Did it come from the tumor samples? To this day nobody knows.

    This highlights valid questions pertaining to the state of the art across the entire field. The apparently simple question about having infected but healthy laboratory animals remains unanswered and important for future research. You can show the presence of gamma or beta retroviral sequences, and image characteristic virions, or even show the presence of antibodies to retroviral proteins, which appear in a number of disease states, without making a case for retroviral etiology. All the definitive examples only appear in connection with acute infectious diseases. There is, at present, no way at all to establish retroviral etiology of any chronic disease state.

    This goes hand-in-hand with another area of confusion: when do ERVs become active, and when can they be ignored? After reading a number of papers on the subject, I will give you the condensed version: any damn thing at all might activate an ERV under some conditions. This goes along with the question of hidden (occult) infections by exogenous retroviruses. When do these become active in response to changing conditions? The answer, once again, is that any damn thing at all might perturb immune function so that an infection which has been held latent in a number of cells too small to be detected becomes active. We now know that even HIV-1 can remain hidden and undetectable for years after it appeared eradicated. The question is not purely academic.

    Recombination was taken as a convenient point to stop looking for explanations, except in the case of HIV. There has been a general misperception that recombination events are rare, (except of course when some particular researcher wants to argue otherwise.) If we consider an exogenous retrovirus invading a cell and inserting a single provirus, in a genome which has perhaps 100 copies of similar ERVs, it ought to be clear that "breeding true" will be a low-probability outcome, and recombination more likely. Since transcription is typically controlled by LTR sequences, and these are the last parts of ERVs to disappear, it seems obvious that the nucleus will be flooded with copies of ERVs under those conditions which trigger transcription of the inserted provirus. Most recombinants will be defective, but it is not wise to assume this will always be the case. When it is not, the result will be a novel sequence not seen in the exogenous retrovirus which initiated the process.
     

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