V. Lombardi, et al, new poster: HERV in pDC as biomarkers & TLR defects

[serg1942]

Hi @anciendaze:

I think a mouse model would more likely have the gene "knocked down" through RNA interference to prevent expression of proteins, rather than "knocked out" by destroying the gene. I think it would be fairly difficult to breed knock-out mice with defective TLR genes in every cell. These are fairly important genes.

The results from the poster strike me as mostly in vitro, based on cultured cells without a complete animal model. This is one of the advantages of using siRNA.

It depends on what you want to look for. The Yu P study (quoted by Lombardi's poster) used a knocked out mice, of course born without the specific removed genes. They wanted to see what happened to them, and found that they developed acute T cell lymphoblastic leukemia, and also retro-viral viremia together with lack of specific antibodies towards the ERVs expressing them. So presumably both deficient acquired Th1 an Th2 response... But as you point out, this model can only be useful if the suppressed genes are compatible with life. It seems in this case they are in mice.

Yes, this is probably an in vitro essay of human pDCs. Actually this would be the normal way to proceed if you want to study the expression of proteins of a given human cell, and siRNA or inhibitors of the receptors in this case, are two different ways of acting at a very different level, that if the hypothesis is right, should give the same result, as it seems it's been the case.

I don't see how a "knock down mouse model" would fit in this kind of study, as a better model. Do you mean that it would have been better for the Yu P study? I could see the benefits when the genes to suppress are not compatible with life, or at least, with the enough long life span needed... I'd appreciate you corrections here.

Comment: I've been noticing quite a number of diseases where genetic causes have long been sought turning up evidence of specific SNPs in genes related to immune function. This strongly suggests to me that these diseases are precipitated by an immune challenge like an infection which exposes a preexisting defect.

Sure, its a matter of finding the defective pathway involved, then SNPs will explain the individual differences responses, as the genetic factors.

With all the evidence that has emerged of active HERVs and retroelements, I am no longer impressed with studies which assume all inheritance is Mendelian.

I think it is already clear that mendelian inheritance can only be applied for those genetic diseases caused either by only one aberrant gene, or by several, which locus are enough separated. For the rest of conditions, it just doesn't fit, because genes interact with each other...

A great deal goes on between the inheritance of a particular allele and the expression of the corresponding protein. It is quite possible some of us are "knock-down" humans with RNA interference blocking the expression of genes we could use. It is also possible methylation has epigenetically repressed genes we actually possess. It is even possible some genes thought to be ours actually belong to our microbial tenants.

I think you're right, but it seems to me that epigenetics are already taken into account as important as genetics. For instance, the role of methylation in suppressing HIV expression is widely accepted, and therapies are being developed based on this....

Best!
Sergio

 

[WNM]

Wouldn't EBV be capable of exactly that? Eco posted this on another thread wrt B cells

There was one study which looked for several viruses (i.e. EBV, HHV-6/7 and Parvovirus B19) in the GI tract of CFS patients. Only Parvovirus B19 DNA was significantly increased in CFS (40% of patients). These same patients did not have Parvovirus B19 in blood suggesting the gut was a reservoir of infection.

This is only one study of a few that have been performed on GI biopsies in ME/CFS. EBV is certainly associated with ME. It activates the intracellular TLRs to induce an IFN/antiviral immune response. So perhaps disruption of this pathway will increase susceptibility to EBV (and other infections). The study posted by Eco is interesting and may suggest EBV can also disrupt TLR signaling once established?

There are probably many viral and bacterial infections which can disrupt TLR signaling. I haven't looked to see what might fit best; I just mentioned Yersinsia enterocolitica as a rough example I was presently aware of. Really as a whole anything in the gut microbiota might be involved, commensal or otherwise. So far we have only one proper study of the gut microbiota using 16s rRNA sequencing. But this was only a genus-level study and performed no correlations with symptoms or biomarkers; hence it is very preliminary.

 

[natasa778]

With all the evidence that has emerged of active HERVs and retroelements, I am no longer impressed with studies which assume all inheritance is Mendelian. If we pay attention to what the data are actually telling us I think we will disregard most newspaper accounts about "the gene" which causes a disease. Most of human genetics and most diseases do not follow the player-piano model of genetics used by journalists. You can learn a great deal from genetic studies, but not if you persist in forcing them into the Procrustean bed of your preconceptions. ...

There is careful genetic work now being done which meets high standards, but not all the rubbish from earlier times has been cleaned up. If this process does not produce dramatic reversals of previous thinking I will be the most surprised person around.

With regards to 'if' - even some of those who have been receiving continuous fat streams of funding to find "the genes" are now realising that "we need to change our assumptions" and "look elswhere, to places like microbiome". Unfortunately at the moment those who make funding decisions still have both feet stuck in the Jurassic.

A huge infrastructure looking for a mission - minutes 23-28 of the NIH round-table illustrates the above more than any words could .

As you say "the genes" that predispose one to ME and similar might easily turn out to lie in places like HERVs - it has already been suggested that HERV-W polymorphisms could be associated with the risk of multiple sclerosis.

 

[anciendaze]

I've stirred up enough trouble to make it hard to know where to start.

Sergio, I did not read that Yu P paper. The problem with results in that case is that the living knockout mice were likely dying of acute T-cell lymphoblastic leukemia, even before the disease reached a clinical stage, and had multiple other problems. This could overwhelm evidence of smaller effects. The use of mice with such severe life-long problems could confound results, leaving researchers arguing about exactly what caused reported results. Using knockdown mice allows you to confirm that the mice were otherwise healthy prior to knockdown. This gives you a much clearer experiment on the immediate effect of a particular gene. There are way too many things that can go wrong in development.

Epigenetics is a huge subject, and still young. If people had followed up the pioneer work of Barbara McClintock we might have been 20 years ahead of where we are. Unfortunately, response to her work was so completely non-comprehending she simply stopped publishing most of it for 20 years. Most people didn't even see a need for turning genes on and off! At that time the "player piano" model of genome unrolling into phenotype was particularly strong, though not the result of much thinking. McClintock had already encountered the problem when she had to decide if "jumping" genes were actually moving, or if they were already present and being switched on and off like a moving display of lights showing headlines. She correctly decided what we call transposons were actually moving before anyone knew about reverse transcription. Her insights about the need for epigenetic regulation were largely ignored until others realized they needed to deal with epigenetics.

We are still learning how complicated expression of genes can be. This is especially important where editing introns can result in multiple ways of expressing the same gene. RNA interference can also be used to prevent some subsequences from being transcribed for protein assembly, and the line between host and pathogen RNA is decidedly fuzzy. There is a combinatorial explosion of possible resulting proteins when you take this into account, and the immune system makes heavy use of such tricks to produce an unbelievable number of specific responses, even to synthetic antigens we are pretty sure never show up in nature.

Researchers have a natural desire to break new ground rather than redo previous work. They also hate to admit past mistakes. In the toxic environment where funding battles are fought any such admission could be fatal to a research program. The result is an unreal world where everything is perfect, and getting more so, if you will only keep funding the same dedicated people who have brought you earlier perfection.

 

[anciendaze]

I've decided I can offer some slight anecdotal evidence for those assertions I made about the toxic environment in research. I will remain vague on significant points to avoid harming innocent people, even though this took place long ago.

I contributed some prose to a proposal relevant to a subject in which I had significant training. This was accepted verbatim into the final draft. It passed a number of stages of review, but the whole proposal failed on cost. Later the favorable impression created led to another, successful proposal, but my name was not on it.

Years later someone working on an entirely different proposal asked me what I meant by some nonsense I had written for a proposal they were working on. I told them I had done no work at all on the subject they mentioned. They presented me with the text described above. It turned out the successful prose I'd turned out had been cut and pasted repeatedly into other proposals which felt the need for some nice words that sounded good to reviewers. These words had little or no relation to the subjects of those proposals.

What this revealed about the review process was alarming. The nice-sounding words had been used in successful proposals where they were meaningless. What happened as a result? Not much.

One thing which proposal writers must never do is say "you know the reasons we presented to get funding at some time in the past? Those were complete bull****." Likewise, you can never embarrass those allocating funding by pointing out evidence they didn't have a clue about some of the objective criteria on which they were said to be making funding decisions.

Absent solid reasoning about objective criteria, upon what basis would you conclude those decisions were made?

In another case, I was handed a proposal to review which used a bibliography plagiarized from my own unpublished work, typos and all. What happened next came closer to justice than you usually see in academia, though this was tempered by a desire to protect the institution involved. A PhD. candidate learned that the labor-saving device of plagiarism could cost far more work than ever anticipated.

 

[Ecoclimber]

As you say "the genes" that predispose one to ME and similar might easily turn out to lie in places like HERVs - it has already been suggested that HERV-W polymorphisms could be associated with the risk of multiple sclerosis.

Not only Herv-W, but HERV-K18, HERV-H and especially HERV-Fc1.
Human Endogenous Retrovirus HERV-Fc1 Association with Multiple Sclerosis Susceptibility: A Meta-Analysis

The Encode Project:
"There is a great amount of information that is still being discovered. The Encode Prolject funded by the NIH is researching the so called 10% of the 'junk' DNA. "We were surprised that disease-linked genetic variants are not in protein-coding regions," said Mike Pazin, Ph.D., an NHGRI program director working on ENCODE. "We expect to find that many genetic changes causing a disorder are within regulatory regions, or switches, that affect how much protein is produced or when the protein is produced, rather than affecting the structure of the protein itself. The medical condition will occur because the gene is aberrantly turned on or turned off or abnormal amounts of the protein are made. Far from being junk DNA, this regulatory DNA clearly makes important contributions to human health and disease."

For example, many regions of the human genome that do not contain protein-coding genes have been associated with disease. Instead, the disease-linked genetic changes appear to occur in vast tracts of sequence between genes where ENCODE has identified many regulatory sites. Further study will be needed to understand how specific variants in these genomic areas contribute to disease.

I believe there are many subsets to ME/CFS but I also looked at the epidemology of this illness. One would have to discard all of the infectious outbreaks throughout the decades from the Royal Hospital, LA Hospital, Incline Village, Lyndonville, Australia, New zealand etc. not to claim an infectious pathogenic cause or genetic predisposition. The pathogen is quite viral with a 3 day incubation period. Some of the proposals do not meet the standard of this fact. So one would have to discard the general meaning of ME/CFs as it refers to these outbreaks to imply a different causation. To take it one step further, is Wessely right then concerning Royal Hospital as mass hysteria as well as for the other outbreaks?

I know that some people who have a predisposition to genetic mutation for H1N1 develope narcolepsy as it wipe out hyrocretins(HCRT) causing narcolepsy, shift in circadian rythyms, temperature homeostatis etc. So I beleive that a possible predisposition may have caused over/under sitmulation of immune dysfunction within the ANS/CNS allowing other pathogens to take advantage of that dysfunction such as in EBV steal capabilities on TLR or HERV.

A fews back science thought gut flora was the caused of MS. http://www.sci-news.com/medicine/article01138-probiotic-microflora-brain.html.
Natural intestinal flora involved in the emergence of multiple sclerosis, study finds

However it still does not explain fully the pathogenic cause of ME/CFS afte an acute viral infection. There is still much to be learned from these new discoveries.

 

[WNM]

A fews back science thought gut flora was the caused of MS. http://www.sci-news.com/medicine/article01138-probiotic-microflora-brain.html.
Natural intestinal flora involved in the emergence of multiple sclerosis, study finds

However it still does not explain fully the pathogenic cause of ME/CFS afte an acute viral infection. There is still much to be learned from these new discoveries.

I think the gut microbiota can be seen as one potentially important environmental factor which increases susceptibility to immunological illness. The gut microbiota interacts directly with potential pathogens and indirectly by regulating the development and phenotype of immune cells in the GALT, and then systemically (for more on this see). Hence an altered microbiota could bias your immune response in different directions making you more susceptible to certain infections and consequent chronic immune dysfunction. Not to mention the immune response accompanying gut infections can disrupt the microbiota.

As a simple example, in ME/CFS there could be a lack of microbiota stimulation of basal NK cell/Th1 activity; whereas in MS a microbiota which favours Th17 over Treg. In either case an acute infection could then light the bonfire. The potential importance of gut microbiota is emphasised by very early reports that Bacteriotherapy, a relative of faecal microbiota transplant (FMT), might cure ME/CFS (in patients with comorbid IBS), and FMT can improve neurological conditions like Parkinson's and MS. This research has all been published by Prof Borody, a pioneer in the field. His team discovered H. pylori as the main cause of gastric ulcers, for which some members went on to win the Nobel prize. Read some of Borody's recent papers in Nature and other journals.

 

[anciendaze]

Please note that the listed HERVs in that last post by Ecoclimber are all presumed derived from gamma retroviruses. HERV-Fc1 is particularly interesting because it is full length, and only disabled by small defects in the pol gene for reverse transcriptase. (One defect is a misplaced stop codon, the other a frame shift. A "patch" for these errors could be a short sequence. This looks like an easy HERV to resurrect.) There is nothing to stop the env gene from producing proteins with immunosuppressive behavior if it is transcribed. Some time ago I even wrote a blog post about evidence that this HERV was transmitted between dogs and humans recently, in evolutionary terms.

Added: When I read that HERV-Fc1 had a defective pol gene, I immediately asked if other HERVs derived from gamma retroviruses had defects in the corresponding genes. Not all do. In particular HERV-W is known to be active during pregnancy, and reverse transcription can be detected. So, we have HERV-Fc1, complete, but with a defective pol gene, and HERV-W with a functional pol gene. We also know that HERV-Fc1 is on the X-chromosome, and MS is twice as common in women, who have two X-chromosomes. I think there is a real possibility HERV-W can function as a helper virus for HERV-Fc1. The odds for recombination do not seem terribly long, if both HERVs are transcribed at the same time.

I have to say I'm in debates elsewhere over the significance of Tregs, Th17 and IL17. These are extremely general indicators of immune function. In acute infectious disease Tregs decrease and Th17 and IL17 increase. If this does not eliminate the pathogen, and the disease becomes chronic, immune tolerance develops as Tregs increase and Th17 and IL17 decrease. Unfortunately, this doesn't give us much clue about the nature of the pathogen. You can find the same sequence of events in diseases caused by parasites, bacteria or viruses, or even in cancers not known to have an infectious cause. I would say this scenario involves either pathogens or host cells with pathological behavior.

The problem with this in testing for a disease is that all the examples I've been able to find are about known pathogens or pathological host cells. If nobody knows the cause, or believes there is one, I can't find a single example where this changed opinions.

The problem in treatment, absent a known pathogen, is that you don't know if the pathological behavior is in the immune cells or other host cells. Suppressing Tregs, for example, might result in either a return to acute infectious disease, which did not resolve earlier, or to an autoimmune disease. We need to find the culprit.

 

[anciendaze]

Speculation: The argument above that recombination between HERV-Fc1 and HERV-W is likely when both are transcribed together leads to the possibility of disease states resulting from this after pregnancy. I don't know that MS is the direct result, but I suspect that postpartum depression is. This condition is so common you don't even have to explain what you mean if you use the term in conversation with women who have had children. It would resolve when the recombinant virus was forced into latency. (Not all cases of postpartum depression do resolve.) If a later immune challenge brought the recombinant virus out of latency that would be consistent with what is known about MS. You can find many papers on postpartum relapse in MS.

HERV-W is active in the formation of a placenta, so actually having a child is not necessary for the recombination I am postulating. It may not even be necessary to test positive for pregnancy. A substantial fraction of pregnancies end in spontaneous abortions, often without official recognition of pregnancy.

 

[serg1942]

Hey guys, I have opened another thread to comment on the new drug being tested for MS:

http://m.neurology.org/content/82/10_Supplement/P2.217.short

I would really appreciate your insights on the subject!:

http://forums.phoenixrising.me/inde...treatment-for-cfs-gnbac1-aganisnt-msrv.29717/


Thanks!
Sergio

 

[Daffodil]

couple of interesting papers in relation to TLR's:

http://www.ncbi.nlm.nih.gov/pubmed/18031246

http://www.ncbi.nlm.nih.gov/pubmed/17979852

 

[Leachim]

Thank you all for a very interesting discussion! I've been wondering what Lombardi and De Meirleir are up to after the study last year, will be interesting to read the article!De Meirleir has started testing Yersinia more, as somebody noted in the thread, since a lot of the patients seem to have had the infection, and some still have an active infection. I had positive IgG but negative IgA (interpreted as past infection, but I'm partially recovered so might have killed it off during treatment). I know a couple of other patients with active infection.

 

[Daffodil]

I really don't understand....so is HERV driving this disease? is the HERV messing up the TLR 7 and 9 functioning?

does the theory regarding EBV-infected autoreactive B cells hold any water? if this theory was right, would dr. Lombardi have found EBV sequences when he did the sequencing of tissue?

someone please explain as I am too foggy to comprehend anything.

this is a quote from a paper on autoimmunity and iinfection:

http://www.jleukbio.org/content/87/3/385.full.pdf

-------------

"IFN-α is largely produced by immature DCs, now known as pDCs, which are stimulated by viruses to produce IFN-α, and this production up-regulates expression of TLR7 by B cells, promotes cell death, increasing the release of certain RNA and DNA autoantigens, and primes pDCs to respond more effectively to immunocomplexes [34] . Recent studies suggested that hypomethylated plasma DNA might be influential in the pathogenesis of SLE. Bacterial and viral DNA, which are hypomethylated, can induce various immune changes that are similar to those observed in SLE, including activation of TLR9 signaling, leading to the overexpression of type I IFN genes, polyclonal B cell activation, and production of autoantibodies such as anti-DNA antibodies, production of IL-6, and resistance to apoptosis, which potentially allows the survival of autoreactive cells [35] . Indeed, induction and/or aggravation of SLE are well known to occur after bacterial or viral infection."

---------------

now they don't even mention HERV here. is our disease still being perpetuated by a virus or bacteria? is the HERV just another mechanism by which problems are arising...but is the main culprit still some virus or bacteria??

thanks a lot

 

[Daffodil]

I want to know what everyone out there thinks about the contagious-seeming aspect of this disease. Why does it appear in such clear-cut clusters at times? Why do some families have every member sick?

What can make a hundred people who happen to live in the same area, so vulnerable to autoimmune disease?

I do not feel that environmental toxins explanation fits.

If it is infection perpetuating it, why didn't Lipkin find it? Something just isn't jiving

 

[cigana]

I want to know what everyone out there thinks about the contagious-seeming aspect of this disease. Why does it appear in such clear-cut clusters at times? Why do some families have every member sick?

What can make a hundred people who happen to live in the same area, so vulnerable to autoimmune disease?

I do not feel that environmental toxins explanation fits.

If it is infection perpetuating it, why didn't Lipkin find it? Something just isn't jiving

I think mold or environmental toxins do fit, certainly as triggers and perpetuators. But that doesn't mean they are the only triggers, explaining why it doesn't occur exclusively in outbreaks