Humoral Immunity Profiling of Subjects with Myalgic Encephalomyelitis

[roller]

burn meds seem to help with HERV-W.
this was lower in the burn-group.

HERV-W is the one which has some similarity to XMRV and also gp120 HIV, which is mentioned in the meirleir study.

from wiki about HERV-W:
"Syncytin-1 shares many structural elements with class I retroviral glycoproteins (such as, Murine Leukemia Virus gp, Ebolavirus gp, and HIVgp120, gp41). It is composed of a surface subunit (SU) and transmembrane subunit (TM), separated by a furin cleavage site"

this is very interesting and should make to wonder if there is a link with protozoan infections.

 

[Valentijn]

could someone please explain what they say about Burkholderia bacteria?

When this sequence is considered in isolation, we have observed it within several other proteins, in particular, the bacteria genus Burkholderia and also in the human protein calcium voltage-gated channel protein CACNA2D3 (Table 2).

A sequence in the peptides which they found in the ME patients occurs in that type of bacteria. But that sequence also occurs in the protein created by at least one gene, CACNA2D3.

It's a pretty short peptide (string of amino acids), which might occur in other pathogens or normal human proteins. But they mention using BLAST to search for the sequences in known pathogens and human DNA, so presumably they've listed all of the known potential sources. I can't currently read the paper closely, however, so I can't be certain that they're claiming that.

 

[justy]

Is it possible for anyone to understand and explain this paper in very simple terms? it is totally beyond me, but I would really like to try and understand some of it as KDM is my Dr.

 

[Rrrr]

"XMRV" was not so long ago. And it was never resolved. Drs. Judy Mikovits and Frank Ruscetti found retroviral material in ME patients that was not Silverman's "XMRV" contamination. Soon after, Drs. Lo and Alter confirmed it. Then it was all put to a halt. (By whom? Why?) It still needs to be researched. The way Dr. Mikovits was treated -- discredited and smeared -- was atrocious and tragic both to her and to our ME community, delaying advancement on this important retroviral research yet another decade.

 

[lansbergen]

Drs. Judy Mikovits and Frank Ruscetti found retroviral material in ME patients that was not Silverman's "XMRV" contamination. Soon after, Drs. Lo and Alter confirmed it.

Thank you.

 

[Valentijn]

Is it possible for anyone to understand and explain this paper in very simple terms? it is totally beyond me, but I would really like to try and understand some of it as KDM is my Dr.

Briefly, they went looking for peptides in ME patients and controls. Peptides are strings of amino acids, often fragments which have broken down from something else.

The basic 20 amino acids are also produced by genes, both in humans and everything else, including bacteria and viruses. In the case of human genes, typically hundreds of these amino acids will be strung together in different orders and with different structures to form the various proteins in our bodies.

So when scanning someone for peptides, it would be expected to consist of fragments of broken down human proteins. But it doesn't really determine if the peptide fragments are coming from our own bodies or from pathogens which we have broken down.

BLASTing the peptides just means that the fragments are compared in databases of known proteins from all sources. So they are able to list some human proteins containing that specific fragment, and some pathogens which contain it as well. To identify the source with certainty, the peptide would have to be fairly long - I'm not sure how long, but the longer it is, the less likely that the sequence occurs in multiple pathogens or even multiple human proteins.

So they can't really determine the source of these peptides, which also means there's no way to know if there is an ongoing pathogen producing those proteins which get fragmented to form the peptides discovered. Or if a normal human protein is getting attacked and broken down into the peptides, which might happen in an autoimmune disorder (speculating here, I have no idea if this happens).

That's why they're saying it is potentially diagnostic, rather than revealing anything about the pathogenesis. It's an abnormality present in the ME patients, but there's no clue yet about the cause of that abnormality.

 

[Helen]

"XMRV" was not so long ago. And it was never resolved. Drs. Judy Mikovits and Frank Ruscetti found retroviral material in ME patients that was not Silverman's "XMRV" contamination. Soon after, Drs. Lo and Alter confirmed it. Then it was all put to a halt. (By whom? Why?)

The study below halted further discussions about XMRV and a correlation to ME/CFS

PLoS One. 2011;6(10):e24602. doi: 10.1371/journal.pone.0024602. Epub 2011 Oct 12.
Murine gammaretrovirus group G3 was not found in Swedish patients with myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia.
Elfaitouri A1, Shao X, Mattsson Ulfstedt J, Muradrasoli S, Bölin Wiener A, Golbob S, Ohrmalm C, Matousek M, Zachrisson O, Gottfries CG, Blomberg J.

 

[anciendaze]

Here's a link to an explanation of the recent discovery that spliced epitopes are surprisingly common. (The paper itself is behind a paywall.) These epitopes are the cell-surface expression of proteins found inside a cell which may indicate pathology to cytotoxic immune cells. Please note that there is a continuum from peptides to polypeptides to proteins. Nothing limits these sequences to expression on cell surfaces, cells may certainly release them. They may or may not count as antibodies. Some may even be peptide transcription factors regulating gene expression.

Peptide signalling between immune cells has been found before, and may either increase or decrease immune activity. Two examples are vasoactive intestinal peptide (VIP) and PEPITEM.

In a very general sense, ME/CFS patients show increased activity against common bacteria in gut flora, and decreased activity against common viruses which are generally considered harmless. Expression of a viral immunosuppression domain could account for this, even without an actively replicating retrovirus.

 

[roller]

In a very general sense, ME/CFS patients show increased activity against common bacteria in gut flora, and decreased activity against common viruses which are generally considered harmless.

A sequence in the peptides which they found in the ME patients occurs in that type of bacteria. But that sequence also occurs in the protein created by at least one gene, CACNA2D3.

thanks!

in table 4 of the report (its also on page 1 of this thread) they list those viruses/bacteria they may have found some activity against in ME ppl.

but there is no mention of anything burkholderia.

where/when/how did they find that or a relation to this?

 

[Jonathan Edwards]

Briefly, they went looking for peptides in ME patients and controls. Peptides are strings of amino acids, often fragments which have broken down from something else.

The basic 20 amino acids are also produced by genes, both in humans and everything else, including bacteria and viruses. In the case of human genes, typically hundreds of these amino acids will be strung together in different orders and with different structures to form the various proteins in our bodies.

So when scanning someone for peptides, it would be expected to consist of fragments of broken down human proteins. But it doesn't really determine if the peptide fragments are coming from our own bodies or from pathogens which we have broken down.

BLASTing the peptides just means that the fragments are compared in databases of known proteins from all sources. So they are able to list some human proteins containing that specific fragment, and some pathogens which contain it as well. To identify the source with certainty, the peptide would have to be fairly long - I'm not sure how long, but the longer it is, the less likely that the sequence occurs in multiple pathogens or even multiple human proteins.

So they can't really determine the source of these peptides, which also means there's no way to know if there is an ongoing pathogen producing those proteins which get fragmented to form the peptides discovered. Or if a normal human protein is getting attacked and broken down into the peptides, which might happen in an autoimmune disorder (speculating here, I have no idea if this happens).

That's why they're saying it is potentially diagnostic, rather than revealing anything about the pathogenesis. It's an abnormality present in the ME patients, but there's no clue yet about the cause of that abnormality.

I was almost as confused as Justy with this paper but as far as I can see they were not looking for peptides but antibodies to peptides. They synthesised a vast array of peptides and looked to see if patients had antibodies to these. That would be a bit like taking a patient serum and looking for autoantibodies by applying it to a set of plasma or tissue proteins run out of a Western blot. Or a bit like looking for antibodies to all the possible viruses and bacteria the patient might have seen.

It is pretty much the ultimate immunological fishing trip in that it seems to try to catch autoantibodies and antibodies to microbes in the same set up. The problem I have is that antibodies do not actually bind to linear peptides in vivo. They bind to quaternary conformations of protein surfaces. And any given peptides are likely to be present as part of all sorts of irrelevant proteins. At least in a Western blot the target is whole protein actually present in human tissue.

And the difficulty with a 'signature' of this sort is in the statistics. In the diseases we now about what we have found is not a signature that relies on a dozen antigens being taken together. It shows up like a sore thumb with one antigen - maybe only in a minority but still a sore thumb compared to normals. I have yet to see this sort of 'signature' approach yield anything useful. I am prepared to believe that one day it might but it does not have a track record yet as far as I know.

 

[anciendaze]

The idea that sequences with short open reading frames were irrelevant was an arbitrary decision made during the Human Genome Project to simplify matters. It was called into question years ago. Other work continues to show just how much was ignored as a result. Added: see this review.

I don't know that any particular sequence is the key to this disease, but I think it is important to see if patients do have more such sequences and antibodies to them. Frankly, I would prefer to test for the sequences themselves, because disturbances in the proteome have been seen in patients before.

 

[Jonathan Edwards]

As far as i can see, anciendaze, the paper is not suggesting that the peptides actually exist as peptides in the patients. The peptide screening systems are just ways of presenting what might be epitopes on proteins in patients to the patients' antibodies. One problem is that they will not have tertiary or quaternary conformational features so may to be seen by the antibodies even if there are antibodies to the proteins.

An underlying supposition seems to be that if a protein is involved in a disease the patient will have more antibodies to it than healthy people. That is not true of most diseases, even if it is true of autoimmune disease and sometimes true of infections.

 

[anciendaze]

If the peptides were neatly confined to cell surfaces this might be true. This would also be a remarkable departure from results of other general research on peptides in blood. I view the antibodies as simply a means of detecting the peptides, though I would prefer more direct evidence. Seen from a conventional immunological standpoint, I can understand your conceptual problem with this paper.

Cell signalling via peptides is a field I've watched move with glacial speed. (Here's a letter from 1970.) At this point we have evidence of very roughly 20,000 human genes and 2,000 short protein sequences probably acting as transcription factors. Very few of these short peptides have been connected with pathological states. Only about 20% of heritable diseases have been tied to sequences in the exome, as typically defined by omitting short open reading frames, the other 80% must be out there in the "dark matter" of the genome. This is also where I see the greatest potential for medical interventions prior to some future millennium when we will be able to edit genes in living individuals at will.

We have repeatedly seen problems related to endothelial function turn up in research on ME/CFS. This would relate to intestinal problems, heart and lung performance, orthostatic intolerance and inadequate supply of oxygenated blood to muscles or brain during exertion. I would be surprised if nothing of this sort turned up.

My prejudice about methods with a "track record" comes from this common sequence of events:
run traditional tests => find nothing => refer patient to psychiatrist.

This is not the result of some vast conspiracy. At the time many objective tests were developed there was scarcely an inkling about physiological anomalies in mental illness, the science simply was not there. A patient without convenient clinical signs must then necessarily be crazy, and there is no point in running extensive medical tests on crazy people. (This benign neglect usually, but not always, stopped short of sending relatives form letters saying: "Der Tod kam als barmherzig Freilassung.") Past attitudes about psychosomatic illness directly affected the setting of diagnostic thresholds for objective laboratory work.

To put it another way, the tests were implicitly designed to get such patients out of the clinic and onto the couch.

Added: link above to Wikipedia article on transcription factors. When you consider evidence that cell metabolism has been throttled down to a "dauer-like" state, and read about transcription factors controlling rates of gene expression, I think you will understand why I am interested in this. The hypothesis that this is the way the pathological state is maintained would also explain why conventional medical tests have failed to find anything significant.

 

[frederic83]

burn meds seem to help with HERV-W.
this was lower in the burn-group.

Which burn group are you referring to ?

 

[alex3619]

To identify the source with certainty, the peptide would have to be fairly long - I'm not sure how long, but the longer it is, the less likely that the sequence occurs in multiple pathogens or even multiple human proteins.

Once you have candidate proteins you can test for them specifically. The issue is in getting the candidates. This research is not nearly definitive, it probably has many false positives, but it does do something important. It gives us candidates for specific testing. If you know which haystack the needle might be in you can save a lot of time.

 

[alex3619]

Expression of a viral immunosuppression domain could account for this, even without an actively replicating retrovirus.

There is another potential explanation. The body likes to focus on specific threats, and may suppress other paths that are not involved but use up energy. This certainly happens with some signaling molecules, particularly in the immune system. If the immune system is hyper-focused on bacteria found in the gut then there should be signaling pathways that direct this to happen, and other pathways that suppress other immune activity. Its a clue, but far from certain.

 

[alex3619]

The problem I have is that antibodies do not actually bind to linear peptides in vivo. They bind to quaternary conformations of protein surfaces.

Yes, its a problem.

 

[alex3619]

A patient without convenient clinical signs must then necessarily be crazy, and there is no point in running extensive medical tests on crazy people.

Which I assert is why so many psych disorders, primarily psychogenic claims, are not re-diagnosed. Its failure to diagnose, and that failure is even used to claim the psych diagnosis must be correct.

More and more I am having a problem with any diagnosis based purely on one symptom, and even a small range of symptoms. Symptomatic diagnosis is most likely to be heterogeneous, which I think is what is wrong with diagnosis on the basis of only depression, or fatigue, or pain. Diagnoses need more than that, and almost certainly need biomarkers.

 

[roller]

if its indeed glanders...

only the german wiki page is helpful
https://de.wikipedia.org/wiki/Rotz_(Krankheit)

very likely that it is at least part of the game.
very bad news.

 

[anciendaze]

Private correspondents have questioned my concentration on peptides, as in my posts above. Antibodies would certainly be important, if these were consistently found only in patients. At this time I'm predicting the pattern will not be consistent. The reason is that there are simply too many possible antibodies to small peptides. What you see in one patient will likely not be found in another, except in the sense that there is some pattern of response to a number of peptides.

Why peptides? My answer is that this represents a huge gap in most research to date which connects with fundamental biology. Peptides may act to control gene expression as transcription factors. They may also fit receptors on membranes to transmit signals between cells. (Several aspects of this illness look like problems of communication between cells to me, which may simply be a prejudice on my part.)

Another way in which relatively small molecules may impact gene expression comes from RNA interference. This is another huge gap in our understanding of pathological states in humans. I'm downplaying this at the moment because naked RNA does not survive long outside cells. It can be transmitted via virions, viral synapses or exosomes, but that gets us into previous controversies. Cell-free DNA also exists, and survives outside cells longer than RNA, but the significance is not yet clear.

With real evidence of abnormal proteomes in patients, and the possibility of small peptide signals acting to control gene expression, I'm putting my bets on peptide signals rather than these other alternatives. My emphasis on signalling could be wrong, but I believe many problems traced to particular cells or organelles are actually reifications of defective signalling.