Latest from Fluge and Mella: ME/CFS Immunosignature Identified

Hufsamor

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We were able to identify a 256-peptide signature that separates ME/CFS samples from healthy controls, suggesting that the hit-and-run hypothesis of immune dysfunction merits further investigation. By extending testing of both our signature and one previously reported in the literature to larger cohorts, and further interrogating the specific peptides we and others have identified, we may deepen our understanding of the origins of ME/CFS and work towards a clinically meaningful diagnostic biomarker.
 

ljimbo423

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This resulted in a 256-peptide immunosignature with the ability to separate ME/CFS cases from controls in the international data sets. We were able to identify a 256-peptide signature that separates ME/CFS samples from healthy controls, suggesting that the hit-and-run hypothesis of immune dysfunction merits further investigation.
This statement above sounds like they are saying there's still something that's causing ongoing immune activation.

By extending testing of both our signature and one previously reported in the literature to larger cohorts, and further interrogating the specific peptides we and others have identified, we may deepen our understanding of the origins of ME/CFS and work towards a clinically meaningful diagnostic biomarker.
When researchers find the origin of ME/CFS, effective treatment(s), I think will be right behind it.

Link to Abstract
 
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Full abstract below. Paper attached.


  • Mol Neurobiol. 2018 Oct 8. doi: 10.1007/s12035-018-1354-8. [Epub ahead of print]
    Immunosignature Analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS).
    Günther OP1, Gardy JL2,3, Stafford P4, Fluge Ø5, Mella O5, Tang P6, Miller RR3, Parker SM7, Johnston SA4, Patrick DM8,9.
    Author information
    Abstract

    A random-sequence peptide microarray can interrogate serum antibodies in a broad, unbiased fashion to generate disease-specific immunosignatures. This approach has been applied to cancer detection, diagnosis of infections, and interrogation of vaccine response. We hypothesized that there is an immunosignature specific to ME/CFS and that this could aid in the diagnosis. We studied two subject groups meeting the Canadian Consensus Definition of ME/CFS. ME/CFS (n = 25) and matched control (n = 25) sera were obtained from a Canadian study. ME/CFS (n = 25) sera were obtained from phase 1/2 Norwegian trials (NCT01156909). Sera from six healthy controls from the USA were included in the analysis. Canadian cases and controls were tested for a disease immunosignature. By combining results from unsupervised and supervised analyses, a candidate immunosignature with 654 peptides was able to differentiate ME/CFS from controls. The immunosignature was tested and further refined using the Norwegian and USA samples. This resulted in a 256-peptide immunosignature with the ability to separate ME/CFS cases from controls in the international data sets. We were able to identify a 256-peptide signature that separates ME/CFS samples from healthy controls, suggesting that the hit-and-run hypothesis of immune dysfunction merits further investigation. By extending testing of both our signature and one previously reported in the literature to larger cohorts, and further interrogating the specific peptides we and others have identified, we may deepen our understanding of the origins of ME/CFS and work towards a clinically meaningful diagnostic biomarker.

    KEYWORDS:
    Diagnosis; Immunosignatures; Myalgic encephalomyelitis/chronic fatigue syndrome; Peptides

    PMID:
    30298340
    DOI:
    10.1007/s12035-018-1354-8
 

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They hunted for groups of peptides that we have antibodies to in levels that healthy people don't.

Then they did some complicated statistical stuff. (not to self: must get to grips with principle component analysis if it's going to be in every damn study.)

And they found a group of 256 peptides such that if you bundle them together, you can use to distinguish healthy people from controls with good accuracy. (graphic on left, which is pretty impressive separation of the groups.

Screen Shot 2018-10-11 at 9.20.50 AM.png

(Note: They say sample handling explains the differences in values between healthy controls in USA and Canada and note how important standardisation is in this field to make the whole exercise worthwhile. It's definitely not good news that you get a stronger separation between healthy USA and Canadian people than sick and well people. It's a shame they didn't have Norwegian health controls.)

Basically it says our immune systems look different to healthy peoples and that suggests the disease has an immune or autoimmune element.

Last point: even though all their peptide groups had lots of peptides in them, there was one that stood out:

A recent publication using the same immunosignature plat- form proposed a 25-peptide ME/CFS signature [de Meirlier, 2016]. There was no direct overlap between this signature and CPS001A, and little overlap with our other candidate signatures (Online Resource 1). The exception was peptide LRVVWLSGVASG, which was found in four of our five candidate signatures, and which might be a good candidate for further biological exploration, as well as a set of similar peptides (EFRAKQWNSVAL, HVVWRVSGVALG, GWKNHRVLSGLS, RLRHLQSWVGVL, VQWWRPALGVAL, LRVVWLSGVASG, WGAVKVGVALSG, and WPRLHLSGVALG)—many containing a VAL or VAS motif—found in CPS002 and CPS006.
 
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JadeD

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Yes it looks like they’ve found a peptide similar to what Lombardi and KDM found back in 2016. Thankfully Lombardi and coworkers have just received the Ramsay award which is an extension to this work. It’s nice to see that similar work is being replicated now by separate groups.
 

Research 1st

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They didn't proof read their own research paper or a bi-lingual hamster took control of the word processor? On page 4 of the PDF at the top it reads:

''Three unsupervised and three supervised analyses were run on the full 122,926 peptide dataset to select peptides best able to discriminate ME/CSF from control samples''.

In the bottom line of the quote below, they mean ME/CFS, not ME/CSF. CSF is Cerebrospinal fluid!

Source: https://link.springer.com/article/10.1007/s12035-018-1354-8
 

Hufsamor

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Stupid question... But what is 256 Peptide? Can anyone explain the results in "laymen terms" lol
Not stupid at all.
I'm reading and reading, but still not sure.

But those peptides, whatever they are, kind of shows how the body's immune system works, and where the immunsystem has a hang up.
And it is like a fingerprint. In a fingerprint you have so and so many lines and points that needs to match, to know who's fingerprint it is.

Many diseases has a petide "fingerprint".
They are used to diagnose cancer and other things.
This me/cfs "fingerprint" has 256 peptides in it, they hope to narrow it down to maybe 25 peptides.

The good thing is that those peptides (whatever they are) can make it easy to diagnose me/CFS in the future. You go to the doctor, they run some tests, and them they will know. Nothing to discuss, they have the proof.

The other good thing is, as far as I understand, that those peptides gives the scientists an idea about what went wrong, why we are sick.
Like the detectives on television, looking for clues, and then able to understand what happened.

Because they found this peptide "fingerprint", they still believe the immunsystem is involved in the sickness. If they had not found a peptide "fingerprint" , the immunsystem would not have been involved and they would have to look elsewhere.

And the more they know, the easier it will be to make a treatment.
 

M Paine

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Peptides are short chains of proteins. Generally speaking, peptides are often a small section of a much larger protein. In humans, there are two major parts of immune surveillance which identify foreign protein peptides.

1. Random proteins found inside a cell are chopped up and presented on the surface of the cell. T-cells bind to cells and check for foreign proteins presented on the cell surface, giving them a window into what's going on inside. Foreign or unexpected protein peptides are indicative of an infection or tumor.

2. Anti-bodies (Immunoglobulin/IgG) produced by mature B-cells, flow through the bloodstream in massive quantity, and bind to proteins, peptides, and many other types of molecules.

This study looks at the second process, the B-cell arm of adaptive immunity.

Proteins are made up of 20 different amino acids parts. The different amino acid molecules are strung together into a long chain, and folded to create little machines (enzymes) inside a cell. Gene's in the human genome are transcribed into RNA and translated into Protein. Those sequences they mention such as "LRVVWLSGVASG" represent amino acids.

What they are looking at, is for patients, is there a common target which the immune system is targeting. That target could be some sort of infectious agent like a virus or bacteria. But the amino acid sequences that they are using may not necessarily come from the virus or bacteria. In fact, they might not be identical to the original infectious agent. Because amino acids are strung together and folded into three dimensional shapes, distinct amino acid sequences may have common binding affinity to non-related sequences. This means a single antibody might cross react with more than one sequence of amino acids.

An analogy would be, if you have 20 pieces of lego, you could string together the pieces in many three dimensional ways. If you call that the 'lock', then a key made of lego might fit a variety of locks.

The take home message, is that they are looking for a common set of biological targets which the immune system of CFS patients is reacting against. In my opinion, this is good evidence of that.
 
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M Paine

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Finally got around to reading the paper...

"These 256 peptides are positioned throughout a phylogenetic tree derived from the complete 125 k-peptide dataset (Supplementary Figure 11 in Online Resource 1), indicating the signature is comprised of diverse peptides and is not reflecting any underlying bias in the design of the array. However, this diversity does not exclude the possibility that these peptides represent immune response to a common antigen—the genetic distance between peptides as represented in a phylogenetic tree does not reflect the physical conformation of epitopes bound by common antibodies. In order to make a valid interpretation of the sequence evaluation of selected peptides, it should be noted that the peptide microarray was created using sequences selected from random space. All possible peptide sequences were created in memory, then compared to each other to select the broadest coverage of 3mer, 4mer and 5mer space, while reducing redundancy as much as possible. When the library of peptides was compared by BLASTP to the latest UniProt UP000005640 proteome consisting of 73,112 sequences, there were 7,051,312 unique hits covering 32.5% of UP000005640. Ninety-eight percent of these hits were 2mer or 3mer perfect matches. Thus, the library is not designed to exclude sequences of natural origin, and any alignments would be by pure chance. At this stage of development, the immunosignature assay is not designed or optimized to allow accurate inference back to source proteins."

That section might answer a few questions for some, who wondered where the peptides originated, what the tree is in the diagrams... and a few other bits and bobs.