NK cells and SNP of specific ion channels and receptor genes in ME/cfs

[alicec]

what is happening in the NK cells

The SNPs are present in all cells, not just NK cells, so the SNP analysis doesn't say anything about what may be going wrong with NK cells.

 

[alex3619]

Let me add that a snp on an ion channel or hormone receptor might alter more than just whether its on or off more often. It might alter how the channel is regulated, or regulates other processes. This might in turn lead to secondary and tertiary effects, some of which might feed back into it all.

 

[Jonathan Edwards]

So it is important to know whether some genes that are supposed to be important for important functions are functioning as they should or have mutated.

I prefer this kind of research, to get to the bottom of things, instead of having a clinician telling me that my brain is freaking out, and the treatment is CBT and GET. This is what is happening currently in many parts of the world. Science, please! We need more of that.

@Jonathan Edwards I believe the Australian team will be present at Invest in ME, so it would be a great opportunity to find out more.

What is bothering alicec, Bob and I is that looking for SNPs in NK cells simply does not do what you would like it to do. It just looks for the SNPs you were born with. It tells you nothing about gene expression, just about genes - the popular press often get these things confused. It is a bit like a policeman stopping somebody in a car and saying 'I don't think you are a legal driver and maybe not insured - show me your birth certificate'. These genes do not mutate in NK cells, unless you have NK cell cancer and NK cell cancer I have never even heard of. If you want to know if they are not expressed properly you look for RNA, not DNA.

I totally agree that this is the sort of science we want. It is just that it is not clear what the point of this particular experiment is - at least to me.

 

[Kati]

What is bothering alicec, Bob and I is that looking for SNPs in NK cells simply does not do what you would like it to do. It just looks for the SNPs you were born with. It tells you nothing about gene expression, just about genes - the popular press often get these things confused. It is a bit like a policeman stopping somebody in a car and saying 'I don't think you are a legal driver and maybe not insured - show me your birth certificate'. These genes do not mutate in NK cells, unless you have NK cell cancer and NK cell cancer I have never even heard of. If you want to know if they are not expressed properly you look for RNA, not DNA.

I totally agree that this is the sort of science we want. It is just that it is not clear what the point of this particular experiment is - at least to me.

So is it not relevant to know there are differences in specific SNP between ME pts vs healthy controls? That the NK cell function was lower in ME pts vs healthy control- and a note on that, these patients's NK cell function with an average of 17%is not as low as could be.

And since we are exchanging , @Jonathan Edwards i am curious to hear what NK cell cytotoxicity means from a rheumatologist point of view. Is that something you kept track of in research or in clinical setting? How about herpes viruses? Thx.

 

[Valentijn]

So is it not relevant to know there are differences in specific SNP between ME pts vs healthy controls?

That's part of the problem. If they had corrected for making multiple (600+?) comparisons, there probably wouldn't have been any statistical differences.

 

[Jonathan Edwards]

So is it not relevant to know there are differences in specific SNP between ME pts vs healthy controls? That the NK cell function was lower in ME pts vs healthy control- and a note on that, these patients's NK cell function with an average of 17%is not as low as could be.

And since we are exchanging , @Jonathan Edwards i am curious to hear what NK cell cytotoxicity means from a rheumatologist point of view. Is that something you kept track of in research or in clinical setting? How about herpes viruses? Thx.

Differences in SNPs between ME pts and controls would certainly be of interest, but the group had already looked at that with unselected PBMC I think. The odd thing is bothering to select out NK cells to look for their 'birth certificate' when all cells have the same version. And there is an implication in the way the paper is written that somehow finding the SNPs in NK cells is relevant - which it isn't (as far as I can see). So no new idea has been tested here.

The low cytotoxicity is something that has been found on many occasions before, as we know, so that is nothing new. The worry is that apparently even Nancy Klimas has had trouble replicating this reliably.

As it turns out one of my work mates in the rheumatology lab has experience with NK assays going back thirty five years. They were of great interest in the 1980s but people found the assays gave very variable results. Then around 1995 we learnt about the huge variation in NK receptors between individuals and people began to see that simply measuring an ability to kill somebody else's K562 cells might actually tell us nothing very interpretable. NK cells do not recognise self and foreign antigens the way T cells do but they recognise self through a different innate mechanism. If you want to measure NK function you should probably look at killing of your own virally infected cells. I am not sure that anyone has set this sort of system up, however.

So generally speaking rheumatologists and others interested in autoimmunity have lost interest in NK cells because we don't really know what to make of the assays. There are extreme cases where people have no NK activity for genetic reasons but they are mostly dealt with by paediatric immunodeficiency specialists.

 

[Bob]

@Kati, as far as my my understanding goes, and in case helpful...

SNPs are genetic (DNA) mutations and are not a measure of gene expression. Gene expression was not measured in this study.

Some specific types of immune cells mutate safely and frequently by design in order to operate normally, but these mutations only occur by design in specific regions of the genome in those cells and are not genome-wide in those cells. NK cells are not one of these cell types, so frequent or unique DNA mutations would not be expected throughout the NK cell population.

We are born with our system-wide genetic mutations (including SNPs) and the mutations occur in the DNA of every cell in our body.

I think others have said that some localised mutations may occur during our lives but I don't know how frequently the mutations are able to survive for long periods or how widely mutations can spread through tissues. The body has a mechanism for spotting most mutations and killing the affected cells.

Some viruses can change our DNA, throughout our body, and such changes can be passed onto offspring.

If all NK cells had the same mutations (rather than occasional random differences in each cell) then you'd expect the mutation to originate from wherever the cells originate from, which may be stem cells and the bone marrow. In which case the same mutations would be widespread and would be detected in all blood cells and many other cell types and tissues. I'm not sure if a random mutation can become so widespread in an individual except by inheritance i.e. passing it to offspring.

In other words, mutations (SNPs) exclusive to NK cells only, doesn't make sense, because you'd expect to see the same SNPs in other cell types, so there doesn't seem to be a reason to test only NK cells for SNPs.

If the occasional NK cell mutated it would likely soon be destroyed and replaced, and if it wasn't destroyed it couldn't create an entire population of NK cells with the same mutation.

Gene expression is a different phenomena and is specific to each cell type, so it would make sense to isolate NK cells to measure gene expression. But gene expression wasn't assessed in this study.

There's nothing wrong with hunting for SNPs in NK cells only, but it seems like an unnecessary extra step to take. They may have had their reasons for isolating NK cells to test for SNPs but I haven't seen it explained in the paper.

We've learned that you need very large studies to reliably gain useful information from genetic studies.

The overall research program may be useful, but this study in isolation doesn't really give us much useful information, as far as I understand it. But I may be wrong.

Disclaimer: any of the above info may be incorrect. It's to the best of my understanding.

 

[anciendaze]

We can agree that gene expression studies would be useful. We may continue to disagree over the question of these mutations being present from birth. If we were talking about cancer or retroviral infection the argument about genetics would be quite different.

Unfortunately, the boundaries between diagnostic categories are not as solid as we would like. Most autoimmune diseases show associations with specific types of cancer, often types that are rare in the general population. Not too long ago I was surprised to learn that paraneoplastic diseases now encompass some in which cancer is never detected.

If simply detecting reverse transcription activity were a reliable clue to retroviral infection most people would be said to have this at some time in life, and at least some HERVs would be classified as provirus. Expression of HERVs in ME/CFS has been found in some limited research, which needs to be followed up.

Even explicit retroviral infection can't easily be ruled out. Expression of HERVs is greatly stimulated by a replication-competent retrovirus, and expression of beta-retroviral sequences has long been known in breast cancer. We now have real evidence that bovine leukemia virus does infect humans and is associated with increased incidence of breast cancer. Nobody has screened the general population for BLV, and you can't simply use antibodies to detect this because antibodies to BLV are widespread in people who consume milk or beef. Anyone who remembers "mad cow disease" can guess the official response to discoveries about BLV in humans.

This must necessarily be an extremely slow retroviral infection, like HTLV-1, which is also loose in humans and associated with rare T-cell leukemia/lymphoma. We know very little about what goes on prior to the appearance of progressive disease in these cases. Most studies find little wrong, just as most studies of CFS patients don't find much wrong. Do I know we are infected with a retrovirus? Not at all.

At the moment I'm distracted by an attempt to make sense of mast-cell activation syndrome, where I also see evidence of unusual variability in immune cell genomes. Is this a real change in DNA? I don't know. I think the question remains open.

Added: can anyone tell me why mast cells showing CD117 would appear at high densities on apparently normal tissues in people who do not have cancer? I'm trying to learn.

 

[lansbergen]

Anyone who remembers "mad cow disease" can guess the official response to discoveries about BLV in humans.

The dutch government was an exception. They hired a good virologist to tell the truth to the public and the public could live with this is what we know now.

 

[Kati]

Thank you @Jonathan Edwards and @Bob and @anciendaze for your explanations. We are (over)due for a breakthrough.

 

[halcyon]

Some viruses can change our DNA, throughout our body, and such changes can be passed onto offspring.

This has to happen in germ line cells to be passed on.

If the occasional NK cell mutated it would likely soon be destroyed and replaced, and if it wasn't destroyed it couldn't create an entire population of NK cells with the same mutation.

I don't believe that NK cells divide or clonally expand, so this wouldn't be possible. As you said, the mutation would have to be in hematopoietic stem cells.

Just to add even more confusion to all of this, according to the recent news coverage, this team supposedly will use these SNPs in their screening test for CFS:

The test targets common genetic variants known as single nucleotide polymorphisms (SNPs), which can predispose a person to chronic fatigue syndrome. According to the researchers, in up to 80 percent of cases, an infectious disease such as glandular fever has triggered the expression of these SNPs to bring on the development of chronic fatigue syndrome.

But then in that article, and in their official press release, they say:

“This illness has traditionally been difficult to diagnose, meaning that people can go for months without getting the care and attention they require. We are confident that the new screening test currently in development will provide efficient and increasingly accurate screening for people with CFS. This test may also be used to monitor and track the progression of their illness,” says Professor Staines.

I don't see how that would be possible using SNPs unless the SNPs they are finding are only occurring in certain cell types and change over time somehow. My assumption is that the media got it wrong and the test won't actually be based on the SNP findings as they haven't official announced that yet.

 

[Jonathan Edwards]

I don't believe that NK cells divide or clonally expand, so this wouldn't be possible. As you said, the mutation would have to be in hematopoietic stem cells.

Things are actually quite weird in this area. As in mitochondrial disease you can get somatically mutated genes 'winning out' over the original alleles by clonal expansion that does not necessarily have to be at stem cell level. I think we are all agreed that none of this is relevant to the ME case but the reality is quite surprising.

 

[Bob]

I don't see how that would be possible using SNPs unless the SNPs they are finding are only occurring in certain cell types and change over time somehow. My assumption is that the media got it wrong and the test won't actually be based on the SNP findings as they haven't official announced that yet.

I think the media got it wrong. Our best guess so far is that they want to use micro RNAs for biomarkers:
http://forums.phoenixrising.me/inde...gue-syndrome-testing.43337/page-3#post-703516

 

[sdmcvicar]

It is possible that the SNPs could be used for diagnosis but it would have to work something like this:

Say these SNPs have an average background rate of 2% in the control population. That means that if you identified 10 SNPs associated with CFS, the control population would average 0.2 SNPs per person. The chance, then, of a healthy person having 6 of these SNPs would be vanishingly small [(0.2)^6 = 0.000064, or about 1 in 15,000]. This would make a good false positive rate for a diagnostic test.

Then, on the other hand, if a person with CFS averaged 8 of these SNPs, and a minimum of 6 was necessary to obtain a positive diagnosis of CFS, you could have a reasonably robust diagnostic test for CFS. (I was going to lay out the math for true positive and false positive, but just too tired tonight).

Again, the physiological effect of these SNPs is totally unknown, and their correlation to CFS in this test population might not bear out in a broader sample size. That happened the majority of the time for other diseases a decade ago when these types of analyses were applied to proteomics data sets.

 

[Jonathan Edwards]

It is possible that the SNPs could be used for diagnosis but it would have to work something like this:

Say these SNPs have an average background rate of 2% in the control population. That means that if you identified 10 SNPs associated with CFS, the control population would average 0.2 SNPs per person. The chance, then, of a healthy person having 6 of these SNPs would be vanishingly small [(0.2)^6 = 0.000064, or about 1 in 15,000]. This would make a good false positive rate for a diagnostic test.

Then, on the other hand, if a person with CFS averaged 8 of these SNPs, and a minimum of 6 was necessary to obtain a positive diagnosis of CFS, you could have a reasonably robust diagnostic test for CFS. (I was going to lay out the math for true positive and false positive, but just too tired tonight).

Again, the physiological effect of these SNPs is totally unknown, and their correlation to CFS in this test population might not bear out in a broader sample size. That happened the majority of the time for other diseases a decade ago when these types of analyses were applied to proteomics data sets.

In the scenario you propose with those figures, yes, you have a diagnostic test. However, in almost no other disease do we get this sort of clear cut result. 98% of people with ankylosing spondylitis have HLA-B27, which is helpful, but there is still a significant minority of normal people with the allele. From memory the sort of results people have been getting with SNPs in ME are at best slight statistical trends. Whatever further studies show we probably already know that these are not black and white enough to make a diagnostic test. I think the problem is that if the genetics are multifactorial, which they would have to be for your scenario, then the links are always going to be variable statistical ones.

There is a story that an English researcher was visiting a US lab at the time when HLA genetics were being looked at for various diseases. One of the US researchers said 'well our test population looks pretty boring but amazingly absolutely all of this control group (ank spond) are B27!' No statistics are needed in that situation.

 

[tango]

The latest version of the research with 13 SNPs identified is of interest to me.
http://www.la-press.com/examination...rphisms-snps-in-transient-recep-article-a4824

I've had 23andme data done. Of the 9 SNPs that were typed I have genetic mutations for 8 of them. I know this is meaningless without knowing whether they are expressing but it's hard data that I can point to and a new thread to pull that might help. Although I have doctors that believe me the vast majority think it's psychosomatic. The old "I believe that you believe that you are in pain.". And doctors asking if I went through some emotional trauma at the time that may have triggered it. Anything that shows that there is a possible scientific cause interests me.

Of course, what interests me more is the potential cure.

Does this Facebook post here make any sense to you? She is saying it's T-cell activation and that anti-histamines are part of the solution.
https://www.facebook.com/byron.bay.health/posts/1146423695382108

 

[Jonathan Edwards]

Does this Facebook post here make any sense to you? She is saying it's T-cell activation and that anti-histamines are part of the solution.
https://www.facebook.com/byron.bay.health/posts/1146423695382108

No, it is gibberish. It comes from a 'certified health coach' which should probably be 'certified advertiser of dubious products'. Whatever Griffith may have found she has no understanding of it whatever I fear!! NK cells are not T cells, for a start.

 

[Gingergrrl]

I just discovered this thread (am not sure how I missed it since it relates to my problem with the calcium channel auto-antibodies) so I have a lot of questions and am looking forward to reading the responses.

We just learned that Gingergrrl has autoantibodies to N-type calcium channels, which play an important role in the release of acetylcholine from the presynaptic side of neuromuscular junctions. This kind of autoimmune problem is less well known than another at the postsynaptic side of neuromuscular junctions which causes the better-known disease myasthenia gravis.

Thanks for mentioning me @anciendaze and yes, I tested positive in Feb for auto-antibodies for the N-Type calcium channels. (I also tested positive for auto-antibodies for anti GAD65 but have no idea if this relates in any way to this research, but wanted to mention it just in case.) As you know I will be seeing a neuromuscular specialist in three weeks (still trying to get sooner appt!) to be evaluated for LEMS, and hopefully rule it out, and then begin treatment to try to reduce this auto-antibody in my system. We do not think I have LEMS and my symptoms do not match it but it can correlate with my antibody.

Finding a connection between weird immune behavior and muscle weakness is significant. I doubt many of us have as many problems or such severe ones as Gingergrrl, but she could be like the canary in the coal mine. She has also reported evidence of mast cell activation syndrome, for which she is being treated. I'm still trying to come up to speed on that confusing problem. At the moment it looks like it could cause practically any symptom.

My muscle weakness is in my lungs/breathing and continues to worsen. No one could understand why until this antibody was found when I took the PAVAL blood test. It's not that I have a huge number of problems versus that the ones I have are very severe (the lung weakness) and completely took away my ability to walk this year. Am hoping I am not the canary in the coal mine (since I think this means that I am the first to die ?) but I would love for my experience and suffering to pay off and for a doctor to apply this discovery and my treatment to help others. That is my wish at least. And yes, I have MCAS since March 2015 (one year) and how this ties in to the antibody discovery, I still am not sure.

There are known associations of both myasthenia gravis and the newer N-type calcium channel autoimmune problems with a range of autoimmune diseases or neoplasms. I think a picture of at least one type of ME/CFS as an unusual autoimmune disease for which we have not known what to test is starting to form, even if the view is still murky.

How new would you say is the discovery of the N-type calcium channel antibody? I think I read somewhere it was around 2006 or 2007 but now I cannot remember where I saw that. If it is ME/CFS, then I have the autoimmune sub-type. I wish I knew if more people on PR have this antibody (but have not been tested) versus even if they were to be tested, they would not have it. I know three others from PR who were tested but do not have it although have other auto-antibodies that I do not have.

I don't know that the ion-channels are identical, but it is a safe bet there are many similarities. Ion channels of many types turn up in every kind of cell you can name. When a particular trick works, evolution uses it over and over again.

So the defect to the calcium channels are throughout the entire body (and not just on the NK cells) if I am understanding the problem with the article correctly? Are they ever focused on the lungs/breathing or am I an anomaly even with this issue?!

The positive side of this is that finding a defective gene in an immune cell does not mean you are doomed because you lost a genetic lottery at birth. It is possible the change took place at a later date due to environmental challenges.

My understanding is that these auto-antibodies for me are post-viral and not something that I was born with since I was basically healthy for 42 years until I got severe mono. Does this (hopefully!) mean that I have a greater chance of treatment reducing or eliminating the auto-antibodies since I was not born with them?

Is it even possible for SNPs to be present on the genome of one cell type but not others? I thought SNPs were body wide and I can't find anything that says otherwise.

My understanding from reading this thread is that they are body-wide but I did not even attempt to read the article b/c I know I will not understand it.

Does this have anything to do with a need for magnesium supplementation? I know magnesium and calcium are antagonists and play a role in these ion channels.

My understanding (someone correct me if I am wrong) is that with the antibody that I have, I do not want to take anything that would further block the calcium channel since it is already under attack. So I would not want to take a calcium channel blocker medication (which I don't) or even Magnesium which I sadly did not know last year when I kept attempting to take Mg.

I am now taking a calcium orotate supplement (just started it yesterday so too early to tell if it will do anything noticeable.) The doctor who tested me (actually it was the PA) told me that it is not so much that the calcium molecules are not there, they may be there in abundance, but the antibodies stops the electrically charged calcium ions from making it across the synapse or neuromuscular junction. So taking calcium may do nothing helpful but anecdotally she had another patient who tried it and noticed some minor improvement in muscle strength.

Or perhaps above pharmacological doses of magnesium would help cover up the symptoms of damaged more calcium channels. In this case magnesium would be much less related to the pathology of this type of CFS.

I am not sure if I understand this but I know I am not supposed to take huge doses of magnesium. But the article might be speaking about a slightly different issue than what I have, I am not sure.

The role of Rituximab is intriguing in this context. Fluge & Mella seem to be quite sure that its delayed effects were attributable to elimination of auto-antibodies after B cell depletion. But how does this fit with the discovery of SNPs causing calcium dysregulation? Perhaps, like everything else associated with this illness, it's more complicated than we've ever previously imagined.

I agree that RTX is intriguing in this context although I remain confused if my antibody is in the B-cells versus all throughout the body so if wiping out the B-cells alone would not be enough. I lack any science background (as you can tell) so my questions are very basic. They have recommended IVIG or plasmapheresis but it will be the local doctor who will decide and my appt not for three more weeks.

My antibody also correlates with small cell lung cancer (an aggressive form of cancer) so I want to reduce it to hopefully also reduce the cancer risk. On lung cat scan mid-March (two weeks ago), I do not have lung cancer and only have very small nodules (under 3 mm) but need to be checked again in 6-12 months to make sure they do not grow or change.

Some of these are calcium channels, and probably most of them (though I have not checked), or are associated with activity in other calcium channels. It points to a possible (as yet unproven) calcium channelopathy, which will involve changes in calcium activated pathways (including acetylcholine related) and intracellular messaging in general. This implies that not only magnesium may have an impact, but also cyclic AMP.

My understanding was that the auto-antibody that I have equals a "calcium channelopathy" but are you saying these are two different things? What is cyclic AMP?

It also suggests, and I do mean its not proven, that there are subtypes of this disorder. In other words, ME might be many different but closely related diseases.

Absolutely agree that there are subtypes or maybe even several different diseases under the same umbrella.

This may be off-topic, but it has considerable relevance. I've started discussing these results with private correspondents who are not on this forum. Part of the dialogue sounds like "Calcium channels? Acetylcholine? These things have been studied for ages. How did such associations with any disease get overlooked?"

One correspondent who had previously been hit with a tirade of mine about neurotransmitters and their effect on immune cells and functions remarked that the words "humility" and "medicine" should not be used in the same sentence unless interactions are mediated by the "lack" verb or modifier. This correspondent has an M.D.

That is fascinating and with the exception of the doctor who tested me, none of my other doctors have any real knowledge of these auto-antibodies or this issue. It seems to be too obscure or they don't want to be bothered with something so complex. Am hoping the neuromuscular doc will have a lot of experience treating this (this is what I have been told) and we also contacted a cancer center who was interested in my case and just sent them my info, hoping that they can steer me in the right direction.

I recall Professor Edwards stating that the process that results in RA involves 50 steps. It's truly a miracle anything that complicated can be sorted out.

I agree and often think this will not be sorted out within my life-time.

SNPs in ion-channels could well be a fruitful avenue of research in CFS/ME but the SNP studies by this group so far are abysmal.

I wish someone would do a solid study with ME/CFS patients testing the PAVAL panel or other auto-antibody tests (vs. just the NK cells) so it would be more thorough and valid. It seems like this would be relatively easy to do?

Let me add that a snp on an ion channel or hormone receptor might alter more than just whether its on or off more often. It might alter how the channel is regulated, or regulates other processes. This might in turn lead to secondary and tertiary effects, some of which might feed back into it all.

Could this relate to weakening the muscles that support breathing?

I totally agree that this is the sort of science we want. It is just that it is not clear what the point of this particular experiment is - at least to me.

Agreed and this research would be amazing!

Does this Facebook post here make any sense to you? She is saying it's T-cell activation and that anti-histamines are part of the solution.

I read the FB link and IMO it sounds like nonsense. I see one of the top ten MCAS doctors in the country and the problem is with the mast cells degranulating and not with the T cells. Also, I have read other links and articles by Alison Vickery and she lists foods as safe for MCAS that would kill most MCAS patients. She does not seem to have any concept of the foods that are high histamine vs. those that are safe to eat. So, I did not personally find that page accurate but maybe someone else might?

 

[tango]

No, it is gibberish. It comes from a 'certified health coach' which should probably be 'certified advertiser of dubious products'. Whatever Griffith may have found she has no understanding of it whatever I fear!! NK cells are not T cells, for a start.

Thanks! I found her post very confusing.

From the little reading I have done it would appear that one theory is pregnenolone may be helpful but I can't remember where I read that as Griffiths University have published so many studies and done a million and one press releases. I think it might have been an analysis by Cort Johnson...

 

[tango]

I read the FB link and IMO it sounds like nonsense. I see one of the top ten MCAS doctors in the country and the problem is with the mast cells degranulating and not with the T cells. Also, I have read other links and articles by Alison Vickery and she lists foods as safe for MCAS that would kill most MCAS patients. She does not seem to have any concept of the foods that are high histamine vs. those that are safe to eat. So, I did not personally find that page accurate but maybe someone else might?

Thanks for that!

Do you have a reliable list of high histamine foods? I seem to find different lists everywhere I go and the low histamine diet is something I want to try. No that's a lie. I do not want to deprive myself of yummy foods but I am thinking it is worth a try.