Genetics: Chromosome 20: ARFGEF2, CSE1L, STAU1

[jnmaciuch]

The size of the peak is very different in Spain (which could be less late EBV) but fairly similar in other countries and at the same time point to within a year in all countries except perhaps Germany. So it doesn't shift in time - it is quite remarkably consistent a bit too early for the kissing disease.

it doesn’t have to line up exactly if what matters is some developmental change that influences some EBV-related response. The unlucky early peak might be people on the tail end of one developmental change and on the start of the EBV spike. In MS we know the relevance of EBV because people who miraculously managed to avoid EBV are strongly protected from the disease. We’d just need to check if there’s a similar tendency in ME/CFS

 

[jnmaciuch]

But why bring in B cells when we have no pathology to link to antibody - which demyelination does beautifully. Why bring in autoreactivity, when we don't even have good evidence for it in MS?

okay, so it doesn’t need to be an auto reactive B cell. Just one that can wreak a lot of damage when it ends up in the wrong place. And EBV might facilitate getting into the wrong place. None of what I’m saying hinges on the auto reactivity.

 

[jnmaciuch]

It would need to be diffuse cytokine specifically in the hypothalamus, presumably? We don't have reason to think cytokines in other bits of brain produce sickness behaviour as far as I know.

Maybe, but not necessarily. In the mouse paper they showed that one face of the endothelial cells bound to circulating IFN, and the cell started dumping out CXCL10 into the parenchyma through its other face. Most neuron types seem to have receptors for CXCL10, and I’ve shared some ex vivo studies showing that it can affect firing rate of e.g. hippocampal neurons. So maybe you get sickness behavior if CXCL10 reaches some hypothalamic neurons, or maybe CXCL10 directly touches lots of different parts of the brain to create symptoms.

 

[ScoutB]

one face of the endothelial cells bound to circulating IFN, and the cell started dumping out CXCL10 into the parenchyma through its other face.

Out of curiosity -- by face do you mean one side of the cell, or does it have a specific meaning?

 

[jnmaciuch]

Out of curiosity -- by face do you mean one side of the cell, or does it have a specific meaning?

One side of the cell, endothelial cells are barrier cells so one side will be structurally different than the other in various ways

 

[ScoutB]

Ah interesting. Makes sense, thanks!

 

[Axel]

In MS we know the relevance of EBV because people who miraculously managed to avoid EBV are strongly protected from the disease. We’d just need to check if there’s a similar tendency in ME/CFS

EBV test result negative here. I am moderate. Mild symptoms appeared well before the first age-related peak, and aggravate right in the second (age 41).

 

[jnmaciuch]

EBV test result negative here. I am moderate. Mild symptoms appeared well before the first age-related peak, and aggravate right in the second (age 41).

Do you know if it was IgG or IgM and what antigen?

 

[Axel]

Do you know if it was IgG or IgM and what antigen?

I’ll let you know as soon as possible.

Edit
It’s simpler than that: we didn’t do it!
Well, I suppose my case is more common after all.

 

[jnmaciuch]

I’ll let you know as soon as possible.

No worries it’s not super important, was just curious because some tests only come back positive if you’re actively in the acute phase of infection

 

[Jonathan Edwards]

Sorry, I had lost this thread.

it doesn’t have to line up exactly if what matters is some developmental change that influences some EBV-related response.

Sure, it doesn't need to but the fact that it does, before the exposure peak, does seem to mean an age dependent susceptibility to the ME/CFS response. But that susceptibility does not need to have any specificity for EBV. It might equally apply to head injury or Q fever.

The thing that worries me is that we start invoking EBV twice - once as a trigger in some and twice as a necessary mediator of the process in general (the type of role in MS).

Audrey and I had quite an intense discussion about this and I agree it is well worth chasing further. If those who escape EBV infection altogether never get ME/CFS that would be important.

 

[Jonathan Edwards]

okay, so it doesn’t need to be an auto reactive B cell. Just one that can wreak a lot of damage when it ends up in the wrong place.

Agreed. Margaret Esiri's in vitro work and the work on B cell survival factors being less necessary in brain suggest that any B cell that starts exporting antibody will produce demyelination as in MS. But there are certainly unanswered questions about why they survive.

 

[Jonathan Edwards]

So maybe you get sickness behavior if CXCL10 reaches some hypothalamic neurons, or maybe CXCL10 directly touches lots of different parts of the brain to create symptoms.

Agreed. My caution here comes from my interest in the biophysics of sensations. Sensations are all encoded in patterns of electrical potential, not in chemical species. They are properties of a neuron 'invented' on the spot in the neuron when the pattern of potentials is right. So it is likely that feeling ill is due to some cells getting a message that codes 'you are feeling ill' through a synaptic potential pattern. If a cell is coming under a fog of CXCL10 there is no reason for any feeling illness in that cell. The feeling ill sensation will be coded in the output of cells specially designed to notice if there are danger signals around (probably in hypothalamus) and sensed in the input to some other cells.

The history of neurosurgery all points to this sort of model. Nastiness can occur in all sorts of brain areas without any sense of nastiness. If you stimulate bits of brain other than hypothaalamus you usually end up with specific sensations like green flashes or sounds or memories.

But as yet we have no real idea where the cells that feel ill, in the way we report, are.

 

[jnmaciuch]

But that susceptibility does not need to have any specificity for EBV. It might equally apply to head injury or Q fever.

That’s fair. I’m really just thinking of EBV here because exposure is so common, there’s a good amount of literature about its host interactions that could help with theorizing, and it might lend itself to explain some miscellaneous observations about ME/CFS.

The thing that worries me is that we start invoking EBV twice - once as a trigger in some and twice as a necessary mediator of the process in general (the type of role in MS).

that may not be a problem if the cases of ME/CFS right after mono are really just the same series of events as everyone else, but happening in quick succession. If whatever entrenches someone in ME/CFS involves EBV-infected cells plus some general infection-response pathways, it makes sense that some proportion of people would be unlucky enough to get the one-two punch right away during that first infection.

The rest who escape it the first time around would just be continually rolling the dice with subsequent infections (or injuries or environmental triggers). That would actually track quite well with the reports of people who had a brief spell of ME/CFS in their youth, recovered for a decade or more, and then fell back into it in middle age. If there’s something happening developmentally in middle age that weighs the dice even heavier around that time, it explains the second peak.

 

[jnmaciuch]

Agreed. My caution here comes from my interest in the biophysics of sensations. Sensations are all encoded in patterns of electrical potential, not in chemical species. They are properties of a neuron 'invented' on the spot in the neuron when the pattern of potentials is right. So it is likely that feeling ill is due to some cells getting a message that codes 'you are feeling ill' through a synaptic potential pattern. If a cell is coming under a fog of CXCL10 there is no reason for any feeling illness in that cell. The feeling ill sensation will be coded in the output of cells specially designed to notice if there are danger signals around (probably in hypothalamus) and sensed in the input to some other cells.

Yes I see your point, though my point is more that the neurons that “encode” malaise could also span several parts of the brain. If it was true that cytokine signals could really only reach the brain at the hypothalamus, then it would make sense for the circuitry for feeling-ill to be concentrated there. But if it is brain endothelial cells churning out CXCL10 into the whole parenchyma, then evolution has no such constraints and it could be a diffuse network acting in concert. Or you’d have the same situation if incoming signal from the DRG branches out quickly to simultaneously engage multiple parts of the brain.

My instinct is that it must be more diffuse, because all of those mouse studies in the CRH thread succeeded in suppressing infection responses but not ablating them completely (even when looking at just one specific symptom). Which makes the existence of a central neural chokepoint somewhat less likely, though of course it just could be because we don’t have the tools to find it yet.

 

[DHagen]

Audrey and I had quite an intense discussion about this and I agree it is well worth chasing further. If those who escape EBV infection altogether never get ME/CFS that would be important.

At least according to my labs, I have never had EBV.

 

[Kitty]

I'm only assuming I've been infected at some stage. When I was a teenager, testing wasn't very common in healthy youngsters with symptoms of glandular fever. I've never had symptoms, so there's been no reason to test for it.

 

[Jonathan Edwards]

Yes I see your point, though my point is more that the neurons that “encode” malaise could also span several parts of the brain.

Yes, I think that is a useful and plausible insight. Brains cells are never just in one place functionally (except maybe short range interneurons I suppose). I am not sure about the mice but remembering that function and transmitter usage may span much bigger distances than is often assumed makes a lot of sense.

 

[ME/CFS Science Blog]

I had a look at the region using ENCODE data on chromatin openness. I used the SCREEN API which organizes the evidence into candidate regulatory elements (CCREs). I looked at 11 core SNPs for the Decode hit (which have more than 80% of the probability of the signal) and found that 7 were in a CCRE.



Next, I could look up scores for these 7 CCRE for various experiments and biosamples. It includes z-scores for open DNA (DNase or ATAC), the active-enhancer mark H3K27ac, the promoter mark H3K4me3, and binding of CTCF (a protein that anchors DNA loops). Using AI I also tried to group the biosamples in meaningful categories (broad_group and fine_group) such as immune, CNS, etc. This help with screening and interpretability but be aware that these are my own categories, not official labels from ENCODE.

Overall, this region doesn’t stand out in chromatin openness and other markers, not more than what would be expected by chance. The most notable results were for immune cells for the SNPs 20:48911205: A: C and 20:48909956:T:G. HL-60 refers to a leukemia cell line.





The graph below plots the CRE position and distance with the location of our core SNPs added. The ARFGEF2 transcription start site is also shown as a comparison of how an active region looks like. The average across all biosamples didn’t show anything interesting in this region but when I restrict to the immune system data, there seems to be a peak at the location where 20:48911205: A: C and 20:48909956:T:G lie.



The average for central nervous system samples didn’t show peaks in our SNPs, so I had a look at a more refined dataset: the Li et al. 2023 brain atlas that used sn-ATAC-seq normalized per 107 cell types. Here I found a minor peak at 20:48917118:T:C (closer to ARFGEF2) that seems to point to GABAergic neurons from the basal ganglia. The FOXP2 finding is interesting because it might be point to eccentric medium spiny neurons found in the RNA analyses of DecodeME (but not so much in the ATAC-analysis).







So, what does all of this mean? I’m not sure. None of hypothesis’s currently seems more convincing that the others. I plan to look closer the eQTL, coloc and AphaGenome predictions but I suspect we’ll need some experimental data from this region to know what it actually points to. It’s the biggest hit from DecodeME so I think it deserves a follow-up!

 

[ME/CFS Science Blog]

Does AlphaGenome give more specific information on the direction of the signal? That would tell me if the variant is associated with opening or closing chromatin at that region.

Sorry for the late reply. Yes they are all negative values so the deletion is predicted to close chromatin and lower active enhancer marks in the myeloma cell lines.