Genetics: Chromosome 6 BTN2A2 and BTN3A3 (BTN2A1)

[Kitty]

Hypothalamus, yes, but most of us have been unconvinced by the role of cortisol and I personally do not see how it could explain the clinical picture.

What did you think about the apparent loss of a specific type of neuron in postmortem ME/CFS brains? It's a very small sample, but the finding looked interesting all the same.

 

[Jonathan Edwards]

It's a very small sample, but the finding looked interesting all the same.

that's what I think.

 

[Hutan]

It's disappointing to see Chris using that Vroegindeweij violin chart on hair cortisol. I've discussed those hair cortisol findings here (see also other posts upthread of that one). That Knoop team's study is small and unreliable, and the 12 people with ME/CFS had a mean hair cortisol level well in excess of the controls after a three month behavioural intervention (despite the increases in hair cortisol not being linked to recovery*). Those people were reportedly able to increase hair cortisol levels in response to the challenge of the intervention, but that did not make them well.

Three other studies did not find differences in hair cortisol.

We urgently need a study to see if that finding of CRH neuron loss is replicated. I understand that it seems like a beguilingly neat answer to the problem of ME/CFS, and perhaps it is the answer, but it is very hard to square with an unbiased assessment of the findings on cortisol in ME/CFS.

* ME/CFS group mean hair cortisol level went from 0.49 at baseline to 0.70 post-intervention. Control mean was 0.59. Edited to add: A major difference in participant mean age could account for the lower baseline value in the ME/CFS group.

 

[ScoutB]

Yeah @Hutan I thought of your cortisol thread when that video first came out.

Chris even mentions he'd like people to tell him he's wrong -- I think it just goes to show what a mess the ME/CFS literature landscape is. Claims get repeated over and over in abstracts as truth, giving everyone (esp. newcomers) the impression something is well established, when that's not the case at all. Researchers almost have to conduct their own critical lit review on every fact they want to know about.

I have fantasized of making some kind of mini 'review' on topics like these. It could just be collecting the studies of the cortisol thread into a table summarizing their findings (and whether or not clinically relevant), anything we can say about reliability (incl. sample size), and any other caveats ("morning cortisol could be affected by patients having later waking times"). Could just go in the first post of the thread? Then we could point researchers to that, not as definitive proof of anything, but so they could easily get a sense of the strength of the evidence for themselves...

 

[Kitty]

We urgently need a study to see if that finding of CRH neuron loss is replicated. I understand that it seems like a beguilingly neat answer to the problem of ME/CFS, and perhaps it is the answer, but it is very hard to square with an unbiased assessment of the findings on cortisol in ME/CFS.

Yes, definitely.

But if the finding's real, it might be more complicated than just cortisol levels. Maybe other tissues secrete enough CRH to keep cortisol levels adequate, and the loss of those specific neurons results in a related but different issue.

 

[SNT Gatchaman]

He talks about the fact that according to an analysis someone did, it's the gene that's disrupted most by rare variants; and about its function in helping a molucule (wasnt clear which) to recognise a metabolite of bacteria, which then allows for the activation of gamma delta T cells.

He asks people to say where he is wrong.

Well I won't go as far as to say "wrong" but I would question the point on bacteria metabolites when we're mostly describing viral infection related onset. (Perhaps gut microbial translocation as a secondary effect? Maybe some other effect on gamma-delta Ts?)

But, I would like to re-up this earlier comment from @jnmaciuch, particularly given Multi-omics identifies lipid accumulation in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome cell lines: a case-control study (2026)

though may have implications for butyrophilins in other roles related to lipid membrane regulation

Just to go back to the GeneCards descriptions for BTN2A1 and BTN2A2 —

This gene encodes a member of the immunoglobulin superfamily. The gene is located in a cluster of butyrophilin-like genes in the juxta-telomeric region of the major histocompatibility complex on chromosome 6. A pseudogene of this gene has been identified in this cluster. The encoded protein is an integral plasma membrane protein involved in lipid, fatty-acid, and sterol metabolism.

Butyrophilin is the major protein associated with fat droplets in the milk. This gene is a member of the BTN2 subfamily of genes, which encode proteins belonging to the butyrophilin protein family. The gene is located in a cluster on chromosome 6, consisting of seven genes belonging to the expanding B7/butyrophilin-like group, a subset of the immunoglobulin gene superfamily. The encoded protein is a type I receptor glycoprotein involved in lipid, fatty-acid and sterol metabolism.

 

[ChronicallyOverIt]

The encoded protein is an integral plasma membrane protein involved in lipid, fatty-acid, and sterol metabolism.

This got me thinking, is there a way to link this to @DMissa newest paper? Would the lipid accumulation seen in that paper trigger the BTN2A1 or BTN3A1, thus triggering the T-cells?

 

[Jonathan Edwards]

I cannot track down much about the supposed role of BTN2A1 n lipid metaboism beyond the interesting fact that variants of the gene confer risk for lipid-linked diseases like coronary artery disease.

I suspect that the relevance to T cells is more about shifting thresholds for innate responses generally than about any specific role of bacterial products.

I need to have another think about this. I think a genetic variant could confer risk in two very different ways. It seems that ME/CFS involves an acquired reset of one or more regulatory mechanisms. I think immune and nervous systems are the only likely candidates. So BTN2A1 could be involved in tripping a 'bistable' regulatory pathway into a bad state. T cells would fit for that. But conceivably so might hypothalamic circuits involved in lipid regulation. The one thing that seems against that is no obvious link between ME/CFS and either high or low weight.

The gene variant might, alternatively, simply make a tissue more susceptible once regulation has shifted. That would apply to organ systems that carry the downstream symptom-generating burden. I think nervous system might be the most likely there and it might be something to do with membrane lipid. T cell gamma delta receptors might be a complete red herring.

 

[ChronicallyOverIt]

This got me thinking, is there a way to link this to @DMissa newest paper? Would the lipid accumulation seen in that paper trigger the BTN2A1 or BTN3A1, thus triggering the T-cells?

I’m trying to piece together my idea of linkage. I think there is precedent of T-cells activating in presence of lipid accumulation, but I’m out my depth here:

Human T Cell Receptor γδ Cells Recognize Endogenous Mevalonate Metabolites in Tumor Cells - PMC

T lymphocytes expressing the T cell receptor (TCR)-γδ recognize unknown antigens on tumor cells. Here we identify metabolites of the mevalonate pathway as the tumor ligands that activate TCR-γδ cells. In tumor cells, blockade of ...

pmc.ncbi.nlm.nih.gov

 

[V.R.T.]

Due to the mention of nucleus acumbens on another thread, I googled it and BTN2A1 together on a whim and got this. Not sure if it means anything.

Brain tissue expression of BTN2A1 in nucleus accumbens - The Human Protein Atlas

Expression of BTN2A1 (BT2.1, BTF1, BTN2.1) in nucleus accumbens tissue.

www.proteinatlas.org

 

[Kitty]

If anyone wants to play with the options on the protein atlas, here it is:

BTN2A1 protein expression summary - The Human Protein Atlas

BTN2A1 (BT2.1, BTF1, BTN2.1) protein expression summary.

www.proteinatlas.org

It doesn't seem to have much specificity to brain region or brain tissue type, and in blood it isn't substantially unregulated in disease.

 

[V.R.T.]

I came across this post in the thread for Nath's checkpoint inhibitor trial

I was reading about how btn2a1-inhibitors can be analogous to PD-1 earlier last week, something possibly connected to that genetic hit?

https://synapse.patsnap.com/article/what-are-btn2a1-inhibitors-and-how-do-they-work?

Thread 'Genetics: Chromosome 6 BTN2A2 and BTN3A3 (BTN2A1)'

Aug 7, 2025

DecodeME candidate ME/CFS gene

In DecodeME, we attempted to link GWAS variants to target genes. Here we discuss the top two tiers of predicted linked genes that we are most confident about –‘Tier 1’ and ’Tier 2’.

We defined genes as Tier 1 genes if: (i) they are protein-coding genes, (ii) they have GTEx-v10 expression quantitative trait loci (eQTLs) lying within one of the FUMA-defined ME/CFS-associated intervals, and (iii) their expression and ME/CFS risk are predicted to share a single causal variant with a posterior probability for colocalisation (H4) of at least 75%. For this...

• Hutan
• btn2a2 decodeme gamma-delta t cells genetics t cell receptor t cells
• Replies: 108
• Forum: Possible causes and predisposing factor discussion

• 

 

[mariovitali]

Using the analytical framework I developed over the years and after having as inputs the genes overlapping with Fibromyalgia, here are the outputs :

1) DNA Methylation that @Chris Ponting mentioned comes up as highly relevant
2) Triglycerides come up for some reason as an important concept connecting these genes.
3) Ubiquitination
4) Mevalonate pathway. Note that mevalonate pathway has been identified previously via machine learning analyses :

https://www.s4me.info/threads/machine-learning-assisted-research-on-me-cfs.5015/page-7#post-185951

 

[Chris Ponting]

Thank you to everyone who has commented on the HPA axis-related hypothesis that I put up in a talk in Newry. Good to read the feedback.
Since then I've heard some say that we know cortisol is not differently abundant in pwME vs healthy controls, and others say that it could yet be so. (I pondered on whether we could ask DecodeME folk to send in their hair clippings! But this won't work as we don't have matched control individuals.)
Also, I've heard researchers say that good hypotheses mostly arise from analysing data rather than from what I'm trying, which is a synthesis drawing from different parts of ME/CFS research. I'm trying to use DecodeME's genetic associations as an evidential foundation upon which to build hypotheses. I don't believe that such a resulting "edifice" will necessarily be true/correct, but I do think that possible hypotheses need to be tested against high quality evidence, and when sufficiently contradicted, torn down allowing the whole hypothesis building process to start again. So please bear with me, and help to create, as well as demolish, hypotheses, knowing that even when we alight on the "right one(s)", far from all data will then support it.

 

[V.R.T.]

Thank you to everyone who has commented on the HPA axis-related hypothesis that I put up in a talk in Newry. Good to read the feedback.
Since then I've heard some say that we know cortisol is not differently abundant in pwME vs healthy controls, and others say that it could yet be so. (I pondered on whether we could ask DecodeME folk to send in their hair clippings! But this won't work as we don't have matched control individuals.)
Also, I've heard researchers say that good hypotheses mostly arise from analysing data rather than from what I'm trying, which is a synthesis drawing from different parts of ME/CFS research. I'm trying to use DecodeME's genetic associations as an evidential foundation upon which to build hypotheses. I don't believe that such a resulting "edifice" will necessarily be true/correct, but I do think that possible hypotheses need to be tested against high quality evidence, and when sufficiently contradicted, torn down allowing the whole hypothesis building process to start again. So please bear with me, and help to create, as well as demolish, hypotheses, knowing that even when we alight on the "right one(s)", far from all data will then support it.

Hi Chris, thanks for commenting here - I was wondering if you could expand a little on what you said in the talk about BTN2A1 likely being the gene as opposed to BTN2A2, and what function you think it might have in the mechanism of MECFS?

 

[Chris Ponting]

Hi Chris, thanks for commenting here - I was wondering if you could expand a little on what you said in the talk about BTN2A1 likely being the gene as opposed to BTN2A2, and what function you think it might have in the mechanism of MECFS?

Thanks. Yes, AstraZeneca analysed the UK Biobank and anyone (who self-reported) ME or CFS had significantly more rare DNA variants that disrupted gene function in the BTN2A1 gene than expected (p = 2.4x10^-5), a level of significance greater than for all other protein-coding genes.

Result is here:
https://azphewas.com/phenotypeView/...sZ2ljIEVuY2VwaGFsb215ZWxpdGlzIChNLkUuKQ==/glr

There were 8 (of 2547) pwME with disruptions in BTN2A1, compared with 50 (of 124,470) population controls. Odds-ratio of 7.7 (95% CI 3.6-16.2). Roughly, this is at the level of statistical significance for a single trait so not definitive. But interesting, I feel, given that BTN2A1 lies within the DecodeME chr6p associated locus.

 

[forestglip]

Thanks. Yes, AstraZeneca analysed the UK Biobank and anyone (who self-reported) ME or CFS had significantly more rare DNA variants that disrupted gene function in the BTN2A1 gene than expected (p = 2.4x10^-5), a level of significance greater than for all other protein-coding genes.

Result is here:
https://azphewas.com/phenotypeView/...sZ2ljIEVuY2VwaGFsb215ZWxpdGlzIChNLkUuKQ==/glr

There were 8 (of 2547) pwME with disruptions in BTN2A1, compared with 50 (of 124,470) population controls. Odds-ratio of 7.7 (95% CI 3.6-16.2). Roughly, this is at the level of statistical significance for a single trait so not definitive. But interesting, I feel, given that BTN2A1 lies within the DecodeME chr6p associated locus.

Wow, B2N2A1 was the most significant gene out of around 17,000 genes. That's pretty compelling considering the DecodeME association, as you say.

These are the criteria for included variants for this gene's result:

Model: raredmgmtr

• Missense variants
• Predicted to be damaging (REVEL score ≥ 0.25)
• Rare (minor allele frequency ≤ 0.00025 within the cohort and ≤ 0.00005 within gnomAD)
• Missense variants must fall within a constrained region (MTR < 0.78 or MTR_centile < 0.5)

Edit: I was mistaken about the 17,000 number specifically since it includes duplicates of genes, but also doesn't seem to include genes with no qualifying variants in the cohort. In any case, impressive result.

 

[Jonathan Edwards]

Since then I've heard some say that we know cortisol is not differently abundant in pwME vs healthy controls, and others say that it could yet be so.

I think we know that it is not different enough to explain the clinical picture of ME/CFS.
Moreover, the clinical picture is unequivocally not that of cortisol deficiency (as in Addison's).

I was not clear why the genetics homes in on HPA specifically? It seems to home in on neural mechanisms and we have seen various clues pointing to nociceptor pathways, hypothalamus, anterior ventral cortex, nucleus accumbens etc. but not specifically HPA axis. (And simple things are missing, like hypotension, sodium loss and adrenal atrophy on CT maybe.)

My guess is that there may be a lot of evidence from elsewhere indicating that CRH is not just the lord and master of cortisol production in the way students may be taught. Hypothalamic damage produces a range of clinical pictures including polyphagy with morbid obesity and growth hormone failure but I am not sure that it commonly leads to hypocortisolism. I rather suspect that CRH may have a more subtle role in cortisol regulation and, importantly, other roles, that we tend to ignore. I wouldn't be surprised if CRH knockouts had fairly normal cortisol levels.

So if we take the post mortem findings on CRH cells seriously (but not as gospel), which seems fair, and add in what we know about narcolepsy (where there isn't symptomatic hypocortisolism either) then my guess is that we should be thinking in terms of some other regulatory role of CRH that has been overlooked. that might have to do with sleep cycles, lipid metabolism, leptin, or whatever.

Also, I've heard researchers say that good hypotheses mostly arise from analysing data rather than from what I'm trying

I can assure you, @Chris Ponting, that these people are as wrong as you think they are.

a synthesis drawing from different parts of ME/CFS research

I would recommend going wider still and looking for every clinical experiment of nature that knocks down one or other option until there is barely one left.

even when we alight on the "right one(s)", far from all data will then support it.

My personal experience is that when you alight on the 'right one' all the data does fit (at least if replicable and robust). It fits with an uncanny precision that only real biology could have thought up. When it happened to me I found it hard to believe that a single experiment with 50 qualitative yes/no predictions could come up with 50 bits of fitting data. I thought God was having me on.

For some strange reason I received an email today from a clinical medical student who was attached to my 'firm' 25 years ago. He wanted to thank me for being the first person to teach him something about how scientific problems can be soluble. He remembered that I had said that there were major medical mysteries that could be solved by the students in the room if they put their minds to it, because the data were available. The difficult part is not interpreting your data but repeatedly building and destroying causal models that draw on information from half a dozen fields time and time again until you hit on one that simply doesn't budge. New bits of data feed in to that but chiefly by prompting a new model from a new angle that suddenly makes sense of everything already there.

I guess really I am writing this to try to persuade the amazing citizen scientists who have gathered around the problem just how possible it is to solve the insoluble. There is only one way the biology will fit with the clinical disease we call ME/CFS. And as is said 'nature is subtle but not vindictive'. When someone hits on the right idea it will prove irrefutable.

 

[Hoopoe]

Presumably the defect in ME/CFS is in a part of physiology that has been overlooked so far, or isn't well understood or easily measurable.

I'm looking at this from the angle of personal experience. A good guess is that the defect is related to inability to sustain or recover from exertion, over time periods days to weeks. This seems to be an area of physiology that hasn't been studied as much. I think we need to move away from studying peak power and pretending that single CPETs can tell us something about total exertion of the patient on that and previous days.

What processes allow the body to endure exertion, recover from it and be functional the next morning? What problems make exertion especially hard on the body? These questions might lead us to the defect in ME/CFS.

Now that I've improved, I'm able to do sports, but am still limited by something that I can only describe as exertion intolerance (where exertion includes mental exertion). I've been able to train enough to improve my peak performance and do sports but a defect still persists, where the following days tend to be unpleasant and unproductive. I'm also still unable to work anything near normal hours. I tried because I felt ready, but discovered that gradually my capacity declined. The sustainable level of serious work I can do for 5 days of the week for months is still seriously abnormal.

The default assumption is that patients have intact ability to recover from exertion and can gradually increase their activity. My experience is that if every day I spent a bit more energy reserves than I am able to recover during sleep, then problems will inevitably come. This ability to adapt and recover is defective in some way.

 

[Jonathan Edwards]

Presumably the defect in ME/CFS is in a part of physiology that has been overlooked so far, or isn't well understood or easily measurable.

I think your analysis is on the money.