Genetics: Chromosome 6 BTN2A2 and BTN3A3 (BTN2A1)

[Jonathan Edwards]

I’ve definitely seen decent evidence of clonal expansion specifically in psoriatic lesions (not so much the blood), almost entirely Th17 if I’m remembering correctly. I will have to go back to find the specific papers to make sure I’m not misremembering. Don’t know off the top of my head about the other conditions

Yes, there has been a recent story about T cell specificity in skin in psoriasis which may turn out valid, although every other story of this sort over the years has fizzled out as far as I know. The real problem with local sampling I guess is that you don't have any 'normal control' T cell spectra. It may be that if you get loads of T cells in skin then you always get some odd clone that recognises an obscure calcium binding protein or something turning up in droves. There really ought to be some crucial clonal specificity involved but it does seem quite hard to prove - people have been looking in these diseases since the 1990s at least.

TCR analysis methods from the past 10 years are largely unbiased sequencing. So long as you sequence enough cells you can detect and quantify even “rare” memory clones (though you generally won’t know what they target unless you can match the CDR3 sequence to one that is well-validated to bind a specific peptide). Good for finding needles

O but has anyone found much in the way of relevant needles?

I’m not sure subfornical organ would make sense since even that mouse paper from last year showed good T cell exchange between it and the blood.

But that wouldn't guarantee numbers in blood which will be dependent on trafficking in and out in various places. It reminds me of the fact that streoid increase neutrophils in blood, which at first seems backwards because steroids reduce inflammation. But they do so by reducing the efflux from blood to elsewhere.

I would buy the arguments if there were a string of diseases where T cell population roles had now been worked out. I may be behnd the times but I haven't heard of anything much in the diseases I used to work on. Even in MS people are still basing their belief in T cell roles on disanalogous mouse models.

 

[Hutan]

We could do that. These are the variants that passed the genome-wide significance threshold at this locus:

Thank you - the list is now in the first post of the thread.

 

[Jonathan Edwards]

Discussion of other roles for CRH came up on this thread I think. We may need a CRH thread. Nightsong has picked up a paper in Science Signalling - on the miscellaneous research findings thread - that indicates CH may be very relevant aside from an HPA axis role:

CRH is expressed in peripheral tissues outside of the central nervous system (CNS) and directly exerts extensive effects on cardiovascular, reproductive, digestive, and immune systems (15). Gastrointestinal CRH delays the motility of the gastrointestinal tract response to stress and even enhances visceral pain, a predominant feature of irritable bowel syndrome (IBS). Immunostaining has revealed CRH-positive neurons in the DRG and TG, as well as CRH-positive fibers in the superficial layer of the spinal cord and trigeminal complex in the medulla, where the central terminals of primary nociceptive neurons end (16). Under the neuropathic state, CRH expression is increased in damaged DRG neurons; however, whether and how CRH tunes pain signals at the DRG and spinal cord level remains unclear (17).
CRH receptors (CRHR1 and CRHR2) belong to the G protein–coupled receptor (GPCR) superfamily, members of which are widely distributed in nervous and peripheral tissues and integrate the responses of these tissues to various internal and external stimuli. Peripheral CRHR1 and CRHR2 mediate diverse functions in different organs. Pharmacologic data have shown that CRHR1 and CRHR2 play a counteracting role in the occurrence of visceral pain induced by colorectal distention (18). Multiple experimental studies have showed that CRH receptors (CRHR1 and CRHR2) are expressed in primary sensory neurons, the spinal cord, and the trigeminal complex in the medulla under normal and neuropathic pain conditions (16, 19–21). Thus, CRH might act on its receptors to tune the pain signals in the DRG and spinal cord after peripheral nerve injury.
Here, we investigated the function of DRG-localized CRH in persistent and chronic neuropathic pain. Through analysis of public datasets and a mouse model, we found that CRH expression in small- and medium-sized neurons of the DRG is induced in a transcription-dependent manner after peripheral nerve injury and mediates a persistent neuropathic pain state through activation of its receptor CRHR2 on dorsal spinal neurons. The findings reveal potential targets for alleviating neuropathic pain caused by peripheral nerve injury.

 

[V.R.T.]

I also discovered that regulatory T cells express FOXP3 (which has been associated with ME iirc) and need TGF beta to differentiate (develop) from naive CD4+ cells. TGF beta has been flagged once or twice as elevated in ME iirc (I know it was mentioned in JE's hypothesis)

https://www.science.org/doi/10.1126/sciimmunol.aeg4759

Also, this paper posted in misc research looks relevant to this post but I cant read it.

Although the post was discussing BTN2A2 not 1. I'm not sure if BTN2A1 has the same links to FOXP3 and Tregs

 

[forestglip]

CRH is expressed in peripheral tissues outside of the central nervous system (CNS)

But isn't the only clue we have that points to CRH that it may be depleted in the hypothalamus? If anything in those paragraphs is relevant, it must basically depend on CRH being globally affected.

 

[Jonathan Edwards]

But isn't the only clue we have that points to CRH that it may be depleted in the hypothalamus? If anything in those paragraphs is relevant, it must basically depend on CRH being globally affected.

Yes, but that might well be the case. If there is an autoantibody to CRH, for instance. Or, alternatively, excessive CRH expression iin dorsal root ganglia might lead to it being switched off in hypothalamus through a negative feedback loop. It is an indirect pointer but I think it could make sense.

 

[V.R.T.]

Is there any link between CRH, especially in hypothalamus and gamma delta T cells or BTN2A1/2A2 generally?

 

[Jonathan Edwards]

Is there any link between CRH, especially in hypothalamus and gamma delta T cells or BTN2A1/2A2 generally?

Not that I am aware of.

 

[ME/CFS Science Blog]

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

That's really interesting, thanks. Perhaps someone should make a separate thread on this?

There are multiple ways to identify ME/CFS patients in the UK biobank as explained here:
Defining a High-Quality Myalgic Encephalomyelitis/Chronic Fatigue Syndrome cohort in UK Biobank - PMC

Looks like there was also an increased odds ratio for BTN2A1 in the G93.3 ICD diagnosis category but not for another question that asked if participants had CFS.

I think this one refers to the pain questionnaire taken in 2019-2020 which asked: “Have you ever been told by a doctor that you have ME/CFS?” It had a prevalence of 0.46%.
Phenotype: 120010#Ever had chronic Fatigue Syndrome or Myalgic Encephalomyelitis (M.E.)
Odds ratio: 7.68
p-value: 2.35e-5
No. cases with QV: 8/2547 (0.31%)

I think this was from an older questionnaire taken before 2010 where there first was a question: "Have you been told by a doctor that you have other serious illnesses or disabilities?” And then the nurse interviewer asked which ones with 'chronic fatigue syndrome' being one of the options. It has a high prevalence of 1.63%.
Phenotype: 20002#1482#chronic fatigue syndrome
Odds ratio: 2.23
p-value: 0.079
No. cases with QV: 5/2049 (0.24%)

I think this refers to all ICD-10 codes for G93.3 which includes postviral fatigue syndrome, ME and CFS. It had a prevalence of 0.31%.
Phenotype: Union#G933#Postviral fatigue syndrome
Odds ratio: 4.70
p-value: 2.36e-4
No. cases with QV: 9/4369 (0.21%)

Not sure what this is but found that it might refer to ICD-10 code for G93.3 being the main reason for hospitalization. It has a low sample size of only 81 (perhaps because ME/CFS is rarely the primary reason for hospitalisation). Results aren't very useful with such low sample size.
Phenotype: 41202#G933#Postviral fatigue syndrome
Odds ratio: 27.9997
p-value: 0.0357
No. cases with QV: 1/81 (1.23%)

 

[ME/CFS Science Blog]

What I don't quite get:

ME/CFS symptoms suggest a disease of T-cell activation
BTN2A1 is involved in activating the T-cell
ME/CFS patients are more likely to have defective BTN2A1
So that doesn't fit with T-cells being overactive after all?
Rather it suggests that at certain times the T-cells of ME/CFS don't get activated while they should.

 

[forestglip]

ME/CFS patients are more likely to have defective BTN2A1

Do we have reason to think it is defective?

As I said previously, I don't think rare missense mutations necessarily imply the protein is "defective". Maybe it is working too well.

 

[ME/CFS Science Blog]

Do we have reason to think it is defective?

Would be my guess: there are many more ways to mess things up than ways to make something work. But you're right that we're not sure of this.

 

[forestglip]

Would be my guess: there are many more ways to mess things up than ways to make something work. But you're right that we're not sure of this.

I agree it intuitively seems more likely for it to impair function.

I'm not sure if there's anything we can do with it, but the qualifying variants in the BTN2A1 gene in the ME/CFS group are listed here: https://azphewas.com/QVView/6319c06...9a8d3d-b11a-4b5d-a129-4327844bcfb1/binary/EUR

To be on par with controls where 0.04% of participants had a qualifying variant, by my calculation, we'd expect around 1 case to have a qualifying variant, but there were 8 cases.

Spoiler: Variants

rsID	Variant	Variant type	Consequence type	Transcript	cDNA change	Amino acid change	Exon rank	Hetero Genotype Cases	Homo Genotype Minor Cases	Case MAC (minor allele count)	Hetero Genotype Controls	Homo Genotype Minor Controls	Control MAC (minor allele count)
rs759384611	6-26468394-C-T	snv	missense_variant	ENST00000312541	c.1429C>T	p.Arg477Cys	8/8	2	0	2	6	0	6
rs775467403	6-26466088-G-A	snv	missense_variant&splice_region_variant	ENST00000312541	c.982G>A	p.Val328Ile	7/8	2	0	2	11	0	11
rs775510675	6-26468013-G-A	snv	missense_variant	ENST00000312541	c.1048G>A	p.Val350Met	8/8	1	0	1	0	0	0
rs747776228	6-26468421-C-A	snv	missense_variant	ENST00000312541	c.1456C>A	p.Pro486Thr	8/8	1	0	1	0	0	0
rs774533122	6-26465188-C-T	snv	missense_variant	ENST00000312541	c.716C>T	p.Ser239Phe	5/8	1	0	1	3	0	3
rs764085206	6-26458679-C-T	snv	missense_variant	ENST00000312541	c.43C>T	p.Leu15Phe	2/8	1	0	1	7	0	7

Edit: Added rsIDs.

 

[Jonathan Edwards]

ME/CFS symptoms suggest a disease of T-cell activation
BTN2A1 is involved in activating the T-cell
ME/CFS patients are more likely to have defective BTN2A1
So that doesn't fit with T-cells being overactive after all?

It's a valid point but I think there are various ways it could make sense. The BTN2A1 variants might not discriminate between intracellular phosphate-linked lipids as well s they should. They might engage in interactions with T cells that trigger other 'danger/misfit' responses. And T cells can come in plus and minus types (minus being Treg) although that might be relevant to this interaction.

We are looking for an interaction that breaks the normal rules more or less by definition. It would be interesting to know more about where the mutations are in relation to protein sequence.

 

[ChronicallyOverIt]

Hey all, I’m still really interested in how this could link to the potential lipid accumulation that dmissa reported, even though I know it’s not 100% fact since it’s immortalized cells, and dmissa was clear we could not trust those results.

I still ran it by AI a few times… I know it’s probably just slop, but it seems pretty interesting since it would be hard to detect outside the cell level, involves BTN, and gamma tcells. I’d just thought I’d post since I don’t have the depth to call bs on Gemini. Feel free to ignore it if it’s slop. I just really thought those two things could be connected. I can delete if it’s absolute garbage.

Spoiler: AI slop of my idea

The ME/CFS "Bistable Trap" Mechanism: A Step-by-Step Outline


1. The Metabolic Stall and Lipid Hoarding


Following an initial trigger (such as a severe viral infection), the patient's cellular metabolism breaks down. Recent multi-omics studies of ME/CFS cells reveal a massive accumulation of triglycerides and saturated fats, alongside the hyperactivation of specific membrane-remodeling enzymes like PTDSS1.[1]


2. The Mevalonate Bottleneck


This cellular dysregulation leads to a highly specific roadblock in the mevalonate pathway—an essential metabolic assembly line used to synthesize cholesterol, coenzyme Q10, and dolichol. Because the pathway is jammed (likely at an enzyme known as FPPS), normal metabolic production halts.


3. The Toxic "Danger Signal" Buildup


With the mevalonate pathway blocked, a specific upstream building block called isopentenyl pyrophosphate (IPP) begins to back up.[2] IPP pools to massive, unphysiological levels inside the cell, acting as a marker of severe cellular distress.[3]


4. The "Molecular Glue" Sensor


The immune system uses a receptor complex made of two proteins, BTN3A1 and BTN2A1, to monitor internal cellular health. When IPP accumulates to toxic levels, it acts literally as a "molecular glue" inside the cell, tightly locking the interior domains of BTN3A1 and BTN2A1 together.[4, 5]


5. The Extracellular Alarm


This rigid internal locking forces a mechanical shift that propagates to the outside of the cell membrane.[4] The shift exposes previously hidden regions of the BTN proteins, creating a "composite ligand" that acts as a permanent biochemical flag waving on the surface of the distressed cell.[4, 6]


6. The Bistable Trap and Immune Exhaustion


A highly specialized subset of immune cells, called Vγ9Vδ2 T cells, are hardwired by evolution to recognize this specific BTN3A1/BTN2A1 alarm.[7] Under normal circumstances, they would kill the infected cell. However, because this is a sterile metabolic misfire, the danger signal never turns off. Years of relentless, futile engagement with this continuous alarm metabolically cripples the T cells, driving them into a state of severe, terminal immune exhaustion. The patient is left locked in a self-sustaining loop of broken cellular energy and burnt-out immunity.

 

[ME/CFS Science Blog]

Perhaps someone should make a separate thread on this?

Made a thread on the Astrazeneca analysis here:

Thread 'Astrazeneca Phewas analysis using the UK biobank'

May 4, 2026

Chris Ponting mentioned this in this thread:

The result can be viewed here:
https://azphewas.com/phenotypeView/...sZ2ljIEVuY2VwaGFsb215ZWxpdGlzIChNLkUuKQ==/glr

• ME/CFS Science Blog
• btn2a1 uk biobank
• Replies: 18
• Forum: ME/CFS research

• 

 

[Adrian]

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.

I find it really encouraging that AstraZeneca is looking and doing some work on ME.

 

[forestglip]

The AstraZeneca study used the entire UK BioBank and all the hundreds of phenotypes it contains, so they didn't specifically focus on ME/CFS.

 

[neophyte32]

The AstraZeneca study used the entire UK BioBank and all the hundreds of phenotypes it contains, so they didn't specifically focus on ME/CFS.

Thank you, too bad, false hope.

 

[jnmaciuch]

What I don't quite get:

ME/CFS symptoms suggest a disease of T-cell activation
BTN2A1 is involved in activating the T-cell
ME/CFS patients are more likely to have defective BTN2A1
So that doesn't fit with T-cells being overactive after all?
Rather it suggests that at certain times the T-cells of ME/CFS don't get activated while they should.

Im inclined to agree. It’s theoretically possible that a given mutation increases protein activity. But in the AZ data it’s multiple different mutations across the protein. The majority seem to be concentrated in the PRY-SPRY domain.

Mutations to the BTN2A1 linker region impact its homodimerization and its cytoplasmic interaction with phosphoantigen-bound BTN3A1 - PMC

Intracellular binding of small molecule phosphoantigens to the HMBPP receptor complex in infected cells leads to extracellular detection by T cells expressing the Vγ9Vδ2 T cell receptor, a non-canonical method of antigen detection. The butyrophilin ...

pmc.ncbi.nlm.nih.gov

This study analyzed the functional effect of some mutations in BTN2A1, unfortunately not the same ones as in the AZ analysis. The two mutations tested in the same general region of the protein blocked gdTCR stimulation.

Phosphoantigens glue butyrophilin 3A1 and 2A1 to activate Vγ9Vδ2 T cells - Nature

Phosphoantigen-mediated BTN2A1 association drives BTN3A1 intracellular fluctuations outwards in a thermodynamically favourable manner, thereby enabling BTN3A1 to push off from the BTN2A1 ectodomain to initiate T cell receptor–mediated γδ T cell activation.

www.nature.com

This paper seems to suggest that unlike BTN3A1, BTN2A1 doesn’t have a binding “pocket” for antigen in that region. Best as I can tell, those corresponding regions on the two proteins seem to bind to each other, with the antigen lodged in BTN3A1 and BTN2A1 homodimerizing and then attaching across like a Tupperware lid. The combined BTN2A1/BTN3A1 complex is what stimulates the gdTCR.

One of the AZ analysis mutations is a proline to threonine substitution. I am no protein structure expert but from my meager knowledge, that seems like it would substantially alter protein shape near a critical binding region. So like I said, theoretically possible that all those mutations create a more “sensitive” protein, but in general seems much more likely that they blunt functionality. In which case the predisposition to ME/CFS might be something more like impaired ability to induce early cell killing during infection (which might get compensated for in other ways). Or, maybe even more likely, it has to do with an as-of-yet unknown function of homodimerized BTN2A1