Genetics: BTN2A2 and BTN3A3

[Hutan]

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 definition, we disregarded the histone genes in the chr6p22.2 HIST1 cluster, as their sequences and functions are highly redundant (1). This prioritisation step yielded 29 Tier 1 genes.

For the intervals without Tier 1 genes, three Tier 2 genes were defined as the closest protein-coding genes without eQTL association: FBXL4 (chr6q16.1), OLFM4 (chr13q14.3), and CCPG1 (chr15q21.3).

CHROMOSOME 6p
Chr6p contained seven Tier 1 genes.

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BTN2A2 (Tier 1)

• Protein: Butyrophilin subfamily 2 member A2. UniProt. GeneCards. The allele that increases the risk of ME/CFS is associated with decreasing BTN2A2 gene expression.

• Molecular function: Mouse Btn2a2 inhibits T-cell activation and promotes the induction of regulatory T cells (Tregs) (31). It also promotes central tolerance to prevent autoimmune disease (32).

• Cellular function: Innate immunity, microbe-sensing.

• Link to disease: Butyrophilins confer immunity against diverse pathogenic bacteria and parasites.

• Potential relevance to ME/CFS: Stoichiometric imbalance of BTN2A and BTN3A levels could alter the ability of Vγ9Vδ2 T cells to discriminate microbial- from self-antigens, and to kill infected cells. Vγ9Vδ2 T cells can be activated by TLR3 and TLR4 ligands. TLR4 variants have been associated with Long Covid in a combinatorial genetics analysis (33).

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BTN3A3 (Tier 1)

• Protein: Butyrophilin subfamily 3 member A3. UniProt. GeneCards.
The allele that increases the risk of ME/CFS is associated with increased BTN3A3 expression in skin not exposed to the sun.

• Molecular function: Co-expression of BTN3A3 synergises with BTN3A1 to greatly boost the efficiency of pAg sensing (42). Confers a chaperone-like function in boosting cell surface expression of BTN3A1 (43).

• Cellular function: Innate immunity, microbe-sensing.

• Link to disease: Butyrophilins confer immunity against diverse pathogenic bacteria and parasites.

• Potential relevance to ME/CFS: Stoichiometric imbalance of BTN2A and BTN3A levels could alter the ability of Vγ9Vδ2 T cells to discriminate microbial- from self-antigens, and to kill infected cells. Vγ9Vδ2 T cells can be activated by TLR3 and TLR4 ligands. TLR4 variants have been associated with Long Covid in a combinatorial genetics analysis (33).



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Reference 31 is
Ammann JU, Cooke A, Trowsdale J. Butyrophilin Btn2a2 inhibits TCR activation and phosphatidylinositol 3-kinase/Akt pathway signaling and induces Foxp3 expression in T lymphocytes. J Immunol. 2013 May 15;190(10):5030–6.

Reference 32 is
Frech M, Danzer H, Uchil P, Azizov V, Schmid E, Schälter F, et al. Butyrophilin 2a2 (Btn2a2) expression on thymic epithelial cells promotes central T cell tolerance and prevents autoimmune disease. J Autoimmun. 2023 Sep;139:103071.

Reference 33 is
Taylor K, Pearson M, Das S, Sardell J, Chocian K, Gardner S. Genetic risk factors for severe and fatigue dominant long COVID and commonalities with ME/CFS identified by combinatorial analysis. J Transl Med. 2023 Nov 1;21(1):775.

Reference 43 is
Vantourout P, Laing A, Woodward MJ, Zlatareva I, Apolonia L, Jones AW, et al. Heteromeric interactions regulate butyrophilin (BTN) and BTN-like molecules governing γδ T cell biology. Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):1039–44.

 

[wigglethemouse]

I think it might be a good idea to add BTN3A3 to this thread @Hutan as they linked the two in the report above. BTN3A3 has increased expression and BTN2A2 has decreased expression.

Potential relevance to ME/CFS: Stoichiometric imbalance of BTN2A and BTN3A levels could alter the ability of Vγ9Vδ2 T cells to discriminate microbial- from self-antigens, and to kill infected cells.

 

[V.R.T.]

Inhibits the proliferation of CD4 and CD8 T-cells activated by anti-CD3 antibodies, T-cell metabolism and IL2 and IFNG secretion.

As we discussed in the preprint thread, the fact this is downregulated and it inhibits CD8 T cells and IFNG might be relevant to JE et al's hypothesis and related theorising.

 

[SNT Gatchaman]

The chr6p22.2 locus includes seven Tier 1 genes, with BTN2A2 and TRIM38 eQTLs colocalised with ME/CFS risk in the most tissues (7 and 5, respectively). Complexes involving butyrophilin3 and -2 homologues (BTN3A1, BTN3A2, BTN3A3, BTN2A1 and BTN2A2) allow innate-like Vγ9Vδ2 T cells to distinguish self-derived from non-self-derived pyrophosphate antigens (pAgs) (47).

[47] is —

A Brief Molecular History of Vγ9Vδ2 TCR-Mediated Phosphoantigen Sensing

Spoiler: Abstract

Vγ9Vδ2 T-cells are universally present in humans and represent one of the most prevalent TCR reactivities, evolutionarily conserved across diverse mammalian species. They are an innate-like subset featuring a semi-invariant TCR repertoire that drives their well-recognized reactivity to small, non-peptidic phosphoantigens (pAg). Crucially, they can distinguish between highly immunostimulatory microbially derived pAg and much less potent host-derived pAg, with the former effectively acting as a pathogen associated molecular pattern (PAMP) and the Vγ9Vδ2 TCR as a surrogate pattern recognition receptor (PRR).

Ample evidence supports important Vγ9Vδ2-mediated contributions to immunity against diverse pathogenic bacteria and parasites, mediated by their potent effector and immunoregulatory functions. The molecular basis of the pAg sensing mechanism underpinning such responses has, however, remained highly mysterious. Despite this, past studies have established that pAg sensing is MHC-independent, extremely fast, exquisitely pAg-sensitive, and dependent upon target cell expression of key BTN-family molecules, notably BTN3A and BTN2A1.

Here we contextualize these findings and several recent studies addressing pAg sensing. We integrate these into a single unified theory of pAg sensing interpretable from different perspectives, both intracellular and extracellular, biophysical, and topological. We prioritize critical questions to address in the context of this proposed model. Finally, we suggest the model will provide a molecular template for antigen recognition by other related γδ T-cell subsets.

Web | PDF | Immunological Reviews | Open Access

See also Butyrophilin 2A1 is essential for phosphoantigen reactivity by γδ T cells (2020, Science)

 

[Hutan]

I think it might be a good idea to add BTN3A3 to this thread @Hutan as they linked the two in the report above. BTN3A3 has increased expression and BTN2A2 has decreased expression.

Thanks Wiggle. Good idea, done

 

[hotblack]

Other s4me threads mentioning these genes

Thread 'Gene discovery and biological insights into anxiety disorders from a large-scale multi-ancestry genome-wide association study, 2025, Friligkou et al'

Jun 22, 2025

Gene discovery and biological insights into anxiety disorders from a large-scale multi-ancestry genome-wide association study

Eleni Friligkou, Solveig Løkhammer, Brenda Cabrera-Mendoza, Jie Shen, Jun He, Giovanni Deiana, Mihaela Diana Zanoaga, Zeynep Asgel, Abigail Pilcher, Luciana Di Lascio, Ana Makharashvili, Dora Koller, Daniel S. Tylee, Gita A. Pathak & Renato Polimanti

[Line breaks added]

Abstract
We leveraged information from more than 1.2 million participants, including 97,383 cases, to investigate the genetics of anxiety disorders across five continental...

• forestglip
• anxiety bipolar depression genetic schizophrenia
• Replies: 15
• Forum: Other health news and research

• 

 

[Hutan]

Regarding the link between these genes and anxiety, the DecodeME results paper says:

Two GWAS (66,67) reported associations to anxiety near BTN2A2. We could not perform coloc analysis because their full summary statistics are not available. However, low LD between lead variants (R2 < 0.05 in the British in England and Scotland [GBR] population) indicate that the genetic signals contributing to ME/CFS and anxiety at the chr6p22.2 locus are distinct.

References to those GWAS looking at anxiety are:

66 Hu J, Lupton MK, Byrne EM, Martin NG, Whiteman DC, Olsen CM, et al. Unravelling Sex Differences in the Genetic Architecture of Anxiety: A Genome-Wide Association Study in the UK Biobank [Internet]. 2025 [cited 2025 Jul 24]. Available from: https://www.medrxiv.org/content/10.1101/2025.02.09.25321968v1

67 Friligkou E, Løkhammer S, Cabrera-Mendoza B, Shen J, He J, Deiana G, et al. Gene discovery and biological insights into anxiety disorders from a large-scale multi-ancestry genome-wide association study. Nat Genet. 2024 Oct;56(10):2036–45.

 

[hotblack]

From the above

The allele that increases the risk of ME/CFS is associated with decreasing BTN2A2 gene expression

Then from another mouse model paper

We found that the human and mouse genes encoding butyrophilin-2A2 (BTN2A2) are regulated by the class II trans-activator and regulatory factor X, two transcription factors dedicated to major histocompatibility complex class II expression, suggesting a role in T cell immunity.

In the Th1 setting, Btn2a2−/− mice developed increased numbers of OVA-specific IFN-γ+ T cells, and these cells produced more IFN-γ after in vitro restimulation (Fig. 2 B).

Btn2a2, a T cell immunomodulatory molecule coregulated with MHC class II genes - PMC

Butyrophilins are proteins secreted during lactation and thought to influence immune function. Sarter et al. generated butyrophilin-2a2–deficient mice to show enhanced effector T cell responses, antitumor responses, and exacerbated EAE due to the ...

pmc.ncbi.nlm.nih.gov

So decreased BTN2A2 means increased interferon gamma from T cells?

 

[Jonathan Edwards]

Mornington Crescent!

 

[Jonathan Edwards]

I rather like the idea that ME/CFS is all down to "regulatory factor X".

 

[Sasha]

I rather like the idea that ME/CFS is all down to "regulatory factor X".

And hot-dog buns!

 

[V.R.T.]

I rather like the idea that ME/CFS is all down to "regulatory factor X".

It has a certain appeal! It sounds like something from an old sci fi film.

This does all look rather relevant to your hypothesis, unless I'm very much mistaken?

 

[hotblack]

This does all look rather relevant to your hypothesis, unless I'm very much mistaken?

Jonathan is obviously better placed and more qualified to respond.

But IMHO it could be but it may not. I doubt they’ll be anything quite as clear and simple, more lots of little things here and there which may slightly shift the balance in favour of whatever is going wrong to happen. Like a finely tuned piece of clockwork machinery but with various cogs slightly off, a little faster or slower or misshapen so the clock tells the wrong time.

So maybe in some people this is one factor which means they’re more likely to end up with the interferon gamma mediated B and T cell conspiracy, maybe not. It’s often possible to find things to suit a hypothesis but that doesn’t mean it’s what is happening or that there aren’t other possibilities. It’s one study, one mouse model, which tbh I found very complicated to read or understand.

So fun as it is to narrow things down maybe it’s wise to also look more broadly and think about other potential mechanisms. We now how evidence of something going wrong immunologically and Jonathan’s theory is one possible mechanism. I’d love it if we could come up with some others

 

[hotblack]

It has a certain appeal! It sounds like something from an old sci fi film.

I suppose we could call our condition Mornington Disease or maybe a study into it the Quatermass Xperiment?

 

[V.R.T.]

Jonathan is obviously better placed and more qualified to respond.

But IMHO it could be but it may not. I doubt they’ll be anything quite as clear and simple, more lots of little things here and there which may slightly shift the balance in favour of whatever is going wrong to happen. Like a finely tuned piece of clockwork machinery but with various cogs slightly off, a little faster or slower or misshapen so the clock tells the wrong time.

So maybe in some people this is one factor which means they’re more likely to end up with the interferon gamma mediated B and T cell conspiracy, maybe not. It’s often possible to find things to suit a hypothesis but that doesn’t mean it’s what is happening or that there aren’t other possibilities. It’s one study, one mouse model, which tbh I found very complicated to read or understand.

So fun as it is to narrow things down maybe it’s wise to also look more broadly and think about other potential mechanisms. We now how evidence of something going wrong immunologically and Jonathan’s theory is one possible mechanism. I’d love it if we could come up with some others

Understood. I certainly didn't think this gene was a definite slam dunk, just something that maybe strengthened the argument for JEs hypothesis. I hadn't realised that the IFNG/CD8 T CellI element was just from that one mouse model paper though.

It would be interesting if we could come up with some other mechanisms. Sadly it's a little beyond me though! Biology was tied with English for my joint best subject at GCSE but my stupid teenage self started smoking in the summer between GSCE and A Level and didn't fancy spending 2 years hearing what a stupid decision that was...

So while I'm relearning enough to spot little patterns in data and (perhaps overenthusiastically) link them to hypotheses, coming up with my own is probably not likely to be very fruitful.

I have to say I would really love something clear and simple though! A nice eureka moment, 'the culprit is factor X, everybody!' Well, I can dream...

 

[hotblack]

I’m also extra cautious of any implications of things I’ve come across, as like you @V.R.T. I didn’t do biology past GCSE, made bad decisions with things like smoking and am learning enough to spot patterns and over-enthusiastically link them to hypotheses!

ME/CFS
M/C
Mornington Crescent… coincidence, I think not

 

[Jonathan Edwards]

things like smoking

Mornington Crescent was where the amazing Art Deco Carreras factory was (now restored).
Coincidences everywhere.

 

[Peter T]

I suppose we could call our condition Mornington Disease or maybe a study into it the Quatermass Xperiment?

Well certainly most of us have had experience of ‘the Pit’.

If only we could unilaterally call ‘Nanan’s Hat’ (sorry an allusion to a word game my goddaughter invented when she was two that is similar to Mornington Crescent which was won when she loudly said ‘Nanan’s Hat’). At present it still feels like a bizarre game for which I/we don’t understand the rules, if there even are any rules, however this research brings hope that the rules may soon be elucidated.