Is the key pathology of ME/CFS in bone marrow?

[jnmaciuch]

I wonder if it is possible for haemopoietic stem cells to acquire mutations in non-coding DNA near Xist or some of these signalling genes that override the normal X inactivation of one X and this gets passed on to daughter cells. The result would be a bit like paroxysmal nocturnal haemoglobinuria where stem cell clones lose expression of CD55 (a complement inactivator) so that red cells are produced that lyse more easily. The clones appear spontaneously in midlife.

Is it even conceivable that in ME/CFS there are rogue clones like this simply overdosing the interferons pathways in such a way that they can be generated locally without due cause?

I like the thinking here, though the concern with a hard coded mutation is that it's harder to explain some of the temporal dynamics. Not impossible, but makes less sense to me than an epigenetic alteration. The explanation for remission would have to be a drop in clone numbers and vice versa for worsening of disease. My sense is that if this mechanism wasn’t something that lead to fatal complications like hemoglobinuria, we’d see much more sporadic worsening and improvement throughout the illness simply due to stochastic fluctuations in clone frequencies.

Epigenetic regulation would fit better to explain both pwME with unchanging disease severity for years, and those with changes due to exertion, infection, or some other processes that happen to involve relevant regulatory pathways.

Epigenetic changes might of course do the same thing more reversibly?

The reason I've been more inclined towards an epigenetic explanation involving interferon is because it would explain both baseline symptoms (from increased transcription of certain ISGs even without canonical interferon stimulation) plus it would prime the pathway to overreact to normal transient stimuli that induce an interferon response, potentially explaining PEM. A disease where baseline symptoms are solely mediated by ISGs themselves would bypass any need to explain the lack of other cytokines from canonical signaling pathways.

A reversible epigenetic change could be maintained long term provided that the signaling pathway gets stimulated often enough, keeping those chromatin regions open. If that stimulation can be achieved by a biological process that happens all the time, like neuron firing or muscle twitching, then you have a solid feedback loop. That's my thought behind calcium flux-mediated mtDNA release and type I interferon signaling via cGAS-STING or TLR9.

 

[jnmaciuch]

Plus mtDNA release through VDAC could absolutely also mean mtRNA release, implicating TLR7 and 8. [edit: Transiently, which would address prior objections about a lack of other cytokine signatures when measured at baseline]

 

[Jonathan Edwards]

And of course I forgot to mention that these clones with drifted genetic/epigenetic programmes may have some growth advantage and become more established with time (as in mitochondrial myopathies) but could conceivably be less good at surviving certain environments and sometimes regress. The latter always seems to happen less often in disease but then again we may miss it.

The other analogy here is MGUS (monoclonal gammopathy of unknown significance) which is a B cell clone that is too busy but not malignant, although it can precede myeloma. The only suggestion I have seen for an increased incidence of malignancy in ME/CFS is B cell lymphoma and I find it hard to link that in.

 

[Hutan]

Main transcription factors upstream of TLR7 (that regulate its gene expression):

• IRF7
• IRF8
• STAT1/STAT2/IRF9 (ISGF3)
• NF-κB
• PU.1
• C/EBPβ
• ERα

Epigenetic regulation would fit better to explain both pwME with unchanging disease severity for years, and those with changes due to exertion, infection, or some other processes that happen to involve relevant regulatory pathways.

There was that (unfortunately very small) Peppercorn 2025 paper that looked at differentially methylated fragments of genes in ME, LC and healthy controls.

STAT5A was found to be hypermethylated in both the LC and MC cohorts compared to the healthy controls. The hypermethylation means the gene is down regulated, there's less expression of it. STAT5A seems to have some female specific roles (it's involved in mammary gland development and milk production). But it also seems to engage (often with other STATs) in immune functions.

Throwing this into the mix:
Differential Contributions of STAT5A and STAT5B to Stress Protection and Tyrosine Kinase Inhibitor Resistance of Chronic Myeloid Leukemia Stem/Progenitor Cells

That 2013 study reported that STAT5 has a crucial role in hematopoietic stem cell maintenance, specifically the protection of the cells from various stresses.

Collectively, our results indicated that STAT5A exhibits the restricted property to limit .. normal stem/progenitor cell stress, independently of its canonical transcriptional activity. In line with these data, STAT5 downregulates ROS production in pre-B leukemic cell lines, in absence of detectable STAT5 tyrosine phosphorylation... Moreover, SRC/ABL kinases differentially affect nuclear translocation of STAT5A and STAT5B; accumulation of ROS correlates with reduced STAT5A—but not STAT5B—activity in aged macrophages; STAT5A shows differential tetramerization potential and selective posttranslational modifications

So, reduced expression of the STAT5A gene could be resulting in poorly functioning immune cells.

STAT5A has plenty to do with interferon.
STAT5 Contributes to Interferon Resistance of Melanoma Cells

The overexpressed STAT5 diminished IFNα-triggered STAT1 activation, most evidently through upregulation of the inhibitor of cytokine-signaling CIS.

So, increased expression of STAT5 was reported as reducing Interferon A triggered STAT1 activation.

However, if STAT5 expression is reduced in ME/CFS, as suggested by the Peppercorn finding, then there might not be that brake on Interferon A triggered STAT1 activation.

 

[Jonathan Edwards]

So, increased expression of STAT5 was reported as reducing Interferon A triggered STAT1 activation.

However, if STAT5 expression is reduced in ME/CFS, as suggested by the Peppercorn finding, then there might not be that brake on Interferon A triggered STAT1 activation.

It looks like the sort of thing you could build a story about every which way. However, if there were a block to one pathway downstream of interferons and not another, that might make some sense, especially if there was also a shift in negative feedback signals such as TGF beta.

 

[V.R.T.]

STAT5A seems to have some female specific roles (it's involved in mammary gland development and milk production).

Could this potentially tie in with the BTN2A2 hit in DecodeME? According to JE's comment here it is expressed in 'breast epithelial cells and milk fat globule membrane'

I have tried to get it bit more information on BTN2A2 / its butyrophyllin protein.

It appears to be an MHC Class I protein. It is not a typical antigen presenting Class I protein as in HLA-A, -B and -C but it is a transmembrane protein of the same immunoglobulin supergene family. It also appears to be quite widely expressed on antigen presenting cells, as are both Class I and II. That includes expression on thymic epithelial cells, which interact specifically with T cells in triage by antigen recognition. It also includes breast epithelial cells and milk fat globule membrane, which expresses other MHC proteins like DR, presumably as part of some sort of immune signalling to fetus, along with maternal antibody transfer. (I remember in 1979 when my brother suggested I looked for HLA-DR [then called IA] in synovium because it was involved in immune response he [a breast tissue biologist] was chuffed because he had heard it was on milk fat globule membrane.)

So although this protein is pretty widely distributed, that is pretty standard for MHC molecules that function via interactions with T cells. Apparently some T cells express BTN2A2 but again, they do for other MHC.

The reviews talk of roles in moderating T cell functions like gamma interferon production. Some focus on regulatory T cells and some on gamma delta. My impression is that the interaction is fairly general. But I have not yet found suggestions that BTN2A2 does much else. I risk from a gene like this would certainly fit with the gist of the model Jo C, Jackie and I suggested - the FcRI aspect was only ever a way to try to make the model consistent with female predominance.

This analysis may be wrong but to me the gene looks like a very important clue. I was initially excited by the idea that DecodeME might have found an HLA link. That turned out to be a bit of a false start, although there still seems to be a suggestion of DQ. But in some ways BTN2A2 looks more relevant because it looks to be involved in a rather general 'innate' signalling mechanism to T cells (in the sense of not being tied to any particular peptide, which seems to me problematic).

I have juat read that this pathway is implicated in a bunch of different cancers, and I have heard cancer is more common in pwME a few times but havent seen study evidence afaik.


Also is this the same Peppercorn study that we (iirc you in particular) had loads of problems with the methodology of?

I suppose if this was the case it might suggest JAK STAT inhibitors as a potential treatment.

 

[V.R.T.]

It looks like the sort of thing you could build a story about every which way. However, if there were a block to one pathway downstream of interferons and not another, that might make some sense, especially if there was also a shift in negative feedback signals such as TGF beta.

I cant remember, do we have evidence of altered TGF beta in ME/CFS?

 

[Jonathan Edwards]

I cant remember, do we have evidence of altered TGF beta in ME/CFS?

It is the one cytokine that did seem to crop up in blood studies more than others (Reviewed by White I think) but I wouldn't put a lot of weight on that.

 

[arnoble]

Epigenetic regulation would fit better to explain both pwME with unchanging disease severity for years, and those with changes due to exertion, infection, or some other processes that happen to involve relevant regulatory pathways.

I really like the ideas in your post #161 - but what part does bone marrow play?

 

[ryanc97]

I wonder if it is possible for haemopoietic stem cells to acquire mutations in non-coding DNA near Xist or some of these signalling genes that override the normal X inactivation of one X and this gets passed on to daughter cells. The result would be a bit like paroxysmal nocturnal haemoglobinuria where stem cell clones lose expression of CD55 (a complement inactivator) so that red cells are produced that lyse more easily. The clones appear spontaneously in midlife.

Is it even conceivable that in ME/CFS there are rogue clones like this simply overdosing the interferons pathways in such a way that they can be generated locally without due cause? Finding such clones would be a very good way to counter the suggestion that disease perpetuation is just due to negative thinking (Dr Garner)! Epigenetic changes might of course do the same thing more reversibly?

I understand none of these words.

 

[arnoble]

I understand none of these words

I find ChatGPT gives me a very useful leg-up with passages like those.

 

[jnmaciuch]

I really like the ideas in your post #161 - but what part does bone marrow play?

Sorry for the confusion--I was just tying together the general ideas of epigenetic dysregulation and abnormal activity happening in a specific niche that would explain lack of particular findings in the blood. Not specifically talking about bone marrow there, I'm just referencing a hypothesis I've been developing for a while related to muscle and brain tissue.

The bone marrow story is hard to make sense of in my opinion, largely because there are very few options that wouldn't have already shown some indication in screens of circulating cells.

 

[jnmaciuch]

STAT1 / STAT2 / IRF9 complex (ISGF3) is something that caught my attention before when I made this thread:

Post in thread 'Unphosphorylated ISGF3 drives constitutive expression of interferon-stimulated genes to protect against viral infections, Wang et al. (2017)'

Sep 30, 2025

What causes the "...simultaneous overexpression of all ISGF3 components..."?

That sentence in the abstract references an experiment where they artificially caused overexpression of those genes to see if it was the complex formed by all three proteins that mediated these effects or just one of its component parts.

If you meant what could cause higher expression of those components in a biological context, unfortunately we don't have an answer. Most likely, all three genes are under the control of one transcription factor. What causes that one transcription factor to be continuously...

• jnmaciuch

• 

Long story short, this is a protein complex that acts downstream of interferon signaling, but it has been observed to be upregulated and capable of inducing expression of several genes in multiple cell lines and tissue cultures, independent of upstream interferon stimulation. Which provides evidence of some common epigenetic mechanism capable of stimulating production of this complex and causing increased transcription of interferon-stimulated genes long term under certain conditions. I'm currently interested in confirming whether this is something that can also be observed in-vivo as well.

But the link to TLR7 provides the perfect structure for a feedback loop: ISGF3 induces expression of nucleic acid TLRs, and TLR signaling stimulates interferon pathways which encourage more transcription of ISGF3 (and would maintain the epigenetic regulation). The trick would be figuring out exactly what inhibitory pathways prevent this loop from occuring in healthy people.

If there's any merit to this idea, hopefully some of the LC trials on JAK-inhibitors will pan out (assuming they're not falling into the trap of selecting an extremely heterogenous patient population). Though some medications in that class have a reputation for paradoxically increasing interferon signaling (at least for a few months).