Uncovering the genetic architecture of ME/CFS: a precision approach reveals impact of rare monogenic variation, 2025, Birch, Younger et al

[Jonathan Edwards]

Agree with post #169 @jnmaciuch .

 

[LizWorthey]

I have a pathogenic variant on one allele of the ACADM gene. I've also had some issues with hypoglycemia which would fit.

The conventional wisdom says that, even if this would lead to a loss of about half of enzyme activity, one defective allele is not enough to cause clinically significant disease. Since ACADM deficiency has been studied extensively in the population this is probably true, but I'm wondering if this mutation could be causing problems when its effects combine with other things.

What is your evidence for this belief? I find it a rather extraordinary and unlikely claim that so many different diseases could cause post exertional malaise and all of these different pathologies could go completely undetected.



What criteria are you referring to here? Surely most sensible people now agree that the presence of PEM is the central defining feature of ME/C\FS, rather than any other symptoms.

Thank you for engaging here.

Sadly diseases often go undiagnosed despite tell tale signs. I've worked in the field of rare disease for 16 years. And so often the symptoms are clear, but the

Agree. High genetic heterogeneity is only a problem is there is high downstream causal heterogeneity. If a huge number of genes have potentially a small impact on the pathological mechanisms, but the mechanisms are conserved, the focus should be on those mechanisms. Now metabolomic, RNA and proteomic sequencing are still relevant until we have identified and understood the mechanisms.

A few of our thoughts on why it can be multiple diseases converging on shared mechanisms and symptoms. Situations where large or small impacts in many diff genes causing the same symptoms are seen. Even though people don't always look in this way. Diabetes is an example; the same picture can stem from single gene disease (HNF1A/HNF4A/GCK/HNF1B) or be complex/polygenic/environmental or not known. Similar “many paths, one phenotype” patterns occur in e.g. dementias and hypercholesterolemia.

This would explains why things that really help some patients (mito cocktails/oxaloacetate) don't help others. When you have a heterogeneous patient group and you look for something that is present, but is only seen in a subset of patients; the noise would drown out the signal. PEM really is seen in many conditions; probably dozens so we used other terms - again all in the paper. LMK if you need me to add here. We did try to put some of these hypotheses in the paper - had to cut out a lot due to size.. but the supplemental will lay out some of the thinking.

 

[LizWorthey]

On Twitter, many of us have placed our trust in Amatica and its RNA sequencing. I know it's not popular here, but we have 120 patients with LC and MECFS and 60 controls. It's a start. In one month we will have the data.
In any case, the results of this study are frightening... this heterogeneity is truly problematic.

Happy to collaborate here if that is of interest... We have the ability to analyse RNA data and would be happy to share what we have. We conducted a lot of this work off our own funds - we are in this as scientists and affected individuals.

 

[LizWorthey]

Sadly diseases often go undiagnosed despite tell tale signs. I've worked in the field of rare disease for 16 years. And so often the symptoms are clear, but the



A few of our thoughts on why it can be multiple diseases converging on shared mechanisms and symptoms. Situations where large or small impacts in many diff genes causing the same symptoms are seen. Even though people don't always look in this way. Diabetes is an example; the same picture can stem from single gene disease (HNF1A/HNF4A/GCK/HNF1B) or be complex/polygenic/environmental or not known. Similar “many paths, one phenotype” patterns occur in e.g. dementias and hypercholesterolemia. This would explains why things that really help some patients (mito cocktails/oxaloacetate) don't help others. When you have a heterogeneous patient group and you look for something that is present, but is only seen in a subset of patients; the noise would drown out the signal. PEM really is seen in many conditions; probably dozens so we used other terms - again all in the paper. LMK if you need me to add here. We did try to put some of these hypotheses in the paper - had to cut out a lot due to size.. but the supplemental will lay out some of the thinking.

We do have another patient with ACADM and two with HADHA (including me). Would you be interested in chatting more on this?

 

[LizWorthey]

I add my thanks to @LizWorthey for joining us to discuss your research and answer questions. I hope you will stick around and join in other research discussions here relevant to your field of research when you have time too.

Yes happy to do so. I didn't know you all had this; it's great! I have been on a bit of a crash and have the flu so will only be in stops and starts.

 

[LizWorthey]

I am not sure if this is relevant, but I think KCNJ18 is a potassium ion gene, as is KCNJ2. They certainly sound similar. Mutations in KCNJ2 are massively pathogenic. We are talking about a major channelopathy when the KCNJ2 variation is at play.

Yes. If you look at the KCNJ18 literature (there isn't a tonne I know); it talks about these variants as being deleterious but as a risk factor essentially. Not all (any?) variants seem to be capable of causing disease outright without other factors such as thyroid dysfunction/illness. Symptoms come perhaps only with the combination of illness, strenuous exercise/other stress, and thyroid dysfunction and only last for a period of time, which can vary amongst people depending on the degree of the different factors.

 

[LizWorthey]

Thanks for all your work on this and your explanations, @LizWorthey, and welcome!

I don't know enough about genetics to contribute, really—except, I guess, to say that the Fukuda criteria ought to have been binned 25 years ago. The sooner researchers make a positive decision to stop using it, the better defined their cohorts will be.

The problem is that it doesn't require PEM, so it doesn't describe ME/CFS. It also allows people to pick and choose from a menu of symptoms, meaning it's too inclusive to be of any practical use. It has led to a lot of research money being wasted—no one can rely on the results of studies on groups that could have had any one of a dozen fatiguing illnesses.

Look forward to hearing more about your work, though!


ETA: cross posted with @V.R.T.

Gotcha. Sorry for the confusion there! Yes; we did the work to make that exact point of how permissive the symptom criteria are (110,000 poss combinations). In our pilot everyone did meet the Canadian Consensus Criteria criteria and they all did have PEM.

 

[Verity]

PEM really is seen in many conditions; probably dozens

Can you tell us what you’re basing this on?

 

[LizWorthey]

Perhaps a rare variant could be useful information but the method in that paper is unlikely to point us to the useful ones. From the replies it’s clear that it was starting with the hypothesis that there is no one such entity known as ME/CFS, and seeing whether symptoms could be alternatively explained by rare variants. Then they combed a person’s genome for rare variants where the monogenic illness matches some of the person’s ME/CFS symptoms, and are essentially interpreting that to mean that being heterozygous for that variant is the more likely cause of symptoms than the people in their cohort having the same acquired disease process. We need an approach like SequenceME to yield any useful information from rare variants

I’d respectfully say that going deep on each individual - looking for trends across both rare and common variants, is the right approach when rare variants may drive a given case. Which I 100% believe to be the case in some people (probably just a fraction). Going deep is what SequenceME is doing and what we did too - the strategy is the same, their scale is wonderfully larger because they’ve attracted the necessary funds. We just can't only look for more common signals. My back-of-the-envelope estimate is that, given heterogeneity, you’d need tens of thousands of cases and same for controls per arm to detect a robust burden signal for a set of rare variants. In the meantime, we can still pursue answers for individual patients by going one by one. If we see nothing of interest; no harm, no foul as long as we don't oversell. If we see something interesting then we need to get that out there; through peer review processes of course; not interested in snake oil.. And even if someone has a common cause finding the rare causes will be very helpful; as they have been in other diseases e.g. dementias.

 

[LizWorthey]

Can you tell us what you’re basing this on?

I know folks will chime in if I'm a bit out of the norm on how I think about PEM since many of you have been thinking about it longer. I mean the delayed post-exertional worsening of symptoms. So I'd count things that are/might "be" ME/CFS like diagnoses of dysautonomia, POTS, or hypermobile EDS/HSD, fibromyalgia. But it is also seen in some autoimmune and inflammatory disorders like Hashimoto’s, SLE/Sjögren’s, inflammatory myopathies as well as perhaps mast cell activation syndrome. The same pattern can also be seen with MS and OXPHOS defects, fatty-acid oxidation disorders, glycogen pathway defects like McArdle's. Might also include certain skeletal muscle channelopathies/periodic paralyses. That trend is also seen in some patients with iron or B12/folate deficiencies and erythrocyte membrane disorders. Something very similar is also seen in cases with certain arrhythmias or cardiomyopathies. You might also include things like adrenal insufficiency, diabetes dysregulation, and hypokalemia disorders states; they can also "mimic"or "be" PEM. Could have more of a fine grained discussion on how people specifically define PEM; that might help me get on the same page as everyone if they think I'm crazy here

 

[jnmaciuch]

I’d respectfully say that going deep on each individual - looking for trends across both rare and common variants, is the right approach when rare variants may drive a given case. Which I 100% believe to be the case in some people (probably not all). Going deep is what SequenceME is doing and what we did too - the strategy is the same, their scale is wonderfully larger because they’ve attracted the necessary funds. We just can't only look for more common signals. My back-of-the-envelope estimate is that, given heterogeneity, you’d need tens of thousands of cases and same for controls per arm to detect a robust burden signal for a set of rare variants. In the meantime, we can still pursue answers for individual patients by going one by one. And even if someone has a common cause finding the rare causes will be very helpful.

But the crucial difference between an individualistic approach and SequenceME is that being able to show a quantitative difference in cases versus controls actually lets you make a conclusion about the relevance of the variant, whereas linking the variant to common symptoms does not (though it might appear to).

Like I already said in the paper's thread, what you'd need to show is that if you took people with e.g. lupus or MS and searched for variants that in their homozygous state were associated with specific symptoms, would you nearly always be able to find seemingly relevant heterozygous variants in a subset of your cohort even when we know that those symptoms would present regardless of genetic background?

Without any sort of control it just leaves the likely possibility that these pathways are only coming up repeatedly because you're searching for variants associated with some of the more specific symptoms of ME/CFS like muscle weakness, even though there's a pretty good chance they simply might not be relevant at all to the person's symptoms (especially when several of the "likely pathogenic" heterozygous variants really only have very weak evidence--one or two case studies specifically highlighted for being unusual--showing that the heterozygous variant ever presents with the same symptoms as the homozygous state).

I understand I'm coming off as overly skeptical here, but I really would be happy to accept it if there was more evidence that the core assumptions of the individualistic approach are valid. And I'd be very excited if your team was able to contribute to something like SequenceME!

 

[LizWorthey]

But the crucial difference between an individualistic approach and SequenceME is that being able to show a quantitative difference in cases versus controls actually lets you make an assumption of relevance of the variant, whereas linking the variant to common symptoms does not (though it might appear to).

Like I already said in the paper's thread, what you'd need to show is that if you took people with e.g. lupus or MS and searched for variants that in their homozygous state were associated with specific symptom, would you nearly always be able to find seemingly relevant heterozygous variants in a subset of your cohort even when we know that those symptoms would present regardless of genetic background?

Without any sort of control it just leaves the likely possibility that these variants are only coming up repeatedly because you're searching for variants associated with some of the more specific symptoms of ME/CFS like muscle weakness, even though there's a pretty good chance they simply might not be relevant at all to the person's symptoms (especially when several of the "likely pathogenic" heterozygous variants really only have very weak evidence--one or two case studies specifically highlighted for being unusual--showing that the heterozygous variant every presents with the same symptoms as the homozygous state).

I understand I'm coming off as overly skeptical here, but I really would be happy if there was more evidence that the core assumptions of the individualistic approach are valid. And I'd be very excited if your team was able to contribute to something like SequenceME!

I really appreciate the debate TBH; it's how science should work. And totally agree-large cohorts are essential to test hypotheses, but IMHO when an individual carries a known pathogenic variant that explains all of their phenotype, we shouldn’t just ignore it just because it’s rare. ME/CFS presentations are heterogeneous; assuming a uniform cause at any point in setting up an experiment risks averaging away real biology.

A back-of-the-envelope calculation from a broad "all cause" (complex and Mendelian genetic) diabetes cohort - you might need on the order of 70,000 cases and 70,000 controls to detect all the genes associated with rare monogenic contributors at usual genome-wide significance levels. The population averages would just bury real signals that are highly relevant for a subset of patients. And knowing the rare causes helps with the complex ones too.

Too often, biomedical disease studies report “no overall effect,” where if you go look you see their plots show large shifts in a minority of participants. Or that claim a group difference - where if you look you see it is driven by a couple of outliers. This is all over in ME/CFS studies; I've been looking. If genetic factors underlie a subset of ME/CFS (and we 100% believe they do), those individuals aren’t noise; they’re critical leads. The path forward is to pair large cohorts (for discovery/replication) with n-of-1 precision analyses (for mechanistic insight), predefine biologically grounded subgroups (genetic, metabolic, immune, autonomic), and analyze them explicitly. Embracing heterogeneity and uniqueness is the only way we’ll stop averaging away what matters for patients.

That said; I've been working on diagnostic odysseys in rare undiagnosed or misdiagnosed diseases since my PhD so I admit I see things through that lens. Others might not agree, I know. And you are, of course, 100% right to be cautious in red herring; totally agree! There have been so many oversold cures .

 

[jnmaciuch]

I really appreciate you continuing to engaging here. I can definitely see the utility from your perspective and understand how your background leads you there. I guess my experience comes from doing a lot of omics analysis myself and seeing first hand how much overfitting and lack of generalizability can so easily lead people become convinced that noise is real biology.

(Mods feel free to move this discussion back to the original thread to avoid derailing)

but IMHO when an individual carries a known pathogenic variant that explains all of their phenotype, we shouldn’t just ignore it just because it’s rare.

I guess that’s the core assumption here—I don’t think the pathogenic variant does actually explain all of their phenotype. When I was looking through each of the heterozygous variants individually, the evidence was very weak for heterozygous variants really ever presenting with the set of symptoms that were listed (which, correct me if I’m wrong, were the symptoms of the homozygous disease not the heterozygous state). Plus I have reason to be skeptical just knowing how thoroughly specific symptoms can get watered down in diagnostic descriptions—flu-like malaise of PEM is not the same as exercise intolerance of some cardiac disorders but they could easily be made to sound the same. [edit: And, like I’ve said previously, it’s possible that you’d frequently find variants to “explain” a phenotype that is already explained by another chronic disease if you looked outside of ME/CFS.]

It doesn’t need to be ignored because it’s rare, it just needs to be held with a lot of skepticism because the way that the analysis is designed will inherently present you with plausible candidates to explain away [edit: part of] someone’s phenotype even though there’s a good chance the variant explains nothing. So there’s no way to differentiate between what’s a variant that reveals real important biology and what’s an expected blip that is just reinforcing confirmation bias.

Given the sheer number of identified genetic disorders, the number of potentially pathogenic variants everyone walks around with, and the number of different symptoms in ME/CFS you could possibly match with a variant, it just seems to me that the odds are substantially more skewed toward irrelevance so you need some reliable way of discerning that before dedicating resources

ME/CFS presentations are heterogeneous; assuming a uniform cause at any point in setting up an experiment risks averaging away real biology.

but I guess the comparable case is lupus—if we went back in time and approached that heterogeneity as evidence against a uniform disease process, you’d just be sending research down endless rabbit holes. Could genetic heterogeneity be important in understanding why someone might be more likely to end up with some symptoms of lupus and not others? Sure. But establishing that definitively would require a massive cohort, because otherwise it’s just likely to give you the same confirmation bias.

The reason to think a unifying disease process is [edit: likely happening rather than a convergence of various genetic contributions] in ME/CFS is that the core of a chronic disease is a self perpetuating disease mechanism. In autoimmune disease that’s antibody (Jonathan on this forum was part of first hypothesizing and proving that). In hypertension it’s the feedback loop between mechanical damage of blood vessels and cytokines responding to that damage. In all those cases genetics do contribute to the likelihood of falling into a disease state and may well contribute to quirks of how it manifests—but unless it’s a monogenic disease you cannot attribute the maintenance of the disease state to those variants.

[Edit: so the TLDR is that genetic heterogeneity could well be important and explain outliers/subgroups in data, but that is to be expected with any chronic disease mechanism (frankly you expect that heterogeneity even in data from mouse clones raised in the same environment). The genes that contribute to someone’s deviance from other ME/CFS cases are relevant, but ultimately there’s no reason to believe the relevant genes interacting with a larger causative mechanism are the same genes identified due to symptom overlap with monogenic illnesses]

 

[Jonathan Edwards]

This would explains why things that really help some patients (mito cocktails/oxaloacetate) don't help others.

It looks as if peope are having a useful discussion here which I don't have time to engage in just for the minute. But I would question this 'really help some patients' motivation. We don't have good evidence anything helps anybody as far as I can see. Rheumatologists used to believe different things helped different people until we realised none of them did much at all.

 

[ScoutB]

The reason to think a unifying disease process is more likely than a scattering of various genetic contributions in ME/CFS is that the core of a chronic disease is a self perpetuating disease mechanism. In autoimmune disease that’s antibody (Jonathan on this forum was part of first hypothesizing and proving that). In hypertension it’s the feedback loop between mechanical damage of blood vessels and cytokines responding to that damage. In all those cases genetics do contribute to the likelihood of falling into a disease state and may well contribute to quirks of how it manifests—but unless it’s a monogenic disease you cannot attribute the maintenance of the disease state to those variants (even if you could prove that the variant is actually some small part in that larger causal mechanism, which you can’t do from this individualistic hypothesis approach)

Thanks for this, it's such a great explanation. It helps me understand why humans are so "lucky" as to mostly get many of the same diseases (rather than our health just chaotically breaking down in ways that are unique to each of us).

 

[arachel]

Rare disease geneticist here. Just wanted to say thank you for this work, it is really valuable. It would be super helpful to have a sense of prevalence of individuals who fit ME/CFS criteria who actually have a pathogenic variant for known rare genetic disorders, and only way this is possible is through painstaking variant classification process.

 

[Verity]

I know folks will chime in if I'm a bit out of the norm on how I think about PEM since many of you have been thinking about it longer. I mean the delayed post-exertional worsening of symptoms. So I'd count things that are/might be ME/CFS like diagnoses of dysautonomia, POTS, or hypermobile EDS/HSD, fibromyalgia. But it is also seen in some autoimmune and inflammatory disorders like Hashimoto’s, SLE/Sjögren’s, inflammatory myopathies as well as maybe mast cell activation syndrome. The same pattern can also be seen with MS and OXPHOS defects, fatty-acid oxidation disorders, glycogen pathway defects like McArdl. Maybe also in certain skeletal muscle channelopathies/periodic paralyses. That trend is also seen in some patients with iron or B12/folate deficiencies and erythrocyte membrane disorders. Something very similar is also seen in cases with arrhythmias or cardiomyopathies. You might also include things like adrenal insufficiency, diabetes dysregulation, and hypokalemia disorders states; they can also "mimic" PEM. Could have more of a fine grained discussion on how people specifically define PEM; that might help me get on the same page as everyone if they think I'm crazy here

I am not sure this is a helpful way to define PEM. As far as I know, the word was created for the phenomenon found in ME. I don’t think the exercise intolerance in at least some of the conditions you listed is similar enough to that found in ME for us to assume they’re the same thing. Broadening the term beyond its intended use to include a bunch of superficially similar types of exercise intolerance could be very misleading.

Also, some of the disorders you listed are being diagnosed when they possibly should not be—hEDS, MCAS, POTS, Sjogren’s. Those might just be patients with ME who are misdiagnosed, as you noted for some of them, so in that case PEM wouldn’t really be caused by all of those disorders. It would just be caused by ME.

 

[V.R.T.]

Hashimoto’s,

I have a friend with Hashimotos. She has fatigue and struggles with it but works a full time job, exercises, and has a full social life. That isn't PEM. PEM stopped me from having those things when my ME/CFS was mild.

I think a lot of autoimmune fatigue is similar.

 

[Jonathan Edwards]

I know folks will chime in if I'm a bit out of the norm on how I think about PEM since many of you have been thinking about it longer. I mean the delayed post-exertional worsening of symptoms. So I'd count things that are/might "be" ME/CFS like diagnoses of dysautonomia, POTS, or hypermobile EDS/HSD, fibromyalgia. But it is also seen in some autoimmune and inflammatory disorders like Hashimoto’s, SLE/Sjögren’s, inflammatory myopathies as well as perhaps mast cell activation syndrome.

I think this is a misunderstanding of PEM. Like a lot of clinical concepts PEM is badly defined and described but I don't think it can be reduced to delayed post-exertional worsening of symptoms. It is specifically a worsening of the sort of symptoms found in ME/CFS and is not only unexpectedly delayed but unexpectedly prolonged. There is a step change down for an extended period.

As you may see from other threads I would not consider dysautonomia, POTS, EDS/HSD (or 'mast cell activation syndrome) as ME/CFS-like diagnoses. They are all dubious concepts based on unproven mechanistic assumptions. They are largely categories used in fringe medicine that I don't think we should get involved in. Fibromyalgia is so vaguely defined that I doubt we have any useful information about whether it can be said to include PEM. A lot of people with ME/CFS would fit fibromyalgia criteria.

I spent my life looking after people with autoimmune disease and I did not come across people with what I regard as ME/CFS PEM. I doubt there is any useful information in this are either because so much of what is written is anecdotal and again from physicians on the fringe. My opinion is also anecdotal but I don't think the literature is reliable on this. A key difference is that for most other illnesses symptom patterns make reasonable sense in terms of what we know about pathology. For ME/CFS they don't really make sense in terms of any pathology we can conceive of - neither metabolic nor inflammatory. Something very different seems to be going on.

I agree that a wide range of genetic defects in different pathways may turn out to be linked to a syndrome like ME/CFS but I don't see that as likely to indicate that the clinical features do not reflect some common causal segment into which different pathways may feed. I don't see it as likely that symptoms arise directly either from ion homeostasis or synaptic signalling or... whatever. The symptomatology of ME/CFS is not generic or vague. It is very specific and very different from any other condition I am aware of, even if that is not very well explained in the literature.

 

[Trish]

I know folks will chime in if I'm a bit out of the norm on how I think about PEM since many of you have been thinking about it longer. I mean the delayed post-exertional worsening of symptoms. So I'd count things that are/might "be" ME/CFS like diagnoses of dysautonomia, POTS, or hypermobile EDS/HSD, fibromyalgia. But it is also seen in some autoimmune and inflammatory disorders like Hashimoto’s, SLE/Sjögren’s, inflammatory myopathies as well as perhaps mast cell activation syndrome. The same pattern can also be seen with MS and OXPHOS defects, fatty-acid oxidation disorders, glycogen pathway defects like McArdle's. Might also include certain skeletal muscle channelopathies/periodic paralyses. That trend is also seen in some patients with iron or B12/folate deficiencies and erythrocyte membrane disorders. Something very similar is also seen in cases with certain arrhythmias or cardiomyopathies. You might also include things like adrenal insufficiency, diabetes dysregulation, and hypokalemia disorders states; they can also "mimic"or "be" PEM. Could have more of a fine grained discussion on how people specifically define PEM; that might help me get on the same page as everyone if they think I'm crazy here

Have you read our PEM fact sheet? PEM is not just worsening of symptoms.