NOD2: A Common pathway that may be disrupted in ME/CFS

kday

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I'm putting this out there so hopefully researchers and others can look into this information to verify my claims.

I have looked through 23 23andMe ME/CFS genomes as well as 3 WGS genomes.

There is a common thread. NOD2 mutations seem to have greatly increased prevalence.

In fact, all 3 WGS samples (100%) have deleterious mutations in NOD2. The first genome has 2 verified pathogenic mutations. The second genome has a single extremely rare predicted damaging variant. And the third genome has two verified pathogenic NOD2 mutations as well as an extremely rare predicted damaging variant (a total of 3 variants). The pathogenic NOD2 mutations were all confirmed with corresponding 23andMe data. And when it comes to 23andMe data, 47.8% of 23 ME/CFS raw data files had a rare and not very common VERIFIED pathogenic mutation. For WGS data specifically, some are predicted by Variant Effect Predictor or Mutation Taster and others are established variants in the NCBI/NIH ClinVar database. 23andMe has some of the important NOD2 variants. But in two WGS samples, there are also predicted NOD2 mutations that are EXTRAORDINARILY rare. The very rare alt allele frequencies were confirmed with gnomAD browser, so they appear to be real variants. The NOD2 mutations range from not very common to rare, but seem to be very common in ME/CFS genomes. And the 23andMe data is self-reported publicly accessible data. So they may be even more common in patients that are verified by ME/CFS expert clinicians. And you need Whole Genome Sequencing to look at the very rare NOD2 damaging variants that I am seeing!

NOD2 is associated with Crohn's Disease, IBD/IBS, and other Autoinflammatory conditions. It's even associated with Fibromyalgia, but no study has been done on NOD2 and it's relationship to ME/CFS. I believe recent GWAS studies completely missed this as well.

NOD2 is important for the recognition and immune response to ssRNA viruses (e.g. Coxsackievirus is an ssRNA virus but herpes viruses are not) and Peptidoglycans (which is a component of the cell wall for almost all bacteria).

I think this is important because what if ME/CFS is an autoinflammatory illness initiated or perpetuated by dysregulation of the NOD-like receptor signaling pathway? What if this could create another negative feedback loop? And most importantly, what if targetted treatments could help ME/CFS symptoms?

Of course, research needs to be done first. This post serves as a call to action for researchers that browse this forum. But to summarize my findings, 100% of ME/CFS Whole Genome Sequence VCF files contained pathogenic and very rare predicted damaging mutations, and 47.8% of 23andMe ME/CFS genomes had pathogenic NOD2 variants that are listed in OMIM.

KEGG NOD-like receptor signaling pathway:
https://www.genome.jp/kegg-bin/show_pathway?ko04621+K10165
 

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kday

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This part is just a theory. But it seems like with NOD2 mutations, the gut isn't particularly good at clearing the harmful microbes and potential overgrowth.

Many chemicals and substances (as well as infections) actually upregulate NOD2. But the chemical 1,3-Butadiene in particular (as well as BPA) downregulates this enzyme and reduces expression of NOD2. What impact can such a common chemical have on an enzyme that may be not working very well in the first place?

1,3-Butadiene is in wood smoke, tobacco smoke, plastics/rubbers, vehicle exhaust, and even contaminated drinking water. Tests aren't available for testing the toxicity of this compound. I don't know if the NOD2 enzyme could be linked to the observed chemical sensitivity, but I find it very interesting that this common chemical decreases the expression of an enzyme that's very important for virus and bacteria recognition and defense.
 
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kday

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There is a 2019 study out of Taiwan that makes a connection between Inflammatory Bowel Disease and increased risk of CFS.

Increased risk of chronic fatigue syndrome in patients with infammatory bowel disease: a population-based retrospective cohort study

http://sci-hub.tw/https://doi.org/10.1186/s12967-019-1797-3

Although the definite pathogenesis of IBD remains unclear, unusual intestinal immune reaction triggered by intestinal fora could lead to inflammation [22] or deficit in the intestinal barrier and bacterial translocation [23]. Noticeably, bacterial translocation has been also proposed as one of the mechanism underlying CFS [9]. This hypothesis could be evidenced by the fact that serum IgA levels against the Lipopolysaccharide (LPS) of enterobacteria were significantly higher in patients with CFS. A study demonstrated the peripheral inflammation is induced by the LPS via binding to the toll-like receptor-4 complex [24]. If there is a mutation of Nucleotide binding oligomerization domain 2 (NOD2), a protein that binds to the peptidoglycan of bacteria resulting in NF-κB activation and inflammatory response, it could lead to CD development [25]. NF-κB is associated with a subjective feeling of fatigue [26] and activation of this pathway is common in both IBD [27] and CFS populations. Moreover, pro-inflammatory cytokines signals could also be relayed to brain by the autonomic nervous system and activated microglia could result in neuroinflammation and increased cytokine levels in brain [28]. There is an association between increased brain Interferon-γ (IFNγ), levels and certain somatic traits such as fatigue and hyperalgesia [29]. The hypothesis of bacterial translocation from the gastrointestinal tract is illustrated as Fig. 3. However, the above hypothesis is one of the possible explanations. Dysbiosis of the gut microbiota and an increased incidence of microbial translocation were suggested to play a principal role in inflammatory symptoms in CFS [30]. Thus, microbiota-gut-brain interactions were indicated essentially in the clinical presentations of a subgroup of patients with CFS [31, 32].
While it doesn't look like this study specifically looked at the rate of NOD2 mutations in ME/CFS, it looks like NOD2 may be an important avenue of research in regards to ME/CFS because of the overlapping pathophysiology of IBD and CFS.

Here's an illustration from the study showing the overlap:
Annotation 2019-07-19 144408.jpg
 
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Great job hypothesizing and looking at the data sets!!!

I'm a little kid, doubled over in the back seat of the car, intestinally distressed....all that occured BEFORE Eppstein Barr.

I just wish we could FIX something, soon, please.:sluggish::sluggish:
 

kday

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Found another ME/CFS genome. All 4 (100%) of WGS samples have not very common and rare NOD2 variants that are in ClinVar or are very rare and predicted damaging variants. This particular one has is a rare variant that is reported in ClinVar. No other rare/deleterious variants identified on further Variant Effect Predictor (VEP) analysis.

Annotation 2019-07-22 025633.jpg
 
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kday

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100% of patients with Ileocecal Crohn's Disease had NOD2 or ATG16L1 mutations. They all also have human enterovirus species B (HEV-B) infections such as Coxsackie B virus and Echovirus. NOD2 is extremely important for recognition and defense against ssRNA viruses such as Coxsackie B and Echovirus.

Could 100% of ME/CFS patients with these enteroviruses have NOD2 mutations? Is Dr. John Chia right about the role of enteroviruses in ME/CFS?
All patients with ICD had disease-associated polymorphisms in NOD2 or ATG16L1. Positive staining for HEV-B was detected both in the mucosa and in myenteric nerve ganglia in all ICD patients, but in none of the volvulus patients. Expression of the cellular receptor for CBV, CAR, was detected in nerve cell ganglia.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696939/
 

kday

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The trend had to stop at some point. I found a 5th genome at OpenHumans.org that was a long-term ME/CFS case that appeared to be well-characterized and confirmed by many institutions. This genome along with the medical data is publicly accessible.

This person DID NOT have any known or predicted damaging NOD2 mutations through SIFT/Polyphen-2. They had one questionable and novel (I believe it was novel if I remember right, but have to double-check) indel variant (a very long dinucleotide repeat) that was predicted "disease causing" by Mutation Taster, but both SIFT and Polyphen did not agree.

It's possible that it is damaging, but because of the uncertainty, I think it's fair to say 4/5 genomes (80%) have rare or not very common damaging variants, and one may or may not have a damaging variant.

One correction:
Earlier I said that one genome had a predicted damaging variant that wasn't in ClinVar. This wasn't true. All 4 genomes with damaging variants have variant(s) that are reported in the ClinVar database.
 
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Sidny

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100% of patients with Ileocecal Crohn's Disease had NOD2 or ATG16L1 mutations. They all also have human enterovirus species B (HEV-B) infections such as Coxsackie B virus and Echovirus. NOD2 is extremely important for recognition and defense against ssRNA viruses such as Coxsackie B and Echovirus.

Could 100% of ME/CFS patients with these enteroviruses have NOD2 mutations? Is Dr. John Chia right about the role of enteroviruses in ME/CFS?


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696939/
Fascinating thread and posts. We always here about Chrons being one of those diseases with “no known cause” clearly something is driving it and a pathogen like Coxsackie Virus B seems to fit the bill really well.
 

kday

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That variant is in about 33% of the population and is benign.

Screenshot_20190729_164701.jpg

Where is shows 0.33 for frequency, you take this number and multiply by 100 for frequency in percentage.

0.33 * 100 = 33

So 33% of the population has this variant. If you click on the "ClinVar" link on that same link. You can see that every submitter agrees that it's a benign variant.
 

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J.G

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Alright. I've combed my 23andme data for NOD2 SNPs/mutations. I was tested on chipset v4 a few years back, so my data is incomplete compared to chipset v5 currently in use. Once I do WGS, I'll revisit this post.

About me: I have clear MECFS with a significant gastro component. In fact I was diagnosed with "IBS" long before CFS, so this thread speaks to me.

For rs2067085 discussed above I am C/C like the majority of the population. My 23andme reported variants are predominantly common, even the "rarest" are well within SNP range:
rs5743289 C / T (frequency T <17%)
rs2076756 A / G (frequency G <25%)
rs17221417 C / G (frequency G 11-29%)
rs2066842 C / T (frequency T 10-26%)
rs2066843 C / T (frequency T 10-26%)
rs17313265 C / T (frequency T 10-27%)

Which pales in comparison to these (possibly pathogenic) NOD2 mutations (of which I have none):
rs2066844 (frequency T <5%)
rs5743271 (frequency G <0.5%)
rs2066845 (frequency C <0.5%)
rs5743272 (frequency G <0.1%)
rs5743299 (frequency T <0.1%)
rs147417132 (frequency T <0.01%)
rs3813758 (frequency T <0.001%)
rs2066847 anything but -/- may be a risk factor for GI ailments

This was an interesting exercise. I hope more n=1 data wil aid your theorisation, @kday!
 
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Bowel issues before any health issues

For rs2067085 I am C/G

As above poster - My 23andme reported variants are predominantly common, even the "rarest" are well within SNP range:

rs5743289 C / T (frequency T <17%)
rs2076756 A / G (frequency G <25%)
rs17221417 C / G (frequency G 11-29%)
rs2066842 C / T (frequency T 10-26%)
rs2066843 C / T (frequency T 10-26%)
rs17313265 C / T (frequency T 10-27%)
Add

rs2066844 (frequency T <5%) (C/T)

No pathogenic calls for
rs5743271 (frequency G <0.5%)
rs2066845 (frequency C <0.5%)
rs5743272 (frequency G <0.1%)
rs5743299 (frequency T <0.1%)
rs147417132 (frequency T <0.01%)
rs3813758 (frequency T <0.001%)
rs2066847 anything but -/- may be a risk factor for GI ailments

Additional “benign” snps on GENOS
rs5743291 G/A
rs1861759 T/G

GENOS does not flag my NOD2’s as pathogenic

BUT

IRGM rs10065172 T/T - very rare in caucasians on SNPEDIA
Associated with Inflammatory bowel disease 19 and poor autophagy efficacy.
 

Moof

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@kday, would the WGS analyser you created pick up on these variants? I just had a quick look at the report I generated when you first made it available to us, and there are no search results on there for 'NOD'. I haven't looked at all the individual SNPs yet, though.
 

kday

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@kday, would the WGS analyser you created pick up on these variants? I just had a quick look at the report I generated when you first made it available to us, and there are no search results on there for 'NOD'. I haven't looked at all the individual SNPs yet, though.
It should, yes. There may have been some corrections to the app since you used it. And there's a button now to save your results as an HTML archive.

It will miss the very rare NOD2 predicted pathogenic variants that are currently not classified. And it seems that some may have extraordinarily rare predicted deleterious variants.
 

stetson28

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Is anyone aware of a good source or forum discussion that describes how to convert the 23andMe "I" numbers that they use to conceal in some cases pathogenic disease causing mutations?
There used to be a member on this site that created a database that would convert many of the "I" numbers to "RS" numbers but she is no longer active.
for those of you who are not aware of what I'm asking 23andMe uses their own internal numbers that start with the letter "I" to marker various things for their own data testing.
In some cases the number simply represents a position that does not have a corresponding snp. However they also concealed particularly high risk snp's to presumably avoid FDA scrutiny.