Severe ME patients have 1.7 broken copies of IDO2

pattismith

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just wondering what this means really.

Broken IDO2 protects again some autoimmune diseases like RA, but produces more susceptibility to LPS toxicity by increasing cytokines and lowering stat3 expression.

IDO2 has very little affinity with tryptophan and is likely to metabolize some other natural substrate.

"Accumulating evidence indicates that IDO2 acts as a pro-inflammatory mediator of autoimmunity, with a functional phenotype distinct from IDO1. IDO2 is expressed in antigen-presenting cells, including B cells and dendritic cells, but affects inflammatory responses in the autoimmune context specifically by acting in B cells to modulate T cell help in multiple model systems. "

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119657/

"IDO1 is expressed in various tissues, whereas IDO2 is expressed in only a subset of these, namely, liver, kidney, and antigen-presenting cells (APCs) of the immune system, including dendritic cells (DCs) and B cells.3,4 Functionally, IDO1 is better able to catabolize Trp to its primary product, N-formylkynurenine, which is subsequently converted to kynurenine.
Enzymatic studies demonstrate that IDO2 is significantly less active, particularly human IDO2, though it remains to be seen if the proper substrate and/or enzymatic assay conditions have been correctly identified, as IDO2 activity toward l-Trp and various Trp derivatives is both highly pH and buffer dependent.57

Unlike IDO1, which efficiently catabolizes l-Trp, there are several Trp derivatives, particularly 5-methoxytryptophan, that are more efficiently catabolized by IDO2 than Trp itself.5
Underscoring the murky relationship between IDO2 and Trp catabolism, deletion of IDO2 in mouse models does not alter serum kynurenine levels, even under chronic inflammatory conditions.3,4
Given the nonenzymatic signaling functions defined for IDO1,812 it is also plausible that IDO2 has a nonenzymatic function yet to be elucidated, a possibility that must certainly be considered given the generally sluggish catalytic activity of IDO2."

"….Together, these data from SLE, RA, and CHS models provide strong evidence for IDO2 as a mediator of inflammatory autoimmunity in multiple systems."


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6206095/

"Abstract
Indoleamine 2,3-dioxygenase 2 (Ido2) is a recently identified catalytic enzyme in the tryptophan-kynurenine pathway that is expressed primarily in monocytes and dendritic cells.

To elucidate the biological role of Ido2 in immune function, we introduced lipopolysaccharide (LPS) endotoxin shock to Ido2 knockout (Ido2 KO) mice, which led to higher mortality than that in the wild type (WT) mice.

LPS-treated Ido2 KO mice had increased production of inflammatory cytokines (including interleukin-6; IL-6) in serum and signal transducer and activator of transcription 3 (stat3) phosphorylation in the spleen.


Moreover, the peritoneal macrophages of LPS-treated Ido2 KO mice produced more cytokines than did the WT mice.

By contrast, the overexpression of Ido2 in the murine macrophage cell line (RAW) suppressed cytokine production and decreased stat3 expression.

Finally, RAW cells overexpressing Ido2 did not alter nuclear factor κB (NF-κB) or stat1 expression, but IL-6 and stat3 expression decreased relative to the control cell line. These results reveal that Ido2 modulates IL-6/stat3 signalling and is induced by LPS, providing novel options for the treatment of immune disorders."



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S-VV

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Interesting. Considering the fact that IDO2 is expressed in the metabolic organs: liver and kindeys, and the antigen presenting cells, it ties metabolism and immunity
 

JES

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The 1.7 broken copies was from Robert Phair's latest study, but the sample size was rather small.

The quoted article, if it is correct, would somewhat contradict the metabolic trap hypothesis. The metabolic trap model predicts that patients lacking IDO2 will potentially get into a trap where they start accumulating tryptophan in cells due to IDO1 not working at high tryptophan concentrations.

The quoted article claims that IDO2 has more of an immune regulatory role and that IDO2 deletion causes increase of inflammatory cytokines. Furthermore, in Phair's study they found low kynurenine levels in patients, whereas the cited paper claims normal kynurenine levels in the IDO2 knockout mice. But it seems that they measured serum levels and not intracellular levels, so there may be a potential pitfall there.
 

pattismith

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The 1.7 broken copies was from Robert Phair's latest study, but the sample size was rather small.

The quoted article, if it is correct, would somewhat contradict the metabolic trap hypothesis. The metabolic trap model predicts that patients lacking IDO2 will potentially get into a trap where they start accumulating tryptophan in cells due to IDO1 not working at high tryptophan concentrations.

The quoted article claims that IDO2 has more of an immune regulatory role and that IDO2 deletion causes increase of inflammatory cytokines. Furthermore, in Phair's study they found low kynurenine levels in patients, whereas the cited paper claims normal kynurenine levels in the IDO2 knockout mice. But it seems that they measured serum levels and not intracellular levels, so there may be a potential pitfall there.
Not sure if the broken IDO2 effect on ME/CFS severe patients is related to tryptophan;

The book I quoted at the end of my post says that IDO2 has a very high Km: it binds at concentrations at more than 100 folds higher than physiological tryptophan concentrations;

For this reasons, authors tend to think that IDO2 immune/inflammatory activity works through a different pathway than the tryptophan pathway, either by binding to another metabolite, either by binding to a receptor.
 
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pattismith

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Phair found that tryptophan/kynurenine is higher in cells patients than control, does someone know which cells were tested?

Also something that I cannot explain, if the metabolic try trap were to be right, then why IDO1 polymorphism is not found in patients?
 

JES

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Also something that I cannot explain, if the metabolic try trap were to be right, then why IDO1 polymorphism is not found in patients?
IDO1 according to the tryptophan trap theory is fully functional, only IDO2 is broken. The problem is that IDO1 has an unusual characteristic of being substrate inhibited, which means at very high tryptophan concentrations IDO1 stops working entirely, hence tryptophan starts accumulating and you end up in the trap.

The real crux here though is whether intracellular tryptophan levels really can get so high that IDO1 stops working. I have seen conflicting information on this so it remains to be seen after more precise lab tests can be performed.
 

pattismith

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IDO1 according to the tryptophan trap theory is fully functional, only IDO2 is broken. The problem is that IDO1 has an unusual characteristic of being substrate inhibited, which means at very high tryptophan concentrations IDO1 stops working entirely, hence tryptophan starts accumulating and you end up in the trap.

The real crux here though is whether intracellular tryptophan levels really can get so high that IDO1 stops working. I have seen conflicting information on this so it remains to be seen after more precise lab tests can be performed.
sorry, I can't understand how tryptophan would increase without IDO1 down regulation at the root
 
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@pattismith Hi Patti,

I’ve been lurking here for a little while almost entirely to follow your research. Fascinatingly you have come to some of the same working conclusions as I have.

I worked on the early iterations of metabolic trap based on the idea that there must be a switch to turn on the dormant ME/CFS from the DNA.

We looked at SREBP1 IIRC and Dr Phair found no evidence using bioinformatics of a switch and we parted ways essentially at that time.

However I continued to work as hard as I could (I’m also a patient) and when Dr Phair announced he had found what he believed to be the trap, I estimated that it was imo probably either HIF-1a or the AhR.

Now that I’ve had some time since the announcement of the IDO hypothesis I’ve tried to make sense of how IDO1 might be inhibited.

I have a paper that indicates that IDO expression depends on AhR activation and it would seem plausible that AhR may be inhibited in the gut (due to pathogenic changes in the Microbiota?) and that this would repress IDO1.

I’m currently trying I3C as it has been shown to activate AhR in the gut and also has some anti-estrogenic properties which should help to adjust the AR/ER balance.

Has your research into AhR led you to any interesting leads?

Just remembered also AhR activation seems to lead to improved tolerance and gut barrier integrity and can resolve peanut allergy for example.
 
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Also IDO1, which was recently reported to have a second function as a nitrite reductase, and this function was pH dependent.

Ambroxol changes the pHi of the mucosal cells in the gut and I’m wondering if it’s helping you by reactivating IDO1 through this mechanism.
 

JES

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However I continued to work as hard as I could (I’m also a patient) and when Dr Phair announced he had found what he believed to be the trap, I estimated that it was imo probably either HIF-1a or the AhR.
This is not what Phair thinks is casing the trap. The hypothesis of Phair, which was simulated in a computer model, predicts that if tryptophan concentrations remain high for a certain period of time, the patient gets stuck in a trap, a bistable state, where there is no easy way out from. This happens because of the unusual enzyme kinetics of IDO1, according to which IDO1 gets inhibited at high concentrations of tryptophan. Hence the patient would need a working IDO2 to get out of the trap.

The interesting thing about Phair's model is that it would potentially explain both ME/CFS outbreaks and also account for why only certain people get hit by the illness. In order for outbreaks to occur, there must be a common predisposing factor among the population, so any rare mutations can automatically be discarded. According to the model, the predisposition to the disease would be common, but the penetrance would be low, due to the fact that only certain set of condition could trigger the trap.

It could of course also be that something else inhibits IDO1, and as you say, the cause could potentially be in the microbiome. However, I'm not sure if it would as elegantly explain ME/CFS outbreaks or the fact that many people get ill overnight and cannot seem to return back to a healthy state.
 
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https://www.ncbi.nlm.nih.gov/m/pubmed/27316681/?i=15&from=ido1 ahr

From the above paper;

Stimulation of DC with IFN-γ and CD40L resulted in rapid induction of IDO1 and IDO2 transcription and recapitulated the in vivo switch from immunogenic to tolerogenic activity. Long-term maintenance of IDO expression was found to be independent of exogenous and autocrine IFN-γ, or the secondary cytokines TGF-β, TNF-α, and IL-6. In contrast, both IDO enzymatic activity and IFN-γ-induced AhR expression were required for continued IDO transcription in vitro and in vivo. Addition of the tryptophan catabolite kynurenine to DC cultures in which IDO activity was blocked restored long-term IDO expression in wild-type DC but not in AhR-deficient DC, establishing the central role of the kynurenine-AhR pathway in maintaining IDO expression in tolerogenic DC.
@JES Thanks for your input I do appreciate it. I have several references that I’ll post here as my CFS energy envelope permits, but I think the above paper is possibly pertinent. Not only do you need IDO enzymatic functioning to confer tolerance but you also need AhR to activate properly when stimulated with IFN-g.

Also in several papers it describes how AhR normally induces transcription and activity of both IDO1/2. It is of interest to me whether our genetic predisposition to IDO2 KO and IDO1 hypofunction causes by TRY accumulation could be blunt forced to work again through AhR activation.

Is there any available information about IDO1 kinetics that would indicate whether TRY accumulation prevents IDO1 activation even in the face of AhR agonism?
 
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nandixon

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sorry, I can't understand how tryptophan would increase without IDO1 down regulation at the root
@JES Also, has Dr Phair discussed here what may cause the initial Tryptophan accumulation if in fact IDO2 is not normally primarily a TRY degrader?
I don't believe he has (?), and he was actually asking for input at one point as to a possible explanation. I meant to reply a long time ago about what I think would be the most obvious possibility for tryptophan (Trp) increasing to levels that might overwhelm IDO1 (although note that I don't think the metabolic trap hypothesis is likely to be correct for a number of reasons I gave when Dr Phair first presented his work months ago).

The most obvious (theoretical) possibility is a failure on the part of the enzyme normally responsible for the removal (catabolism) of the largest quantity (90+%) of Trp in the human body, which is Trp 2,3-dioxygenase (TDO2).

TDO2 is mainly but not exclusively found in the liver and is induced by glucocorticoids (whereas IDO1 is mainly induced by pro-inflammatory cytokines like IFN-g and TNF-a). So the possibility exists for desensitization of the TDO2 glucocorticoid receptors during, for example, sustained periods of elevated HPA axis activity, in which case TDO2 may not be sufficiently induced to perform its function and Trp blood levels might (speculatively) rise to abnormally high levels, potentially subjecting IDO1 to detrimentally high (i.e., inhibitory) levels.

But this is all a moot point as it stands now because Phair has found that the original data from the tracer experiments on the 6 patients that had appeared to show decreased intracellular kynurenine formation may be bad.
 
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pattismith

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on the other hand, TDO enzymes are suposed to regulate blood tryptophan levels, so if they were downregulated, wouldn't we find high blood tryptophan in CFS/ME patients?

On the other hand, IDO2 SNPs that result in a non-functional IDO2 are extremely common. So the finding of an average of 1.7 damaged copies (alleles) in the severe patients is probably not very significant given that over 40% of the relevant general population (i.e., European-derived ethnic ancestry) already has 2.0 non-functional alleles (i.e., they are either homozygous or compound heterozygous for the IDO2 SNPs).

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I agree with all you answered to me, but even if the metabolic try trap is wrong, a down regulated IDO2 could still be real.

I read IDO2 depends only on Aryl receptors (see the abstract quoted at the end), which are downregulated by sport and by some plastic compounds:

https://forums.phoenixrising.me/thr...were-plastic-particles-pr.52498/#post-2183125

;;
https://www.researchgate.net/publication/269186596_IDO2_in_Immunomodulation_and_Autoimmune_Disease

"Gene expression studies indicate that IDO2 is a basally and more narrowly expressed gene than IDO1 and that IDO2 is uniquely regulated by AhR, which serves as a physiological receptor for the tryptophan catabolite kynurenine. In the established KRN transgenic mouse model of rheumatoid arthritis, where IDO1 gene deletion has no effect, IDO2 deletion selectively blunts responses to autoantigen but has no effect on responses to neoantigen challenge"
 
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nandixon

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on the other hand, TDO enzymes are suposed to regulate blood tryptophan levels, so if they were downregulated, wouldn't we find high blood tryptophan in CFS/ME patients?
The hypothetical downregulation of TDO2 and correspondingly high levels of tryptophan would be part of the trigger for developing ME/CFS and happen just at the beginning or early stage of the disease under this scenario. Thereafter, under Dr Phair's metabolic trap hypothesis it would be the non-functional IDO2 that would cause IDO1 to remain inhibited (and this would be seen intracellularly).

Tryptophan blood levels in established ME/CFS patients are more likely to be low, as you suggest.

I read IDO2 depends only on Aryl receptors (see the abstract quoted at the end), which are downregulated by sport and by some plastic compounds:
The abstract isn't saying that IDO2 only depends on AhR receptors. It's saying that IDO2 is influenced by AhR receptors but that IDO1 apparently is not. IDO2 is certainly not just regulated only by AhR receptors.
 
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The most obvious (theoretical) possibility is a failure on the part of the enzyme normally responsible for the removal (catabolism) of the largest quantity (90+%) of Trp in the human body, which is Trp 2,3-dioxygenase (TDO2).
Fwiw this has been seen before in human disease, namely a pediatric cancer called Ewing Sarcoma. The sequelae is TDO2 failure > Tryp Accumulation > AhR hypoactivation

Our data suggest that EWS-FLI1 suppresses autocrine AHR signaling by inhibiting TDO2-catalyzed TRP breakdown
https://www.ncbi.nlm.nih.gov/m/pubmed/27282934/?i=6&from=tdo2 ahr

EWS-FLI1 is a protein by the way (shout out to Ron Davis)
 
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