Metabolic Trap, wouldn't we suffer from serotonin abnormality?

[alex3619]

I have several hypotheses about this trap. First we need to realise that as its intracellular, then not all cells expressing IDO2 may be affected.

Hypothesis 1 is that total numbers of cells affected may contribute to ME severity.

Hypothesis 2 is the pattern of distribution of affected cells might contribute to ME symptoms expression.

 

[Neunistiva]

We cannot infer much about this as the trap hypothesis is for intracellular levels. Blood levels are irrelevant.

Yeah I know that from this post and this one You took the first half of the wikipedia quote whereas I was including that quote because of the second half

consuming purified tryptophan increases the serotonin level in the brain, whereas eating foods containing tryptophan does not.
​

I can't remember where, but Dr. Phair or Dr. Davis (or was it in one of Dr. Janet Dafoe's forum posts?) said that eating food will not affect intracellular levels of tryptophan because cells already have enough (too much!) and don't allow more tryptophan to enter. I don't know why it's different when it's purified tryptophan.

What impresses me is the fact that every single patient in the severe patient study has a problem with this gene. This is very unlikely to be by chance.

I can't imagine this being a coincidence either and it gives me a lot of hope. Then again a lot of things I couldn't imagine happenend....

Its also unlikely to be the only factor in ME. If maybe 40% of the population have an inactivating IDO2 mutation, and less than 1% have ME (possibly more like 0.2%) and only about 10% of patients (sometimes up to 20%) who have a severe infection get ME, then some other factors are involved.

Dr. Phair said

In my view (as of October 2018), there are many unlikely combinations of events that can drive a person into this trap.
​

If this turns out to be correct then that's the explanation why only 1 in 40, or less, people with the mutation don't fall into the trap. Those lucky 39 people simply never found themselves in the unlikely combination of events.

From my understanding of this, as for why some patients are more severe, that should be explained by the number of mutations. Every ME/CFS patient has that common mutation, but more severe patients have additional mutations.

This is so intriguing, and I would enjoy the riddle even more if my life didn't depend on it, but I really can't understand researchers and doctors who have no scientific curiosity and would rather label us all crazy and proclaim everything known. What sad little brains.

 

[Murph]

I can't imagine this being a coincidence either and it gives me a lot of hope. Then again a lot of things I couldn't imagine happenend....

IWhat impresses me is the fact that every single patient in the severe patient study has a problem with this gene. This is very unlikely to be by chance.

I'm far less impressed by this finding, from a statistical perspective. There are a lot of common mutations in the gene for IDO2, and Phair's table of p-values left me ice-cold.

Perhaps Phair omitted some details here that give him more confidence than we can infer from what we saw. But it seems to me perfectly likely that a group of 20 people could all have at least one of a group of common mutations in a certain gene. @Simon shares my concerns, here's a quote of his from *elsewhere*.

The mutation he focused on was R248W, with a P value of 0.036, just inside the nominal P value of 0.05. However, he looked at multiple mutations, I am pretty sure more than the 5 shown here. And once you start making more than one comparison, you need to adjust P value downwards to correct for the resulting problem of false positives. 0.05 only applies to a single comparison.

And 0.036 would not survive any kind of statistical correction for multiple comparisons. That means that the original clue identifying IDO2 doesn't really hold up, which strikes me as a problem.

Phair's approach to the question is also relevant for figuring out whether this is a needle in a haystack or a needle in a haberdashers.

If he had a bunch of potential traps and then went hunting in the severely ill patient data to find one that mapped onto a slightly-more-than-usually mutated gene, that's the haberdasher scenario.

I hope he first found an unusually mutated gene and then discovered - omg - it has a potential metabolic trap. But it's not clear to me which way the process went.

To my eye the much better evidence for the trap is the kinetics data. If, in comparing patients to well-chosen controls, we can observe constrained flow from trp->kyn then we may really have something. So far we have a tantalising sample of three and this is where I want to see much more work done!!

 

[alex3619]

I hope he first found an unusually mutated gene and then discovered - omg - it has a potential metabolic trap.

He came into this looking for problems in a small range of genes, which include bistable responses. If this was a broad analysis and they just went looking for abnormalities, then the concerns would be more valid. Its not. Its a specific hypothesis driven search, with a very high rate for a specific enzyme type. In the more general case of microRNA issues they found over 2000 abnormalities. Many of those will indeed be false positives.

Take metabolomic findings for example. Currently its estimated that I think 15% of the original findings are false positives.

Then there is a potential link to African Sleeping Sickness, which I have not examined, that has as a primary symptom many of the circadian sleep issues we face.

Having said that most findings in science are wrong. I expect this and others are likely wrong based on that alone. They will continue to be wrong, making more wrong findings ... until they get one that is not wrong. This finding, or the next, or one made before, could turn out to be the key. We will only know after the science is done.

Statistics always has to be interpreted in terms of theory. Much of statistical science is not science, its arbitrary, like what p value to choose. In physics a p value of 0.001 is absurdly high, and would indicate the hypothesis is probably wrong. Most things meeting a p value of 0.05 in biomedicine are possible wrong or limited in some way. The p value is set very high because of the issues of researching biological systems and people.

 

[Wishful]

The abnormal Trp/Kyn is also shown in six out of six patients

Was the abnormality high or low, and was it serum or some other sample? My Trp/kyn serum level was abnormally low. Darn, now I can't remember what it was. I do remember that it was opposite of what I expected, but that led me to ask whether kynurenines cross the BBB (where they could cause my symptoms) and found out that they don't cross easily.

 

[FMMM1]

Was the abnormality high or low, and was it serum or some other sample? My Trp/kyn serum level was abnormally low. Darn, now I can't remember what it was. I do remember that it was opposite of what I expected, but that led me to ask whether kynurenines cross the BBB (where they could cause my symptoms) and found out that they don't cross easily.

Hi, regarding the tryptophan levels these are intracellular (cytoplasm?) levels i.e. not in plasma. The OMF folks on this site (Janet Defoe and @Ben H) and Alex have been emphasising that it's intracellular tryptophan. I was also wondering if they were referring to intracellular kynurenine; I assume they are but you could confirm from Phair's presentation.

If I recall correctly kynurenine is low since IDO1 is not working (substrate inhibition), and IDO2 is not functioning (non functioning mutation), i.e. converting tryptophan to kynurenine. Intracellular tryptophan is high. A higher concentration than normal (tryptophan) divided by a lower concentration than normal (kynurenine) gives a higher ratio than normal.

Ignore your plasma levels since OMF have not, to my knowledge, provided data showing intracellular levels compared to plasma/serum levels.
[Added 13 November]. Further thought, Fluge and Mella (& Armstrong) demonstrated low plasma levels of amino acids (including tryptophan) in ME/CFS. Therefore, I would ignore plasma/serum tryptophan levels. Here's an extract from Fluge and Mella's paper [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161229/]:
"All the 6 amino acids in category II were significantly reduced in nonfasting ME/CFS patients compared with nonfasting healthy controls, with P values of less than 0.001 for Ile, Leu, Phe, and Tyr and P values of 0.001 and 0.009 for Lys and Trp [tryptophan],".

I think the fact that these are intracellular levels may help to explain why this has been missed i.e. testing is normally done on blood (plasma/serum). Makes this theory more plausible to me.


Consider writing to your elected representative i.e. to request funding for ME/CFS research including the development of a diagnostic test.
I've written to the European Union Committee on the Environment, Public Health and Food Safety (ENVI) requesting that they lobby for funding for research into ME/CFS including the development of a diagnostic test [https://forums.phoenixrising.me/ind...ch-theyre-working-for-you.61516/#post-1003111].
Currently the ENVI Committee is lobbying for increased funding for research into Lyme disease and the development of a diagnostic test.
In 2016 the European Commission [European Union civil service] said [regarding Lyme disease] that "Both basic research and the development of new diagnostics, treatments and vaccines for Lyme borreliosis are funded by EU research and innovation framework programmes. The total EU contribution to such projects since 2007 amounts to EUR 33.9 million [US dollars]" [http://www.europarl.europa.eu/doceo/document/E-8-2016-008631-ASW_EN.html].

ME/CFS received no funding from the European Union [http://www.europarl.europa.eu/doceo/document/E-8-2017-006901-ASW_EN.html].

 

[FMMM1]

---
Then there is a potential link to African Sleeping Sickness, which I have not examined, that has as a primary symptom many of the circadian sleep issues we face.---

Thanks Alex. Based on a search on Google for "african sleeping sickness tryptophan", and a few minutes scanning of the results (and very little understanding), there's a lot of research which seems relevant; e.g. this mentions "CNS inflammatory" [https://www.ncbi.nlm.nih.gov/pubmed/28013248].

Also, Ron Davis said that a gene expression study, comparing ME/CFS to other illnesses, found that the closest match was to African sleeping sickness [Ron's talk at the 2018 Symposium etc.].

Looks like they may be on to something but we need to know if this is a general problem in ME/CFS i.e. high intracellular tryptophan/low kynurenine. OMF are looking for a test for intracellular tryptophan i.e. to replace the current Mass Spectrometry test [Janet Defoe on Health Rising].

 

[alex3619]

Also, Ron Davis said that a gene expression study, comparing ME/CFS to other illnesses, found that the closest match was to African sleeping sickness [Ron's talk at the 2018 Symposium etc.].

That is why I keep looking at ASS (hmmm, first time I wrote it as as acronym, but it fits). I started looking at AfSlSi (might be a worse acronym) a long time back, trying to understand the problems we have with sleeping, but I was looking at sleep mechanisms and not circadian reversal.

 

[FMMM1]

Given that 40% of the healthy population has mutations with the gene I'm feeling skeptical

I think the hypothesis that high intracellular tryptophan is the cause of ME/CFS is testable. I.e. test a lot of people with ME/CFS to see if their intracellular levels of tryptophan are higher than the normal range (people who do not have ME/CFS). OMF already have a test for intracellular tryptophan [mass spectrometry] and are looking for a cheaper test [Janet Defoe on Health Rising]. Next, lower the levels of intracellular tryptophan; there's talk of drugs (and re-feeding syndrome approach?) to lower intracellular tryptophan. If high intracellular tryptophan is the cause of ME/CFS then lowering it will "cure" ME/CFS. If high intracellular tryptophan is a consequence (downstream effect) of ME/CFS then lowering it will not "cure" ME/CFS - it might however give you a diagnostic test for ME/CFS i.e. intracellular tryptophan.

Also Ron Davis (and others in the OMF group) are world class geneticists. There been no talk of making IDO2 from the presumed defective genes but (as a non geneticist) that appears to be deliverable. That way you could check whether these forms of IDO2 are capable of converting tryptophan to kynurenine.


Consider writing to your elected representative i.e. to request funding for ME/CFS research including the development of a diagnostic test.
I've written to the European Union Committee on the Environment, Public Health and Food Safety (ENVI) requesting that they lobby for funding for research into ME/CFS including the development of a diagnostic test [https://forums.phoenixrising.me/ind...ch-theyre-working-for-you.61516/#post-1003111].
Currently the ENVI Committee is lobbying for increased funding for research into Lyme disease and the development of a diagnostic test.
In 2016 the European Commission [European Union civil service] said [regarding Lyme disease] that "Both basic research and the development of new diagnostics, treatments and vaccines for Lyme borreliosis are funded by EU research and innovation framework programmes. The total EU contribution to such projects since 2007 amounts to EUR 33.9 million [US dollars]" [http://www.europarl.europa.eu/doceo/document/E-8-2016-008631-ASW_EN.html].

ME/CFS received no funding from the European Union [http://www.europarl.europa.eu/doceo/document/E-8-2017-006901-ASW_EN.html].

 

[FMMM1]

Did you hear or read what the specific type of immune cell is? I realized a couple of days ago that if they used lymphocytes, for example, that the expression of IDO1 apparently isn't upregulated by interferon-gamma (IFNg) in that type of cell, versus if they simply used the general class of PBMCs (which includes lymphocytes) that IDO1 would be found to be upregulated by IFNg (due to the monocytes in the PBMCs, for example). Knowing what type of cell they used potentially changes the analysis of what they found. Thanks.

I think everyone is using peripheral blood mononuclear cells* (PBMCs) since (I assume) these are readily accessible [e.g. this test for intracellular phenylalanine uses PBMCs - https://sci-hub.se/10.1039/C8AN01437J].

In terms of IFNg upregulating IDO1 in monocytes. Does this matter since IDO1 is substrate inhibited [by high intracellular tryptophan] and presumably isn't working? I assume you could check whether IDO1 is inhibited by measuring the intracellular tryptophan levels in lymphocytes, and monocytes, and compare this to the level at which IDO1 is inhibited.

I'm guessing that you can use PMBCs as the basis of a diagnostic test and to test a drug/or other treatment (e.g. refeeding syndrome approach) to see if it lowers intracellular tryptophan. They've found a couple in potential drugs using the Nano needle/PBMCs.

Hope this is of some benefit.

*Peripheral blood mononuclear cell - Wikipedia
https://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell
A peripheral blood mononuclear cell (PBMC) is any peripheral blood cell having a round nucleus. These cells consist of lymphocytes (T cells, B cells, NK cells) and monocytes, whereas erythrocytes and platelets have no nuclei, and granulocytes (neutrophils, basophils, and eosinophils) have multi-lobed nuclei



Consider writing to your elected representative i.e. to request funding for ME/CFS research including the development of a diagnostic test.
I've written to the European Union Committee on the Environment, Public Health and Food Safety (ENVI) requesting that they lobby for funding for research into ME/CFS including the development of a diagnostic test [https://forums.phoenixrising.me/ind...ch-theyre-working-for-you.61516/#post-1003111].
Currently the ENVI Committee is lobbying for increased funding for research into Lyme disease and the development of a diagnostic test.
In 2016 the European Commission [European Union civil service] said [regarding Lyme disease] that "Both basic research and the development of new diagnostics, treatments and vaccines for Lyme borreliosis are funded by EU research and innovation framework programmes. The total EU contribution to such projects since 2007 amounts to EUR 33.9 million [US dollars]" [http://www.europarl.europa.eu/doceo/document/E-8-2016-008631-ASW_EN.html].

ME/CFS received no funding from the European Union [http://www.europarl.europa.eu/doceo/document/E-8-2017-006901-ASW_EN.html].

 

[nandixon]

In terms of IFNg upregulating IDO1 in monocytes. Does this matter since IDO1 is substrate inhibited [by high intracellular tryptophan] and presumably isn't working?

In the case of using interferon-gamma, we're mainly talking about upregulating IDO1 gene expression and hence the quantity of the IDO1 protein (enzyme) subsequently made. The more enzyme that's present then the more that higher levels of tryptophan can be offset.

Some subsets of PBMCs apparently aren't affected by INFg with respect to expression of IDO1, though. Lymphocytes are one example if I remember correctly. (I can't remember whether dendritic cells, which may be more important in this context, are or not.)

 

[Wishful]

I'd want the test to be done on microglial cells, since I believe that's where my symptoms arise from. I expect that will be done much later, since it's less convenient.

 

[JaimeS]

One thing that strikes me as odd is that if the Metabolic Trap is correct shouldn't we all have Serotonin Syndrome if we are very high? We don't generally suffer most of those symptoms.

On the flip if we were too low wouldn't we all be depressed?

Given that 40% of the healthy population has mutations with the gene I'm feeling skeptical

Not to counter your skepticism, which is healthy.

Quite a few smaller studies found higher levels of serotonin in ME. There are seemingly contradictory studies that show low serotonin in the bloodstream, but serotonin levels there have zip to do with what's on the other side of the blood-brain barrier.

I think we do either have high brain serotonin or high sensitivity to serotonin. At onset, I took 5-HTP and had full-blown serotonin syndrome symptoms (which you can probably find here if you search under my name and "serotonin").

To 'spring' the metabolic trap, you wouldn't need high serotonin as a chronic thing, anyway -- you'd just need a burst at onset.

What could cause that?

Serious infection.

 

[Wishful]

I haven't noticed any symptoms of high or low serotonin. My guess is that some ME victims might have problems with it, other don't.
< 5% of TRP gets converted to serotonin in the brain, so the effects from altered serotonin/kynurenine ratio might be a lot smaller than the effects from the kynurenines.

 

[FMMM1]

Not to counter your skepticism, which is healthy.

Quite a few smaller studies found higher levels of serotonin in ME. There are seemingly contradictory studies that show low serotonin in the bloodstream, but serotonin levels there have zip to do with what's on the other side of the blood-brain barrier.

I think we do either have high brain serotonin or high sensitivity to serotonin. At onset, I took 5-HTP and had full-blown serotonin syndrome symptoms (which you can probably find here if you search under my name and "serotonin").

To 'spring' the metabolic trap, you wouldn't need high serotonin as a chronic thing, anyway -- you'd just need a burst at onset.

What could cause that?

Serious infection.

Thanks,
Does infection result in high serotonin?
Does high serotonin result in high intracellular tryptophan?

 

[FMMM1]

In the case of using interferon-gamma, we're mainly talking about upregulating IDO1 gene expression and hence the quantity of the IDO1 protein (enzyme) subsequently made. The more enzyme that's present then the more that higher levels of tryptophan can be offset.

Some subsets of PBMCs apparently aren't affected by INFg with respect to expression of IDO1, though. Lymphocytes are one example if I remember correctly. (I can't remember whether dendritic cells, which may be more important in this context, are or not.)

I'm guessing but if you have e.g. twice as much IDO1 (effect of INFg) then you could clear twice as much tryptophan. However, lets say IDO1 is substrate inhibited by tryptophan levels of 100 units or more; higher concentrations of IDO1 will make it more difficult get to that value (100 units) but if you do IDO1 will still stop working.

 

[nandixon]

I'm guessing but if you have e.g. twice as much IDO1 (effect of INFg) then you could clear twice as much tryptophan. However, lets say IDO1 is substrate inhibited by tryptophan levels of 100 units or more; higher concentrations of IDO1 will make it more difficult get to that value (100 units) but if you do IDO1 will still stop working.

The charts that Phair showed for the utilization of tryptophan and the production of kynurenine in the in vitro tracer experiments (on the 6 patients and 6 controls) are indicating that increasing IDO1 by a few fold should be more than enough to correct the problem.

However, I now believe that Phair's tracer experiments are showing not that IDO1 is inhibited as required by the metabolic trap hypothesis, but rather that a reduced amount of IDO1 is present instead.

I believe the latter is more consistent with the known immunomodulatory abilities of IDO2, which can potentially both directly and indirectly affect the gene expression of IDO1, and which also appears capable of affecting the rate of degradation of IDO1 (i.e., the rate of degradation seems more likely to be increased when a person has the inactivating IDO2 SNPs).

I talk about this in a recent post here:
https://forums.phoenixrising.me/ind...ic-trap-for-me-cfs.58606/page-18#post-1012430

(including the possibility that the results of Phair's tracer experiment might actually be perfectly normal).

 

[nandixon]

Just FYI, I had looked into the possibility of serotonin being a problem a few years ago (when I had much less biochemistry and genetics knowledge, unfortunately), and I may have been the first person to suggest that IDO1 might need to be increased in ME/CFS, but I gave it short shrift at the time because I'm homozygous for the most important common SNP of that gene, rs7820268, which appears to be an upregulation.

I'm doubtful anything will be helpful but both these posts are from Jan 2015:

I'm guessing that an additional defect, e.g., a down-regulation in the serotonin transporter (SLC6A4), and/or a defect in tryptophan catabolism (i.e., the kynurenine pathway, e.g., IDO1), etc, may also be needed to have a serotonin excess problem, in addition to perhaps a necessary SNP upregulation in TPH2.

To lower serotonin, I'm looking to inhibit tryptophan hydroxylase 2 (TPH2) and induce indoleamine 2,3-dioxygenase (IDO1), and avoid the opposite.

 

[JaimeS]

Does infection result in high serotonin?

It should, yeah.

Does high serotonin result in high intracellular tryptophan?

Less certain. That would rely on feedback inhibition to be the case.

Your serotonin would have to bounce, which would have to inhibit the process that changes tryp into serotonin. Then tryp would build up. Theoretically.

I'm doubtful anything will be helpful but both these posts are from Jan 2015:

Weird! I think I remember this convo! Mostly because I have a downregulation in the serotonin transporter. I'm a slow processer of serotonin.

 

[Research 1st]

In light of the OMF scientists proposing that CFS serotonin receptors could be negatively affected in order to cope with high serotonin levels (due to the tryptophan/kyneurenine issue), this interested me as years ago ME doctor/researcher from Belgium, Kenny De Meirleir, mentioned that he believes ME patients have altered hormone receptors, e.g. effectively giving patient signs of hypothyroidism, yet their blood thyroid markers (sans RT3) are essentially normal.

So I wonder if it's 'just' the serotonin receptors 'adapt' (potentially causing a functional depression without actual depression), but other receptors could have adapted like this also in ME CFS, such as KDM mentioned?

Also I was thinking if that happened, all of these effects, including low GH due to pituitary problems may be explained by a process of wide spread neuroinflammation affecting the way our brains control hormones? If so, this might explain why so many of our hormone levels although altered, aren't altered enough to meet clinical definitions of deficiency or excess states, yet in long term ME CFS patients we can still have the classic symptoms of these conditions - such as hair loss, premature greying of hair, weight gain/weight loss, female health problems etc.

It always interested me why the tragic fatal ME CFS subsets with dorsal root ganglionitis found on autopsy, not only are usually female, but I've read at least one of these young women reported entering the menopause in their 20's, which now might make sense if the brain is getting zapped on it's receptors, or in some way, trying to adapt?

Just a thought.