New research update video with Prof. Ron Davis, March 29th 2021

BrightCandle

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Small rant: Old non functioning equipment just epitomises the issue ME research faces, its underfunded so badly, surely the NIH can fund the purchase of a new robot!

It is great news he is moving on to testing drugs to see what gets the yeast and then human cells out of the metabolic trap having confirmed it could happen, from theory to seeing yeast doesn't grow when trapped. Fascinating, I hope they are onto something here and find something that works and they can trial out of the drugs or the herb extracts.

I would laugh my arse off if it turns out one of the banned psychedelics is and always has been the cure to ME.
 

Ben H

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Here is a rough transcript I did for patients that cannot watch or listen to the video:




-Intro from Ron. Ron's sole focus is ME/CFS.

-Working on treatments/cure.

-Metabolic Trap idea. This is where critical enzyme gets trapped in it's function.

-Difficult to test in human cells, testing in bakers yeast. Have great technology for this.

-Have taken bakers yeast + put in critical gene that gets trapped (function gets trapped) + that is IDO1 gene.

-IDO1 converts tryptophan (in diet) to kynurenine.

- Kynurenine v. important-regulates immune system, can suppress inflammation etc.

- Placing gene into yeast can control it, but it makes the same protein that is made in humans.

- Many human genes will work in yeast and vice versa.

- Yeast doesn't really have this level of pathway so kynurenine can be used to make NAD.

- NAD is chemical compound that is extensively used in metabolism of organisms, human + yeast.

- In humans NAD used in ~400 chemical reactions, really essential.

- Required for production of energy in mitochondria.

- What they have done is make kynurenine in yeast with this enzyme + require it to make NAD.

- Yeast has multiple ways to make NAD so have removed all genes involved in the production of NAD.

- So ONLY way yeast can make NAD is to have this pathway on.

- If they trigger the metabolic trap, will shut down the enzymatic activity of ido1 then it can't kynurenine, and it can't make NAD. If can't make NAD, won't grow.

-One problem is don't want yeast to consume tryptophan by any other pathway.

-Looked into yeast, all genes have been sequenced + understand their function, found several genes that consume tryptophan for other purposes.

-Have removed these genes.

-This new developed yeast is now suitable for a test.

-Grew on low tryptophan, cells grew fine.

-If raise tryptophan concentration, high level of tryptophan can inhibit enzyme.

-This is very strange.

-Here is an enzyme (IDO1) that converts tryptophan to kynurenine. Would guess that if raised tryptophan would simply make more kynurenine.

-Not true-the high tryptophan inhibits the enzyme and can't make kynurenine.

-If it can't make kynurenine can't grow-so if raise concentration of tryptophan gets to point where it stops growing.

-As long as you leave tryptophan in at a high level, can't grow.

-If you then wash out the high level of tryptophan + put in low level of tryptophan, starts growing again.

-OR if leave high level of tryptophan but give yeast kynurenine (required for NAD) starts growing again even in presence of high tryptophan and absence of activity of enzyme.

-Why are they doing all this? One is to test the Metabolic Trap-something you can do in a test tube-does it work in a cell?

-This experiment shows it CAN work in a cell. It's yeast, but can still work in a cell.

- This is a possibility what is happening in humans.

-There is another reason to do this. Now have system where can shut down the enzyme in metabolic trap + the only way cell can grow is to get rid of tryptophan.

-Human cells not quite the same, it's not growth, it's making kynurenine which is critical factor.

-If this true in human cells, only way to make kynurenine would be to get rid of the tryptophan. The only way to get rid of tryptophan is to convert it to kynurenine.

-That's why it's called a trap, you get into it, you can't get out.

-However if they can find compound-that will 'block the block'-the inhibition that tryptophan has over the enzyme/IDO1 this then will reactivate IDO1, IDO1 will consume the tryptophan and cells will produce kynurenine.

-That's the stage are at at the moment with yeast.

-Fairly simple to do with yeast. Put in high tryptophan + can add drug(s) at different concentrations + look for growth.

- Have a robot that can do all of this, can do 96 at a time + have 3 robots, can do this with different concentrations of drugs.

-Can set up + leave to do experiments. Robot can do lots of experiments! Is being set up now.

-Unfortunately it's an old robot, needs some repairs + is in the process of repair.

-Getting help + are going to get fixed. So is just about ready to start doing drug screens.

-Have all FDA-approved drugs in their freezer. Have already screened all those drugs for their effect on yeast + know concentration that has some effect.

- Ron excited about this, has no idea what the probability is but is optimistic. Lots of things to try at lots of different concentrations.

-Also, if it works out + don't find any FDA-approved drugs, will start screening herbal extracts.

-Wants to have something patients can take + a new compound would take updated approval + take years to do. Doesn't want to do that.

-Optimistic can find something. If metabolic trap is real they have something can treat it with.

-Next thing is move to human cells. In process of doing that.

-Ron says thank you.
 

nerd

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Assuming this is the main lead, wouldn't the tryptophan levels be too high in CFS/ME patients? Or wouldn't Niacin supplementation or another NAD+ booster help? Not in my case. My intracellular tryptophan levels were even a bit low.

Here is my opinion. This research is focused on the manifestation pathway of CFS/ME but not on the causality.

Genetics could be a causality. But there is nothing special in my IDO1 gene. No loss of function, major deletion, or rare mutation at least.

Given the assumption that EBV is the major cause of EBV and that it is immunologically mediated, you can find evidence of EBV involvement in the IDO1 pathway. EBV-mutated B cells could produce EBV-IDO which competes with human IDO (10.1016/j.imlet.2011.01.009). Maybe EBV-IDO even has a greater affinity than human IDO and thereby enhancing its relative concentration factor. Maybe EBV-IDO is not as functional in the Tryptophan metabolism as human IDO but it seems to be functional in suppressing L-kynurenine signaling and thereby evade immune recognition (10.1016/j.imlet.2011.01.009). I've pointed out similar observations with EBV-IL-10 vs. human IL-10.

Moreover, the activation of IDO in response to EBV infection of MDMs suppressed the proliferation of T cells and impaired the cytotoxic activity of CD8+ T cells, whereas the inhibition of IDO activity with 1-methyl-l-tryptophan (1-MT) did not affect T cell proliferation and function. These findings indicate that EBV-induced IDO expression in MDMs is substantially mediated by IL-6- and TNF-α-dependent mechanisms via the p38/MAPK and NF-κB pathways, suggesting that a possible role of EBV-mediated IDO expression in tumor stroma of NPC may be to create a microenvironment of suppressed T cell immune responses.
This is from another study (10.1128/JVI.03678-13) on EBV-IDO and I see similarities with the pathology of CFS/ME.
  1. CFS/ME is associated with a suppressed cytotoxic activity of CD8+ T cells (Selin et Gil).
  2. CFS/ME is associated with a decrease in CD8+ T cell ratio, indicating a problem with the proliferation or maturation of CD8+ T cells (Selin et Gil).
  3. CFS/ME is associated with an increase in Foxp3+Helios+ T/-reg cells (Selin et Gil). IDO signaling is known to induce this conversion to Foxp3+ Tregs (10.3892/mmr.2018.8537).
  4. CFS/ME is associated with elevated NF-κB (10.1016/j.mehy.2012.07.034).
  5. CFS/ME is associated with enhanced IL-17/Th17 signaling (Selin et Gil). EBV-induced EGR1/p38/MAPK/IL-17 signaling is speculated to be the reason (10.3390/biom10111484).
Another thing to consider. Many CFS/ME patients who report remission, within a few days report a relapse. I recently experienced this myself. Given the assumption that the IDO1 function is the explanation for the major CFS/ME symptoms, why do you have such a fast and immediate relapse? Something must push you back into the metabolic trap and whatever it is, it seems to adapt to the metabolic conditions given by the approached therapy. This also supports my theory that there is an active pathology behind the metabolic trap and this pathology won't disappear by trying to fix the trap only.
 

Ben H

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Ben, thanks for doing this. And of course the Davis/Defoe family !
Does anyone remember if we are have low kynurenine in our lymphocytes or dendritic cells?
Thanks
No worries, yes big thanks to Ashley and the whole Davis/Dafoe family.

I think the consensus (based on this theory) is it would be low, but I can't remember specifically to that question if it's been measured-someone else may know.

There is the Kynurenine trial being run at Uppsala University, one of the CRC's :

https://www.omf.ngo/kynurenine-clinical-trial-for-me-cfs/


B
 

Ben H

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Assuming this is the main lead, wouldn't the tryptophan levels be too high in CFS/ME patients? Or wouldn't Niacin supplementation or another NAD+ booster help? Not in my case. My intracellular tryptophan levels were even a bit low.

Here is my opinion. This research is focused on the manifestation pathway of CFS/ME but not on the causality.

Genetics could be a causality. But there is nothing special in my IDO1 gene. No loss of function, major deletion, or rare mutation at least.

Given the assumption that EBV is the major cause of EBV and that it is immunologically mediated, you can find evidence of EBV involvement in the IDO1 pathway. EBV-mutated B cells could produce EBV-IDO which competes with human IDO (10.1016/j.imlet.2011.01.009). Maybe EBV-IDO even has a greater affinity than human IDO and thereby enhancing its relative concentration factor. Maybe EBV-IDO is not as functional in the Tryptophan metabolism as human IDO but it seems to be functional in suppressing L-kynurenine signaling and thereby evade immune recognition (10.1016/j.imlet.2011.01.009). I've pointed out similar observations with EBV-IL-10 vs. human IL-10.



This is from another study (10.1128/JVI.03678-13) on EBV-IDO and I see similarities with the pathology of CFS/ME.
  1. CFS/ME is associated with a suppressed cytotoxic activity of CD8+ T cells (Selin et Gil).
  2. CFS/ME is associated with a decrease in CD8+ T cell ratio, indicating a problem with the proliferation or maturation of CD8+ T cells (Selin et Gil).
  3. CFS/ME is associated with an increase in Foxp3+Helios+ T/-reg cells (Selin et Gil). IDO signaling is known to induce this conversion to Foxp3+ Tregs (10.3892/mmr.2018.8537).
  4. CFS/ME is associated with elevated NF-κB (10.1016/j.mehy.2012.07.034).
  5. CFS/ME is associated with enhanced IL-17/Th17 signaling (Selin et Gil). EBV-induced EGR1/p38/MAPK/IL-17 signaling is speculated to be the reason (10.3390/biom10111484).
Another thing to consider. Many CFS/ME patients who report remission, within a few days report a relapse. I recently experienced this myself. Given the assumption that the IDO1 function is the explanation for the major CFS/ME symptoms, why do you have such a fast and immediate relapse? Something must push you back into the metabolic trap and whatever it is, it seems to adapt to the metabolic conditions given by the approached therapy. This also supports my theory that there is an active pathology behind the metabolic trap and this pathology won't disappear by trying to fix the trap only.
It's one of many leads/hypothesis (nanoneedle, RBC's etc) but some interesting points. We need the human cell experiments. It may be just a subset, it may be a majority, or it may not be relevant at all. However the research so far, and now the research on yeast (as well as the technology used in this) looks promising.

One might expect (if the theory is correct) that raising intracellular NAD levels could help, but that alone may not be enough. Again it comes back to the human cell and future experiments.

Thanks for the research links, I'll try and take a look when I am able.

Yes the rapid remission stories are interesting, it's interesting to theorise how that may fit into the metabolic trap (or not).


B
 
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nerd

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Yes the rapid remission stories are interesting, it's interesting to theorise how that may fit into the metabolic trap (or not).
Thanks for looking into it.

This isn't the only theory I have in the context of EBV residual activity as ongoing background pathology. Selin et Gil also showed elevated levels of CD4+CD8+ T cells, which indicates a problem with the differentiation during T cell maturation. So I'm quite surprised that I couldn't find any studies on the thymuses of CFS/ME patients. Are they enlarged? In my case, it is. MG is the typical thymus hyperplasia disease, but I'm seronegative and I don't think seronegative MG is "real" MG and that the other cases are just confused with CFS/ME, which can also trigger mild levels of AChR Abs. But for MG, residual EBV activity can be found in many patients, whether they have thymomas/thymic tumors or not (10.1186/s13027-019-0254-5). It might be up to 100%, depending on the detection method. If residual EBV activity could be found in the thymic B cells or otherwise, this could explain this abnormal maturation to CD4+CD8+ T cells and a lack of CD8+ T cells because EBV's BDLF3 gene is able to induce a downregulation of MHC-I and MHC-II (maybe with differing affinity) (10.1128/JVI.02183-15).

I'm also looking into the involvement of EBI 2, which is elevated 40-fold in my case despite negative EBV IgM and the lack of EBV-specific symptoms (=> no acute EBV) (10.1016/j.immuni.2019.04.001).
 

Janet Dafoe

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Assuming this is the main lead, wouldn't the tryptophan levels be too high in CFS/ME patients? Or wouldn't Niacin supplementation or another NAD+ booster help? Not in my case. My intracellular tryptophan levels were even a bit low.

Here is my opinion. This research is focused on the manifestation pathway of CFS/ME but not on the causality.

Genetics could be a causality. But there is nothing special in my IDO1 gene. No loss of function, major deletion, or rare mutation at least.

Given the assumption that EBV is the major cause of EBV and that it is immunologically mediated, you can find evidence of EBV involvement in the IDO1 pathway. EBV-mutated B cells could produce EBV-IDO which competes with human IDO (10.1016/j.imlet.2011.01.009). Maybe EBV-IDO even has a greater affinity than human IDO and thereby enhancing its relative concentration factor. Maybe EBV-IDO is not as functional in the Tryptophan metabolism as human IDO but it seems to be functional in suppressing L-kynurenine signaling and thereby evade immune recognition (10.1016/j.imlet.2011.01.009). I've pointed out similar observations with EBV-IL-10 vs. human IL-10.



This is from another study (10.1128/JVI.03678-13) on EBV-IDO and I see similarities with the pathology of CFS/ME.
  1. CFS/ME is associated with a suppressed cytotoxic activity of CD8+ T cells (Selin et Gil).
  2. CFS/ME is associated with a decrease in CD8+ T cell ratio, indicating a problem with the proliferation or maturation of CD8+ T cells (Selin et Gil).
  3. CFS/ME is associated with an increase in Foxp3+Helios+ T/-reg cells (Selin et Gil). IDO signaling is known to induce this conversion to Foxp3+ Tregs (10.3892/mmr.2018.8537).
  4. CFS/ME is associated with elevated NF-κB (10.1016/j.mehy.2012.07.034).
  5. CFS/ME is associated with enhanced IL-17/Th17 signaling (Selin et Gil). EBV-induced EGR1/p38/MAPK/IL-17 signaling is speculated to be the reason (10.3390/biom10111484).
Another thing to consider. Many CFS/ME patients who report remission, within a few days report a relapse. I recently experienced this myself. Given the assumption that the IDO1 function is the explanation for the major CFS/ME symptoms, why do you have such a fast and immediate relapse? Something must push you back into the metabolic trap and whatever it is, it seems to adapt to the metabolic conditions given by the approached therapy. This also supports my theory that there is an active pathology behind the metabolic trap and this pathology won't disappear by trying to fix the trap only.
A few points. Kynutenine would have to be low in certain cells, but not necessarily the cells that are measured in blood tests. Also it’s not the ODO1 gene that is defective. In humans when IDO1 gets suppressed, most of us have an ODO2 gene that takes over the processing of tryptophan. That gene has mutations in all CFS patients that the lab has Analyzed. Without the IDO2 Gene there is no way to process tryptophan and you’re in the trap.
 
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nerd

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Also it’s not the IDO1 gene that is defective. In humans when IDO1 gets suppressed, most of us have an IDO2 gene that takes over the processing of tryptophan.
Thanks for pointing out.

Kynutenine would have to be low in certain cells, but not necessarily the cells that are measured in blood tests.
I also think it's short-sighted to draw conclusions from blood tests only. This is why I'm so interested in results from the lymphoid system and also from the CSF.

That gene has mutations in all CFS patients that the lab has Analyzed.
Are these mutations published by any chance? Is rs4503083 among them? Regardless, there are a lot of mutations in my IDO2 gene indeed. And yet, why is IDO1 suppressed in the first place?
 
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Another thing to consider. Many CFS/ME patients who report remission, within a few days report a relapse. I recently experienced this myself. Given the assumption that the IDO1 function is the explanation for the major CFS/ME symptoms, why do you have such a fast and immediate relapse?
It's a good question @nerd and one of the big puzzles of me/cfs.
 

nerd

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It’s the way that gene works. It’s called substrate Inhibition. When the substrate, tryptophan, gets too high, it stops working
I think I get it now. Even with normal Tryptophan levels in the average blood cells, we could have elevated Tryptophan inside certain cell types and there, IDO1 would be suppressed due to substrate inhibition and IDO2 would be dysfunctional due to the genotype.
 
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Hi @Janet Dafoe,

Would it be possible to get an update on the kynurenine trial that’s happening in Sweden? The last anyone knew was back in December when someone from India found a speech Dr. Bergquist made in mid-November where he said the trial was postponed until March 2021 due to Covid infection concerns. Has the trial begun or are they waiting until the EU has a higher vaccination rate?
 

nerd

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Interestingly, other pathogens could also intervene with the IDO pathway.

The pathogen with the strongest evidence is Toxoplasma gondii (10.1038/s41419-019-1420-9).

We propose that T. gondii selectively utilizes tryptophan to produce the antioxidant, melatonin, thus prolonging the survival of infected cells through functional AKT and β-catenin activity for better parasite replication. Stable IDO1 in the presence of IFN-γ catabolized tryptophan into kynurenine, promoting cell death by suppressing phospho-AKT and phospho-β-catenin levels, and circumvented parasite replication. Treatment of infected cells with kynurenine or its analogue, teriflunomide suppressed kinase activity of AKT, and phosphorylation of β-catenin triggering caspase-3 dependent apoptosis of infected cells to inhibit parasite growth.
In this case, tryptophan or melatonin wouldn't be beneficial.

They also discuss potential drugs.

Currently, there are several analogues of kynurenine, either commercially available or under clinical trials. Teriflunomide, for example, increases the synthesis of kynurenines in brain, and offers protection from seizures.
Earlier, niacin was used as a drug because it is final product of kynurenine pathway, but niacin has feed-back effects, as higher amounts of niacin exhausts the enzymatic activity of IDO1.
This finding supposedly is from this study (10.1016/0306-3623(92)90017-E), but I couldn't find any mentioning of niacin suppressing IDO1 in it and how the feedback effect is supposed to work.

Maybe someone else shares this experience as well. As previously mentioned, I tried Niacin already. It was a high dose. For a few days, I might have felt a little improvement, but no remission. And after 5 days or so, I got significantly worse. I had GI issues, my extremities felt extremely cold. I was freezing and had tremors that came in waves. 10 seconds tremor, 20 seconds relaxing, and so on. On top of that, tachycardia and low blood pressure etc.

From the herpes family, CMV and HHV6 also have been linked to the IDO1 gene, and this again is linked with Alzheimer's disease (10.1038/s41598-019-45129-8). This reminds me of my other theory of early-onset Alzheimer's in that the Alzheimer's manifestation pathology just is a manifestation of Diabetes-like neuropathy and the causality actually is CFS/ME and its glycolysis issues.
 
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Abrin

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I have been thinking about this update for the last couple of days.

After having time to roll it around in my head, I've got to say, I am hesitantly excited by it.

I know things are still moving forward super slowly but I am still hesitantly excited because things seem to be moving forward.

I am sure that hesitantly excited might not seem like a lot for some people but seeing I've been sick the majority of my life I have got to say it has been a long time since I've been hesitantly excited about anything. :)
 

bensmith

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Dont want to derail, but does niacin feedback mean we shouldnt take it? I have been since becoming ill. It seems to help, at least for a little bit after ingestion. Nad+ didnt work for me really. For some reason.

Also too ill to read the update atm but I’m glad people are feeling positive About it. Thanks for the update Ben and ron/dafoes