Pre-Illness Data reveals Differences in Multiple Metabolites and Metabolic Pathways in Those Who Do and Do Not Recover from IM, 2022, Jason et al

That spermidine / spermine relationship looks potentially interesting. Spermidine is an intermediate precursor of spermine. From Wikipedia —

So the pathway is ornithine -> putrescine -> spermidine -> spermine (the latter two via the enzymes spermidine synthase and then spermine synthase).

The page also notes "Spermidine inhibits neuronal nitric oxide synthase (nNOS)".

Two of the most significant differences in @chillier's chart above are spermidine (up in ME) and spermine (down in ME), which might suggest something is preventing the action of spermine synthase?

The thread paper comments on oxidative stress —

I wonder if other ways spermine could relate to ME/CFS beyond this include RBC deformability (relating to nitric oxide and acetylcholine). From the abstract in Effects of acetylcholine and SpermineNONOate on erythrocyte hemorheologic and oxygen carrying properties (2001, Clinical Hemorheology and Microcirculation) —

(Spermine NONOate is a nitric oxid donor.) So possibly reduced spermine may impact nitric oxide function and reduce RBC deformability.

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Spermine synthase (2009, Cellular and Molecular Life Sciences)

Nonneuronal Cholinergic System in Human Erythrocytes: Biological Role and Clinical Relevance (2010, Journal of Membrane Biology)

The function of spermine (2014, IUBMB Life)

 

My understanding from Lenny a couple years ago was that they did plan to do this. Certainly it would be possible, given the samples they have, I would guess.

 

The pre-illness approach is great. The weird categorisation is worrying because it makes no sense, which raises the possibility it is post hoc, created to get some decent results. It was a huge study with a lot riding on it, so a lot of pressure.

I'm glad you have found something in it, and appreciate you redoing it with an FDR of 0.05. Can you see any obvious way those metabolite results might lead to an increased risk of poor recovery from an infection? My ability to 'read' metabolites is non-existent.

For those to whom FDR is jargon,
a p=0.05 means (loosely) there is a 5% or one in 20 chance of a false positive. By contrast, an FDR (False Discovery Rate) of 0.05 means you would expect only one in 20 positive results to be false positives, i.e. you would expect most results to be good (assuming a model experimental design...).

Bonferroni is very strict (I'm not a fan as it inevitably leads to a high rate of false negatives) - and if only 1 in 20 positive results are false positives, I am happy - at least with the stats side of things.

 

Spermidine is the second most significant hit in the NIH intramural study's metabolomic data, as well as other polyamine related metabolites nearby (N-acetylputrescine).

Lots of other interesting things in there too in particular pyrroline-5-carboxylate/ arginine - these weren't seen in jason's data but have been seen in a few other places.

EDIT: I've just noticed that many of those p values are higher than the adjusted p values. This is... odd. How is spermidine not significant at p=0.056 but significant after it has been corrected for multiple testing correction at p=0.0036? Am I getting confused here?

 

Oh yeah very good point.

I haven't gone into that myself but if @LarsSG is right about this that's reassuring.

To me it looks like maybe three pathways involved here. Purine metabolism, Urea cycle, Glutathione metabolism. Urea cycle and glutathione metabolism are linked closely to nitrogen metabolism more generally (through glutamate). You could maybe argue purine metabolism is linked to this too. Here's a plot of enriched pathways:

 

Urea cycle:
Carbamoyl phosphate synthesis is the rate limiting step of the urea cycle, it's formed from the combination of ammonia and bicarbonate. It's then attached to ornithine by ornithine transcarbamoylase.
Ornithine is the precursor to putrescine which goes on to make spermidine and spermine as @SNT Gatchaman mentioned.

Glutathione metabolism:
Glutathione has antioxidant properties, it's involved in redox reactions detoxifying various things. Glutathione disulfide is its spent oxidised form which needs to be regenerated back to glutathione. The synthesis of it requires glutamate, as well as cysteine, which can be produced from the transulfuration pathway from S-Adenosyl-L-methionine and produces 2-Hydroxybutyrate as a byproduct.

Purine nucleotide metabolism:
Purine bases Adenine and Guanine, and their nucleotide forms ATP, ADP, GTP, and GDP are synthesised from inositol monophosphate, which itself requires glutamine for synthesis. Xanthine and hypoxanthine are degradation products of purine nucleotides and go on to form uric acid for excretion. They can also be reused to make inositol monophosphate, maybe to regenerate purine nucleotides in the absence of glutamine? (ok this is conjecture territory now I admit).

Obviously the disease relevance of all this is pure speculation I'm just thinking out loud here: Maybe urea cycle problems lead to a build up of ammonia after exercise? Problems at the centre of nitrogen metabolism like this could lead to a difficulty synthesizing all kinds of important nitrogen based molecules. Problems with glutathione leading a difficulty removing free radicals and detoxifying in a very general way?

Here's a schematic I made of the pathways represented here:

(*transulfation should be transsulfuration)