Systems Modeling Reveals Shared Metabolic Dysregulation and Novel Therapeutic Treatments in ME/CFS and Long COVID, 2024, Gong-Hua et al

[Andy]

Now published - link to abstract


Preprint
Abstract

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Long COVID are complex, multisystemic conditions that pose ongoing challenges to healthcare professionals. Emerging research suggests that ME/CFS and Long COVID exhibit overlapping metabolic symptoms, indicating possible shared metabolic dysfunctions.

This study aims to systematically explore these shared metabolic disturbances and their potential treatments. Utilizing our novel metabolic modeling method, GPMM, we identified the key metabolic irregularities in patients with ME/CFS and Long COVID, notably the downregulation of the alanine and aspartate metabolism pathway, and the arginine and proline metabolism pathway. Genome-wide knockout analyses indicated that supplementation with aspartate (ASP) or asparagine (ASN) could potentially ameliorate these metabolic deficiencies. Further metabolic assessments in Long COVID patients highlighted the significant downregulation of ASP in both blood and muscle, supporting our predictions.

Consequently, we propose that the combination of l-ornithine and l-aspartate (LOLA) offers a promising approach to alleviate metabolic symptoms in both ME/CFS and Long COVID patients. This study not only elucidates the shared metabolic pathways in ME/CFS and Long COVID but also positions LOLA as a viable candidate for future clinical trials.

https://www.biorxiv.org/content/10.1101/2024.06.17.599450v1?ct=

 

[EndME]

First off it’s good to see research on LC and ME/CFS coming out of China.

It seems like they used a novel metabolic modeling method called GPMM (Genome-wide precision metabolic modeling), which is something the authors for example used, or possibly introduced, in this paper https://pubmed.ncbi.nlm.nih.gov/35343058/ (not well cited).

To run their model on ME the authors simply used the data from the intramural study. Which means that it seems to have sparked some international interest. To run their model on LC they used the data by Wüst et al.

 

[Andy]

First off it’s good to see research on LC and ME/CFS coming out of China.

Also, two of the authors are listed as at Massachusetts General Hospital, Harvard Medical School.

 

[mariovitali]

I have been taking part on meetings with the team of Wenzhong Xiao since last November and witnessed their work on using computational methods to identify research "hotspots". Really impressed with their work and there are more upcoming targets which are very interesting IMHO. Note that LOLA is used for managing hepatic encephalopathy :

https://www.elsevier.es/en-revista-...-l-ornithine-l-aspartate-in-S1665268119316084

 

[SNT Gatchaman]

Quoting Hutan from another thread.

I listened to Wenzhong Xiao who comes across as a safe pair of hands. I think he said that he feels confident that, with the tools available including the metabolomics that he concentrates on, they are unravelling the causes of ME/CFS. Praise be! - he was sensible about cortisol, noting the changes in lifestyle including sleep problems that of course will flatten the morning cortisol peak. He also notes other issues that metabolomics researchers need to be aware of, including how different techniques can produce different results. He says that there needs to be more work done on techniques in order to get better data.

 

[EndME]

I cannot comment on the merits of their method, but I think it's excellent that people on this forum and elsewhere are analysing and re-analysing some of the data from the intramural study. I do think it contains some valuable information (for example on diagnostic accuracy, POTS/POT/OI, etc).

One of the more interesting findings of the intramural study to me, which wasn't reported in the paper, were the differences in ANA levels between patients and controls. 24% of ME/CFS patients had positive antinuclear antibodies and only 5% of controls (supplementary material 9). @MelbME do you think there is any aspect under which this can be re-analysed or dived into?

 

[MelbME]

I cannot comment on the merits of their method, but I think it's excellent that people on this forum and elsewhere are analysing and re-analysing some of the data from the intramural study. I do think it contains some valuable information (for example on diagnostic accuracy, POTS/POT/OI, etc).

One of the more interesting findings of the intramural study to me, which wasn't reported in the paper, were the differences in ANA levels between patients and controls. 24% of ME/CFS patients had positive antinuclear antibodies and only 5% of controls (supplementary material 9). @MelbME do you think there is any aspect under which this can be re-analysed or dived into?

ANA levels have been observed to be elevated in ME cohorts on several occasions from memory. It would be good to know if this is a predisposing factor or an issue of under diagnosing other autoimmune issues or if it's a developed phenomenon.

I will chat to Wenzhong next week and ask him about the data, I'll ask if he's looking into it more.

 

[MelbME]

I think this is an interesting paper. I would be interested in the outcome of this treatment concept as well. Difficult part is working out how to get metabolites like these to the tissues of need.

 

[Hutan]

Quoting Hutan from another thread.

Ha, thank you SNT. I did not recognise the name.

It's terrific that Wenzhong is working with people in Kunming, China. We hear so little about how ME/CFS is regarded in China, let alone in Yunnan. There's a decent understanding of ME/CFS and Long Covid here:

Both conditions have been associated with a wide range of debilitating symptoms, including but not limited to profound fatigue, cognitive impairment, and post-exertional malaise, which severely impacting the quality of life of affected individuals2.

Edit to add:

This work was supported by grants from Open Medicine Foundation and the Stupski Foundation (WX). Yunnan Ten Thousand Talents Plan Young & Elite Talents Project (G.-H.L.), Yunnan Fundamental Research Projects (202101AS070058).

 

[Hutan]

I'm a bit puzzled.

Metabolic Modeling of ME/CFS Patient Muscle Reveals Altered Metabolism

To investigate metabolic changes in ME/CFS, we conducted metabolic modeling using muscle samples from the ME/CFS dataset5. This dataset comprises 13 ME/CFS patients and 12 healthy controls. The modeling process involved 2841 reactions, with 65 reactions showing significant up-regulation and 52 reactions significantly down-regulated (Figure 2A). Pathway analysis revealed that several metabolic pathways were affected. Specifically, Alanine and aspartate metabolism, Pyrimidine catabolism, Aminosugar metabolism, and Arginine and proline metabolism pathways were significantly down-regulated (FDR < 0.05). Conversely, the Pentose phosphate pathway exhibited significant up-regulation (FDR < 0.05). Notably, the most prominently down-regulated pathway was Alanine and aspartate metabolism (Figure 2B).

Furthermore, our all-against-all knockout analysis highlighted ASN and ASP as agonist metabolites. Administering these two amino acids could potentially rescue the metabolic changes observed in ME/CFS patients. This knockout result aligned with the modeling findings and supported the notion of dysfunction in Alanine and aspartate metabolism among ME/CFS patients4.

Metabolism of Long COVID Reveals Down-Regulated Asparagine (ASN) in Blood and Muscle

Given the similarity in symptoms between long COVID and ME/CFS, weanalyzed the metabolic profile in Long COVID patients. As post-exertional malaise (PEM) is a common metabolic symptom shared by both conditions, we performed pairwise comparisons between pre- and post-exercise samples from Long COVID patients and healthy controls using data from a post-exertional malaise Long COVID study6(Supplementary Data S1). Significant changes were noted in muscle tissue, particularly with asparagine and dihydroxyacetone-P being down-regulated.. Notably, Asparagine emerged as the top-ranked down-regulated metabolite in muscle samples of Long COVID patients (Figure 3A). Similarly, in blood samples, Asparagine also ranked highest among down-regulated metabolites following PEM in Long COVID patients (Figure 3B).
Collectively, these findings from both ME/CFS and Long COVID studies consistently highlighted that the most significant metabolic alteration was the down-regulation of the ASN/ASP metabolism.

For ME/CFS, they find issues with alanine and aspartate, and then "ASN" is mentioned out of nowhere, with no explanation of the acronym.
Then in Long Covid, there's no mention of alanine and aspartate, but there are issues with Asparagine, which is also referred to as ASN.

The lack of detail in the ME/CFS section about where the asparagine comes into the picture is puzzling, especially as that is the link with the Long Covid findings. And they later say

1) L-Aspartate aligns with the commonly observed down-regulation of ASN/ASP in both ME/CFS and Long COVID, suggesting it could help counteract this deficiency.

even though aspartate isn't specifically mentioned in the LC section.


Googling, I think the three molecules may convert between themselves. But, if so, then I think we needed that connection spelled out in the results in order to follow the links the authors are making.

The Long Covid work uses data from
Appelman B, Charlton BT, Goulding RP, et al. Muscle abnormalities worsen after post-exertional malaise in long COVID. Nat Commun 2024; 15(1): 17.
That's the Wust paper - thread here:
Muscle abnormalities worsen after post-exertional malaise in long COVID, 2023/4, Wüst, van Vugt, Appelman et al

Assuming there is some tight connection between alanine, aspartate and asparagine, these findings from muscle metabolites are really interesting, and the field of metabolic modelling is fascinating.

 

[SNT Gatchaman]

According to KEGG - ASN is asparagine (link to abbreviations)

From Pathway for alanine, aspartate, glutamate

L-alanine <----- L-aspartate -----> L-asparagine

 

[DMissa]

If I am reading this right their ME/CFS data is the RNAseq data from the Wallitt study muscle samples.

DNA -> RNA -> protein -> metabolic function.

This paper seems to say: RNA = metabolic function = treatment target.

Am I missing something?

"GPMM 10 integrates protein abundance estimates from gene expression data" from RNAseq?

"significant metabolic commonalities" using RNA data in one disease case and metabolite data in the other?

Quoting Hutan from another thread.

"I think he said that he feels confident that...they are unravelling the causes of ME/CFS"

Back to the paper:
"Consequently, we propose that the combination of l-ornithine and l-aspartate (LOLA) offers a promising approach to alleviate metabolic symptoms in both ME/CFS and Long COVID patients. This study not only elucidates the shared metabolic pathways in ME/CFS and Long COVID but also positions LOLA as a viable candidate for future clinical trials"

I suspect that this isn't at where they think it is yet. That is my good-faith assessment.

 

[MelbME]

I'm a bit puzzled.




For ME/CFS, they find issues with alanine and aspartate, and then "ASN" is mentioned out of nowhere, with no explanation of the acronym.
Then in Long Covid, there's no mention of alanine and aspartate, but there are issues with Asparagine, which is also referred to as ASN.

The lack of detail in the ME/CFS section about where the asparagine comes into the picture is puzzling, especially as that is the link with the Long Covid findings. And they later say

even though aspartate isn't specifically mentioned in the LC section.


Googling, I think the three molecules may convert between themselves. But, if so, then I think we needed that connection spelled out in the results in order to follow the links the authors are making.

The Long Covid work uses data from
Appelman B, Charlton BT, Goulding RP, et al. Muscle abnormalities worsen after post-exertional malaise in long COVID. Nat Commun 2024; 15(1): 17.
That's the Wust paper - thread here:
Muscle abnormalities worsen after post-exertional malaise in long COVID, 2023/4, Wüst, van Vugt, Appelman et al

Assuming there is some tight connection between alanine, aspartate and asparagine, these findings from muscle metabolites are really interesting, and the field of metabolic modelling is fascinating.

Pathway analyses are a bit clunky. They are simply a guide to suggest that metabolites in this network of pathways are enriched.

They help to focus ideas.

Aspartate and alanine pathway includes aspartate and asparagine.

 

[Hutan]

Pathway analyses are a bit clunky. They are simply a guide to suggest that metabolites in this network of pathways are enriched.

They help to focus ideas.

Aspartate and alanine pathway includes aspartate and asparagine.

Great. The point though is that in the Long covid data, they only talk about asparagine being down regulated. I think the paper should have made clear that asparagine is part of the alanine and aspartate pathway and when it is down-regulated that means that the whole pathway is down regulated, as part of the process of saying 'look we are finding the same sort of thing in these two cohorts'. They needed to tie the two together more conclusively if they were going to propose the same treatment for both. For all we know from this paper, the identified down-regulated reactions in the ME/CFS group and the metabolites in the Long Covid group might have been indicating quite different functioning of the aspartate and alanine pathway in each group.

I mean, I think that's unlikely, I think ME/CFS and ME/CFS-like Long Covid are the same things, but to goes to @DMissa's point on another thread that a bit more thought needs to be given to what is actually happening in a pathway. Perhaps these investigators know exactly what is happening in the pathway or have very good ideas - I just think they should have told us something.

 

[Arnie Pye]

Edit : Asparagine is referred to as a non-essential amino acid i.e. the body can make it.

It occurs to me that if ASN turns out to be important in keeping people well, and in avoiding ME/CFS, then perhaps there are genetic problems in the creation of ASN in some people.

Edit 2 : I've just managed to screw up my post by unwise deletion of bits of it!

 

[Hutan]

ASN is mentioned in the top line of your second quote.

Yes, it is mentioned in the Long Covid section. But, in the ME/CFS section, which comes first, it is just mentioned as an acronym 'ASN', with no explanation how it fits in an Alanine and Aspartame pathway.

 

[MelbME]

Great. The point though is that in the Long covid data, they only talk about asparagine being down regulated. I think the paper should have made clear that asparagine is part of the alanine and aspartate pathway and when it is down-regulated that means that the whole pathway is down regulated, as part of the process of saying 'look we are finding the same sort of thing in these two cohorts'. They needed to tie the two together more conclusively if they were going to propose the same treatment for both. For all we know from this paper, the identified down-regulated reactions in the ME/CFS group and the metabolites in the Long Covid group might have been indicating quite different functioning of the aspartate and alanine pathway in each group.

I mean, I think that's unlikely, I think ME/CFS and ME/CFS-like Long Covid are the same things, but to goes to @DMissa's point on another thread that a bit more thought needs to be given to what is actually happening in a pathway. Perhaps these investigators know exactly what is happening in the pathway or have very good ideas - I just think they should have told us something.

I don't know if they do know what's happening in the pathway. Statisticians typically stick to reporting facts rather than interpreting them in my experience.

My guess is that the conclusion of asp and asn is largely driven by what they saw in the pathway. But yes, that doesn't seem to be revealed explicitly from what I can see.

 

[MelbME]

Yes, it is mentioned in the Long Covid section. But, in the ME/CFS section, which comes first, it is just mentioned as an acronym 'ASN', with no explanation how it fits in an Alanine and Aspartame pathway.

Asparagine is simply aspartate with an NH3 added.
Alanine is pyruvate with an NH3 added.

Adding Asparagine or Aspartate would probably produce a similar outcome though asparagine comes with more NH3.

 

[Jonathan Edwards]

The increasing emphasis on amino acid metabolism in ME/CFS seems interesting. A shift in metabolism that might in a crude sense be 'anti-inflammatory rather than inflammatory might make some sense.

I doubt, however, that simply increasing availability of substrates for down regulated pathways would be likely to help. It is very likely that the pathways are down regulated as part of an adaptive diversion of resources and adding in substrate may simply aggravate things. An analogy would be pouring in protein to patients with nephrotic syndrome.

The solution will be to find out why the pathway is downrgulated and address that mechanism I think.

 

[DMissa]

The increasing emphasis on amino acid metabolism in ME/CFS seems interesting. A shift in metabolism that might in a crude sense be 'anti-inflammatory rather than inflammatory might make some sense.

I doubt, however, that simply increasing availability of substrates for down regulated pathways would be likely to help. It is very likely that the pathways are down regulated as part of an adaptive diversion of resources and adding in substrate may simply aggravate things. An analogy would be pouring in protein to patients with nephrotic syndrome.

The solution will be to find out why the pathway is downrgulated and address that mechanism I think.

In strongly agreeing with this I would also add as a general comment to readers that I think tissue context always needs to be front and centre when we think about these metabolic questions. Eg a T cell upregulating glycolysis or a muscle cell doing so can be driven by mechanisms not even present in the other cell type.