Dysregulated Provision of Oxidisable Substrates to the Mitochondria in ME/CFS Lymphoblasts, 2021, Missailidis et al

Can someone tell me the significance of all the significant up and downregulations in the gene pathways? Seemed to be a lot, but I dont know much about proteomics/transciptomics

Edit: Mentioned here i guess: "A feature of our results is the striking difference in the pattern of expression changes at the RNA and protein levels. The proteomics revealed a broad pattern of elevated ex-pression of proteins involved in alternatives to glycolytic provision and catabolism of ox-idisable substrates for mitochondrial respiration. By contrast, the levels of transcripts en-coding these proteins were, in many cases, either unchanged or decreased. This is an un-expected but important insight into the underlying cytopathological mechanisms of ME/CFS. It suggests that the overall pattern of dysregulation in ME/CFS cells is a result of a network of normally homeostatic pathways, including competing antagonistic elements like elevated mTORC1 and AMPK activities, that regulate gene expression and metabo-lism at the transcriptional, translational and posttranslational levels [65]. The major path-ways we found to be dysregulated in this way are β-oxidation of fatty acids, glutamine metabolism, branched-chain amino acid catabolism and proteasomal protein degradation."

 

In his 2019 Australian conference talk Dr Fisher said he has used Lymphoblasts in several past mitochondria studies - one might have been parkinsons I think. He described that they continue to grow and you can siphon of a portion to do more studies so that what you are comparing is from the same source and not another patient time point.

So for example they found Complex V issues on patient sample ABC1. At a later date they can take some more cells from this ABC1 sample and do proteomics and metabolomics. The results from the various experiments can be correlated due to being based on the the same cells with the same properties. You don't need to keep going back to the same patient and ask for another blood draw at a different time point, and where the cells may have different characteristic.

I hope I understand and remembered that right?

 

Mitochondrial complex V is also called ATP synthase. A decline in its function seems like it would be a big deal (especially if this affects all cells). It's not the only source of energy in the body but it's a big one.

 

@Hutan Here is the video - starting about 6 mins. The problem with lymphocytes are that they are small - harder to measure energy - and that they are continually dying. Detailed info about lympoblasts at 8:30mins
https://mecfsconference.org.au/videos/paulfisher/

 

Just got through the paper.. Learned quite a bit by reading up on the side. Its very thorough, probably one of the more thorough ive read in this field.

I like that they have concrete hypothesizes, not only "more research on X is warranted".

Id say its time to replicate these findings by an independent group, and also look at other cells.

 

I've wondered too about what the immortalisation process does, and is that a key part of the experiment.

Bhupesh Prusty has taken model cells cultured in patient and control plasma and then exposed them to H1N1 & HSV1. Most cells cultured in patient plasma showed a strong antiviral response if I remember right. I wonder if the process of exposing the patient lymphocytes to EBV programs an antiviral response in the lymphocytes of patients that then stays with the cells as they become lymphoblasts and that antiviral response is stronger than with controls........

 

Williams and Ariza at Ohio State University have been studying EBV in ME/CFS for quite some time. I wonder if they would have any ideas about looking for differences in antiviral properties of the cell such as quantifying herpes virus proteins/dUTPases in the lymphoblast culture. Or maybe that will not be relevant when the cells are washed after the immortalisation................ Just guessing/brainstorming

 

It may well feel like so, but note that they say in your quotation, it would not reach statistical relevance, in my understanding they say, they found a(nother) tendency, or in a likely interpretation, it may well be a downstream-effect,

as

quotes:

 

I was curious what exactly they meant with "energy stress signalling"

 

Because peripheral blood is very easy to sample and in blood you basically only have white blood cells, red blood cells, and platelets. The latter two aren’t useful to study in this context, so lymphocytes are selected from WBC. They could’ve selected other WBC types though not sure if there’s any value add there.

 

... completely right.

my understanding was, that they meant an altered energy utilization for any purpose not known right now (maybe a response to an supposed infection or within wound healing pathways; or a counter for that). This would not be a genuine ansewere to impaired glycolysis (which they say indeed, in Michel Tacks quote, would not be the case).

But maybe they mean that an impaired energy utilization elsewhere affects lymphoblasts? - (for a technical reason I am not prepared to read the paper rn)

 

Thanks, thats probably what they meant

 

Look up AMPK function

 

It wasn't easy. I knew that something in high-protein foods was making my symptoms worse. Peanut and soy butter had the same effect, so it wasn't meat-only. Then I remembered that I had some gelatin in my cupboard. That was the worst trigger yet, and it's essentially amino acids, and three of those--glycine, proline and alanine--were 15-20x higher than the ratios in peanuts, so they were my top suspects. I then checked the AA content of other foods that I did or didn't react to, which allowed me to cross off some of the other AAs, such as lysine. Next step was to establish the level needed to trigger the symptoms. Two strips of bacon didn't cause problems, but four did.

One issue that led to confusion was that I tested those other foods with bread or pancakes, since 'those are safe!'. Nope, the amounts of wheat-based food was just under my threshold for triggering symptoms. Once I figured that out, I found that the amount of bacon that triggered my symptoms contained ~1400 mg of proline. I then took my hypothesis of '1400 mg of total proline will trigger symptoms' and tested it with several other foods. They all matched expectations. Whole wheat flour is particularly rich in proline, so there goes a big part of my dietary choices. Meat too.

Here's a useful tool for determining amino acid content: https://tools.myfooddata.com/protein-calculator It doesn't list all foods, but I still found it useful.

 

Aaah very cool