Micro-RNA in ME/CFS

Hutan

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Prompted by a recent paper claiming to have identified a micro-RNA signature for endometriosis in saliva:
I have been sceptical about the power of miRNA analysis to help with ME/CFS. I mentioned this to my pain genetics colleagues who have an interest in long non-coding RNAs and they agreed. But I wonder if we should discuss miRNAs in a bit more detail on a thread.

I can see that endometriosis cells and nearby peritoneal cells might chuck out miRNAs of a particular pattern just through random leakage, in the way that prostate specific antigen leaks out of prostate cancer cells.

What I find odd is that they should need to study 109 miRNAs to show the pattern. For most diseases where biomarkers make use of combinations of molecules it is 2, 3 or maybe 4. Presumably the 109 just reflects throwing in anything that adds a little bit more discrimination but it remains puzzling.

My main puzzlement about miRNAs is that I find it hard to see how they could be much use as deliberate biological signals, perhaps passed from one cell to another in extracellular vesicles, as is claimed. If a cell threw out vesicles then why should they reach any other particular cell rather than just got gobbled up by spleen. On the other hand if these are non-specific danger signals or possibly specific signals for lack of something specific like insulin or blood flow then maybe that would not be a worry, if specific vesicle-grabbing cells in immune organs, liver or even brainstem got the message. But then maybe you wouldn't expect any very fancy pattern of miRNAs?

In ME/CFS we do not so far have any indication that any very unusual cells, like endometrial cells, are signalling. Which makes me still sceptical that they would ever be an miRNA signature. On the other hand maybe miRNA analysis might at least tell us about immune cell populations that at present we cannot track by blood tests but which are behaving badly in a way that is reflected in miRNA output. My memory is that there have been studies from Canada but I haven't heard more about that recently.

There have been some studies of micro-RNA in the blood of people with ME/CFS. It's worth having another look at the papers to see where we have got to.
 

Differential expression of miR-558, miR-146a, miR-150, miR-124, and miR-143 was significantly down regulated and notably interfered with pain intensity and frequency in patients with CFS.
We weren't too impressed with this paper.
 
Nor this one that had 9 participants and aimed to identify changes in microRNA after sessions of yoga. There were no healthy controls.

 
This one is from Maureen Hanson's lab - microRNA in PBMCs and EVs. I'm not sure if we have heard more from them?



PBMCs
Over-expressed (p<0.05)

  • miR-374a-5p
  • miRNA-4516
  • miR-340–5p
  • miR-140-5p
  • miR-18a-5p
  • miR-146a-5p
  • miR-106a-5p
  • miR-17-5p
  • miR-106b
p<0.1
  • miR-21-5p
Under-expressed (p<0.05)
  • miR-644a
  • miR-451a
  • miR-4454
  • miR-7975
  • miR-549a
  • miR361-3p
  • miR-1253
  • miR-590-5p
EVs
Over-expressed (p<0.05)
  • miR-4454
  • miR-7975
  • miR-150-5p
  • miR-15a-5p
  • let-7d-5p
  • miR-423-5p
  • miR-374a-5p
  • miR-130a-3p
p<0.1
  • miR-21-5p
  • miR-320e
  • miR-185-5p
  • let-7g-5p
  • miR-126-3p
  • miR-223-3p
  • miR-93-5p
Under-expressed (p<0.05)
  • miR-183-3p
  • miR-33a-5p
p<0.1
  • miR-203a-5p
  • miR-607
  • miR-369-3p
Bold are miRs that are differentially expressed in both the PBMCs and EVs. Note that miR-4454 and miR-7975 are over-expressed in EVs but under-expressed in PBMCs. The paper says "At present, the significance of these differences is not understood." (I don't know if one possibility would be that PBMCs are off-loading those particular miRs via EVs.)
 
There was this thesis.
 
This one was from Klimas' lab. The results were underwhelming, just a couple of microRNAs were different from healthy controls only in males:
miRNA-423-5p and miRNA-4443

 
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This one was from the Moreau lab. It looked at microRNA before and after the application of an inflatable cuff stressor (like a blood pressure cuff). to people with severe ME/CFS.

We don't seem to have discussed the microRNA findings much. Nepotchatykh is the primary author of the study (her thesis is in post #6 of this thread.



"In the present study, we performed extensive profiling of circulating miRNAs on plasma samples of patients with severe ME/CFS (housebound), both at baseline and in response to the application of a post-exertional stress challenge. This unique experimental design led us to determine distinct molecular footprints of ME/CFS by comparing the differential expression plasma miRNA levels before and after 90 min of stimulation, which induced PEM, compared to age- and sex-matched controls. With implementa-tion of a machine learning algorithm (i.e., Random Forest), we validated eleven microRNAs (
hsa-miR-28-5p,
hsa-miR-29a-3p,
hsa-miR-127-3p,
hsa-miR-140-5p,
hsa-miR-150-5p,
hsa-miR-181b-5p,
hsa-miR-374b-5p,
hsa-miR-486-5p,
hsa-miR-3620-3p,
hsa-miR-4433a-5p, and
hsa-miR-6819-3p),
the first diagnostic panel of its kind.

Differential expression of these eleven circulating miRNAs led to the identification of four ME/CFS clusters with distinct miRNA profiles and specific symptom severities"
 
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This one is another from the Moreau team, from 2023, working with plasma samples. We had some questions about whether there might have been some technical problems with the fibromyalgia samples, but the ME/CFS results might be worth checking out.

It was noted by the people doing the endometriosis study that saliva samples are a lot easier to work with than blood samples.



These are the three miRNA that were different between the ME/CFS samples and the healthy controls (all of which made the short list in the 2020 study). I think the levels were higher in ME/CFS but need to check that.

hsa-miR-127-3p
hsa-miR-374b-5p
hsa-miR-140-5p
 
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So possibly Moreau's lab identified miR-374b-5p as having a higher expression in ME/CFS compared to controls , and Hanson's lab identified miR-374a-5p as being over-expressed (in PBMCs and in EVs). I'm not sure how consequential the 'a' and 'b' difference is.

If you click on those links in my last post (copied from @SNT Gatchaman), it takes you to a database where you can click through to see the known targets of the specific miRNA. There are number of X chromosome targets for miR374b-5p.

I think I need to read the discussion section of the Hanson and Moreau papers. It would be interesting to have a good look at the targets of the miR374.
 
Super interesting.

Differential expression of these eleven circulating miRNAs led to the identification of four ME/CFS clusters with distinct miRNA profiles and specific symptom severities"
I need to read this study but this was exactly what I was wondering: could a large study potentially find subtypes (if they exist) in an unbiased way.

I’m going to try and read up on just the basics of miRNA. I’m curious how far along they’ve gone as a biomarker in other diseases (looks like a lot of the interest has been in various cancers?). Im also wondering how consistent salivary miRNA is. Do people have similar profiles day to day?

AI summaries from https://mirbase.org (hard to know how accurate these are):
Ooo this AI summary at least provides references, which helps a lot.
 
I’m going to try and read up on just the basics of miRNA. I’m curious how far along they’ve gone as a biomarker in other diseases (looks like a lot of the interest has been in various cancers?). Im also wondering how consistent salivary miRNA is. Do people have similar profiles day to day?
A lot of miRNA screens have been done in almost every context, especially cancer, largely because the technology for it is pretty cheap these days. It’s similar to differential gene expression where nearly every comparison will show some differences, but those findings often won’t replicate between cohorts or it’s very hard to draw conclusions on what those differences really mean. And compared to genomic studies, we tend to have even less information about what the miRNAs in question actually do.

There are a couple instances I know of where miRNAs were experimentally confirmed to be actually central to the disease process—Hep C infection is the example that comes to mind.
 
Finally had a break from the brain fog long enough to write a reply here..

@Jonathan Edwards raised this point in another thread:
My main puzzlement about miRNAs is that I find it hard to see how they could be much use as deliberate biological signals, perhaps passed from one cell to another in extracellular vesicles, as is claimed. If a cell threw out vesicles then why should they reach any other particular cell rather than just got gobbled up by spleen. On the other hand if these are non-specific danger signals or possibly specific signals for lack of something specific like insulin or blood flow then maybe that would not be a worry, if specific vesicle-grabbing cells in immune organs, liver or even brainstem got the message. But then maybe you wouldn't expect any very fancy pattern of miRNAs?

I came across a review (Extracellular miRNAs: From Biomarkers to Mediators of Physiology and Disease) which, tbh, doesn't really answer that question but at least gave me some background on why researchers are even *thinking* miRNA might be travelling between cells/tissues. They were discussing experiments where mice were genetically altered to (mostly) not produce miRNAs in specific tissues (e.g. knock-out only in fat, or only in liver) and the resulting phenotype was studied.
For example, fat-specific DICER knockout mice [ie. mice who's fat cells can't produce miRNA normally] exhibit changes in hepatic gene expression which are reversed when mice are transplanted with normal adipose tissue, suggesting that these changes are controlled by miRNAs secreted from the adipose tissue (Thomou et al., 2017).
This raises the hypothesis that the miRNA pool of each cell is the sum of endogenous miRNA production and uptake of exogenous miRNAs. This hypothesis may explain why following [disrupting miRNA production] in hepatocytes, only 45 of the several hundred miRNAs detected in liver are downregulated (Sekine et al., 2009).

Sounds like they don't know how the miRNA would be sent to specific target cells:
Also, different types of extracellular particles may be taken up by cells differently (Horibe et al., 2018; McKelvey et al., 2015), and this could affect both effectiveness of entry and which miRNAs will remain active in the host cell. Proteins located on the EV membrane and the host cell membrane are thought to determine host cell selectivity and the mechanism of EV uptake, although details of this mechanism and how this varies from cell to cell is not clear (McKelvey et al., 2015).

Also, a possible confounder to any studies in ME/CFS, this quote from the same paper suggests exercise/activity-level impacts miRNAs:
In addition, changes in levels of circulating miRNAs and EVs have been shown to correlate with differences in lifestyle activities, such as exercise (Flowers et al., 2015; Rome, 2015; Safdar et al., 2016; Whitham et al., 2018), and the composition of gut microbiota (Beatty et al., 2014), suggesting that extracellular miRNAs may serve as circulating indicators of the physiological status of the individual
 
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