Perturbation of effector and regulatory T cell subsets in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) (2019) Karhan, Unutmaz et al

So are a lot of the t-cells "old cells"? Im just thinking how that could explain the chronic nature of ME
 
Marky said:
So are a lot of the t-cells "old cells"? Im just thinking how that could explain the chronic nature of ME
Click to expand...

Presumably T cell clones educated during infancy are still around to protect against measles in old age but they Amy have undergone many divisions during that time I guess. Immune responses tend to get fixed in memory mechanisms that are pretty much life long and most, although not all, immune mediated disorders seem to continue long term.
 
Merged thread - the pre-print is now available.

Abstract

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disorder of unknown etiology, and diagnosis of the disease is largely based on clinical symptoms. We hypothesized that immunological disruption is the major driver of this disease and analyzed a large cohort of ME/CFS patient or control blood samples for differences in T cell subset frequencies and functions.

We found that the ratio of CD4+ to CD8+ T cells and the proportion of CD8+ effector memory T cells were increased, whereas NK cells were reduced in ME/CFS patients younger than 50 years old compared to a healthy control group. Remarkably, major differences were observed in Th1, Th2, Th17 and mucosal-associated invariant T (MAIT) T cell subset functions across all ages of patients compared to healthy subjects. While CCR6+ Th17 cells in ME/CFS secreted less IL-17 compared to controls, their overall frequency was higher. Similarly, MAIT cells from patients secreted lower IFNgamma;, GranzymeA and IL-17 upon activation.

Together, these findings suggest chronic stimulation of these T cell populations in ME/CFS patients. In contrast, the frequency of regulatory T cells (Tregs), which control excessive immune activation, was higher in ME/CFS patients. Finally, using a machine learning algorithm called random forest, we determined that the set of T cell parameters analyzed could identify more than 90% of the subjects in the ME/CFS cohort as patients (93% true positive rate or sensitivity).

In conclusion, these multiple and major perturbations or dysfunctions in T cell subsets in ME/CFS patients suggest potential chronic infections or microbiome dysbiosis. These findings also have implications for development of ME/CFS specific immune biomarkers and reveal potential targets for novel therapeutic interventions.
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https://www.biorxiv.org/content/10.1101/2019.12.23.887505v1

This is a pre-print that has not been peer reviewed.
 
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Could you change the title from Unutmaz et al. to Karhan et al.?

One can always indicate who the foremost author is (the person that helps us to recognize the research team) in the post below but for titles, the first author is normally used and it can be confusing if you use another name.

Apologies for nitpicking.
 
Just for easier reading

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disorder of unknown etiology, and diagnosis of the disease is largely based on clinical symptoms.

We hypothesized that immunological disruption is the major driver of this disease and analyzed a large cohort of ME/CFS patient or control blood samples for differences in T cell subset frequencies and functions.

We found that the ratio of CD4+ to CD8+ T cells and the proportion of CD8+ effector memory T cells were increased, whereas NK cells were reduced in ME/CFS patients younger than 50 years old compared to a healthy control group.

Remarkably, major differences were observed in Th1, Th2, Th17 and mucosal-associated invariant T (MAIT) T cell subset functions across all ages of patients compared to healthy subjects.

While CCR6+ Th17 cells in ME/CFS secreted less IL-17 compared to controls, their overall frequency was higher.
Similarly, MAIT cells from patients secreted lower IFNgamma;, GranzymeA and IL-17 upon activation.

Together, these findings suggest chronic stimulation of these T cell populations in ME/CFS patients.

In contrast, the frequency of regulatory T cells (Tregs), which control excessive immune activation, was higher in ME/CFS patients.

Finally, using a machine learning algorithm called random forest, we determined that the set of T cell parameters analyzed could identify more than 90% of the subjects in the ME/CFS cohort as patients (93% true positive rate or sensitivity).

In conclusion, these multiple and major perturbations or dysfunctions in T cell subsets in ME/CFS patients suggest potential chronic infections or microbiome dysbiosis.

These findings also have implications for development of ME/CFS specific immune biomarkers and reveal potential targets for novel therapeutic interventions.
Click to expand...
 
It'd be great if these findings can be replicated with a larger group and in more than one lab. I imagine that interpreting the T-cell perturbations will be complex work and subject to a lot of debate, but if the specific 'ME profile' held up in even 60% of patients, it would be a big step forward.
 
There is a bunch of graphs in the paper. I don't know how to interpret this imunology but the overall impression is that of there being little differences between patients and controls. With a large sample size, even small differences can become statistically significant. A few graphs seem to show something that might be a meaningful difference (eg. interferon gamma of MAIT cells).

My question to any expert: are these findings potentially important clues to the disease process?
 
strategist said:
don't know how to interpret this imunology but the overall impression is that of there being little differences between patients and controls.
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I also got that impression. But there were much more datapoints for the ME/CFS group than the control group and all compressed on a small figure. So it could be that there's a bit of an optical misinterpretation where we underestimate the datapoints that are clustered togehter in the lower ME/CFS range.

The figures look a lot like christmas trees, by the way. Hope that's a good omen.
 
@strategist Looked at this very briefly and I certainly am no expert.

I recall Chris Armstrong's:
  • 2014 paper [https://www.ncbi.nlm.nih.gov/pubmed/25344988] which showed changes from using glucose (normal) to certain amino acids in energy production in ME; and

  • 2016 webinar [] where he discussed how this change in energy production could result in the observed changes in microbiota (microbiome/gut bugs) i.e. to a more pathogenic state.


This is an extract from the Karhan & Unutmaz (and others) paper:
"In conclusion, these multiple and major perturbations or dysfunctions in T cell 36 subsets in ME/CFS patients suggest potential chronic infections or microbiome dysbiosis".
So possibly this paper provides more evidence of gut dysbiosis, but without necessarily explaining how this dysbiosis comes about.

In his 2016 webinar (50.45 minutes) Chris highlighted that the change in energy production (switch from using glucose to amino acids) may result in gut pH changing (less acid in gut) to favour pathogenic species, which in turn maintains the altered energy state ---. So possibly Karhan & Unutmaz (and others) paper has provided more evidence to support Chris's explanation.

If Karhan & Unutmaz (and others) paper results in a biomarker, which helps doctors to diagnose ME, then that would be helpful (understatement). However, I think we need to understand the rest of the cycle:
  • how is the altered cellular energy production maintained -- what is the "something in the blood";
  • is there leaky gut and if so is it a consequence of altered energy production (protein scavenging from the gut - check out Chris's webinar);
and how do we progress this to diagnosis and treatments?

I think we'll have to wait to see how important this paper is --- views from immunologists -- Mark Davis -- Jonathan Edwards +++ welcome.
 
strategist said:
There is a bunch of graphs in the paper. I don't know how to interpret this imunology but the overall impression is that of there being little differences between patients and controls. With a large sample size, even small differences can become statistically significant. A few graphs seem to show something that might be a meaningful difference (eg. interferon gamma of MAIT cells).

My question to any expert: are these findings potentially important clues to the disease process?
Click to expand...

I agree, most of the differences do not look major. I think it is a pity that the authors keep referring to 'profound' differences when it all looks pretty marginal.

I don't think one can draw any very specific conclusions from the findings so far. It would have been interesting if this study had replicated the findings of Cliff but it does not look as if it did. I certainly would not want to say the findings have any special implications for gut bacteria.

As I have said before, the trouble with studying functions of circulating cells is that circulating cells by and large are in transit and not doing anything particularly interesting.
 
How do I interpret Figure 9? Does this mean you could use the model that has the 10 features with highest importance and select 50% of patients correctly, and almost 0% of controls as false positive?

upload_2019-12-26_15-44-31.png
Figure 9. Random forest clustering of immune features in ME/CFS and control subjects. To generate a receiver operating characteristic (ROC) curve using random forest (RF) clustering algorithm, a training set with 231 samples (80% of total samples) was selected and the remaining data, corresponding to 58 samples (20% of total samples), was left as the test set. Missing values in the training and test sets were replaced by the corresponding median value in the training set. A K-fold cross-validation method was used (K=3) to tube the hyperparameters of the model and was trained using a distinct set of features as input; all 65 immune profile features, the 40 significantly different features, the top 10 significantly different features and the top 10 features that received the highest importance score are plotted.
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If yes, What is special about this 50% and could it be considered a subset? Actually I'm surprised any possible subsets are not discussed, and what about outlier patients whose results could possibly indicate an alternate disease be investigated?
 
This paper is the culmination of three plus years work and $2.6MM in funding. Since this paper is focusing mainly on T-cells I wonder why they did no gene expression studies on these cells, to compare patients and controls.

Just checked NIH reporter and the project description does say they intended to do gene expression studies....... maybe that is to come
https://projectreporter.nih.gov/project_info_description.cfm?aid=9716375&icde=31258613
 
I am interested in the MAIT cells and interferon gamma.

There seem to be difference between patients and controls. Do I see that correct?
 
Jonathan Edwards said:
I agree, most of the differences do not look major. I think it is a pity that the authors keep referring to 'profound' differences when it all looks pretty marginal.

I don't think one can draw any very specific conclusions from the findings so far. It would have been interesting if this study had replicated the findings of Cliff but it does not look as if it did. I certainly would not want to say the findings have any special implications for gut bacteria.

As I have said before, the trouble with studying functions of circulating cells is that circulating cells by and large are in transit and not doing anything particularly interesting.
Click to expand...

Would tissue resident immune cells show the same abnormalities, but more pronounced?
 
Jonathan Edwards said:
I agree, most of the differences do not look major. I think it is a pity that the authors keep referring to 'profound' differences when it all looks pretty marginal.

I don't think one can draw any very specific conclusions from the findings so far. It would have been interesting if this study had replicated the findings of Cliff but it does not look as if it did. I certainly would not want to say the findings have any special implications for gut bacteria.

As I have said before, the trouble with studying functions of circulating cells is that circulating cells by and large are in transit and not doing anything particularly interesting.
Click to expand...

Are 'mucosal-associated invariant T cells' (MAIT cells) transient or are they resident i.e. in the gut lining (mucous)?

There has been some evidence of problems with the microbiome in ME e.g. Ron Davis has repeatedly highlighted that Indolepropionate, a neuroprotectant produced by clostridium, is low in people with ME*.

If the findings don't indicate "any special implications for gut bacteria" then do they indicate increased gut permeability? Here's an extract from the paper:
"Together these findings suggest chronic activation of the Th17 subset that potentially induces an “exhausted” state, as when their numbers are increased due to chronic stimulation, they become more dysfunctional."
On the face of it exhausted MAIT cells could result from a more permeable gut.

Ron Davis commented that you need so much data to get an NIH grant that you've basically done the study. Cort Johnson did an article a few years ago highlighting that Unutmaz had discovered that MAIT cells were basically exhausted. So perhaps most of what's in this paper was already public.

*Around 10 minutes in this video
 
wigglethemouse said:
This paper is the culmination of three plus years work and $2.6MM in funding. Since this paper is focusing mainly on T-cells I wonder why they did no gene expression studies on these cells, to compare patients and controls.

Just checked NIH reporter and the project description does say they intended to do gene expression studies....... maybe that is to come
https://projectreporter.nih.gov/project_info_description.cfm?aid=9716375&icde=31258613
Click to expand...

I'm sure you're aware of this gene expression data which shows ME is similar to Systemic inflammatory response syndrome (SIRS)

Not suggesting another study would not be useful/informative.
 
I'm getting a little cynical with statements in papers; here's an extract from the Abstract:
"using a machine learning algorithm called random forest, we determined that the set of T cell parameters analyzed could identify more than 90% of the subjects in the ME/CFS cohort as patients (93% true positive rate or sensitivity). ---- suggest potential chronic infections or microbiome dysbiosis. These findings also have implications for development of ME/CFS specific immune biomarkers ---."

So MAIT cells can be used to diagnose ME? Can MAIT cells differentiate ME from other forms of persistent gut disbiosis?
Wonder how a "diagnostic test" based on MAIT would compare to the nano-needle?
 
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