Transcriptional reprogramming primes CD8+ T cells toward exhaustion in Myalgic encephalomyelitis/chronic fatigue syndrome, 2024, Iu, Hanson et al

[Snow Leopard]

T cell exhaustion isn’t an idea it’s a measurable phenomenon.

Is it? They're just looking at the phenotype of T-cells in circulation and as I linked above, (a) T-cells in circulation aren't the ones that are really doing anything (b) that phenotype can be the result of lower turnover due to differences in activity levels and exposure to new pathogens and (c) I cited a study that showed that even "exhausted" T-cells were still able to proliferate, execute antimicrobial functions and form quiescent memory cells upon further stimulation.

 

[Jonathan Edwards]

Pretty sure there are dozens of papers showing it to correlate with reduced survival in human cancer patients

There may well be but it is hard to know what on earth that would mean. Cytokines released in association with cancer may shift traffic in all sorts of ways so you may be measuring a quite different subset of cells. And of course almost any abnormality will correlate with reduced survival in cancer patients. There is an industry (likely thousands of papers) based on trying to show that T cells are relevant to cancer. Recent work has shown that you can kill cancer with targeted T cells, yes, but much of the other stuff I would be wary of. But then my brother is a breast cancer biologist and writes articles on that!

 

[leokitten]

Is it? They're just looking at the phenotype of T-cells in circulation and as I linked above, (a) T-cells in circulation aren't the ones that are really doing anything (b) that phenotype can be the result of lower turnover due to differences in activity levels and exposure to new pathogens and (c) I cited a study that showed that even "exhausted" T-cells were still able to proliferate, execute antimicrobial functions and form quiescent memory cells upon further stimulation.

The current state and future of T-cell exhaustion research
https://pmc.ncbi.nlm.nih.gov/articles/PMC10352049/

There have been different definitions of exhaustion based on varying combinations of metabolic, epigenetic, transcriptomic, and activation based phenotypic markers in this research field. For this reason you might see papers that don’t quite align with others. Doesn’t mean this is just a nebulous idea.

The research community is slowly working towards a consensus, and that being said all of the definitions so far have been based on combinations of measurable phenotypes. A useful excerpt

We recommend creating a ‘M.E.T.A’, i.e. metabolic, epigenetic, transcriptional and activation-based set of phenotypic markers for use in capturing the surface profiles, and cytokine production and killing activities of exhausted T cells generated in vitro. These four sets of markers comprise overlapping measures of exhaustion so that if at least two of these criteria are met, there will likely be good agreement that truly exhausted-state T cells are being studied.

 

[Jonathan Edwards]

"exhaustion at the molecular level remains poorly defined and inconsistent across the literature."

Seems to sum it up.

 

[leokitten]

"exhaustion at the molecular level remains poorly defined and inconsistent across the literature."

Seems to sum it up.

Again, it doesn’t mean it’s just some nebulous idea, each varying definition is clearly based on a signature of measurable phenotypic markers

 

[Snow Leopard]

Doesn’t mean this is just a nebulous idea.

Does it matter though? Most of this research is sampling cells from circulation which isn't relevant to what is going on in specific tissues and is also confounded by other factors that affect T-cell lifespan/turnover in circulation.

On top of all of that, there aren't any reasonable hypotheses as to how T-cell exhaustion leads to ME/CFS pathology.

 

[Dolphin]

ME Research UK

Researchers suggest that ME/CFS leaves genetic changes on immune cells, known as T cells, making them more prone to T cell exhaustion - a state where they are overworked and eventually stop functioning properly.

Read more - https://bit.ly/tcellexhaustionmecfs

 

[wigglethemouse]

This video at 6hrs:27min to 6hrs:33min is interesting. Dr Hanson describes the teams work on CD8 T-cells that have been exposed to an antigen not only show markers of "exhaustion" differences they also show changes in energy production - metabolically from an energy measurement, ROS, AND gene expression.


Chris Armstong and colleagues identified energy differences in naive B cells that lead to changed differentiation upon maturation. Could that be similar to what is happening in T cells in the paper of this thread. It could be the energy pathway changes that are driving the expression of "exhaustion" markers.

 

[wigglethemouse]

Shout out to @forestglip who posted a Cornell Chronicle news article in the NIH news thread that describes this work in laymans terms.
https://news.cornell.edu/stories/20...e-exhausted-chronic-fatigue-syndrome-patients

This quote near the end of the article describes what they hope to do next

Future work will try to determine whether a virus is in fact involved, which is currently not known. “We need to understand what is pushing them to this exhausted state,” Grimson said.

The team also plans to take cells from patients and controls, purify those cells and treat patients with drugs that reverse exhaustion and see if the immune cells resume normal function. If CD8+ T cell exhaustion can be reversed, the next question is whether such reversal actually benefits a patient, as exhaustion can have protective qualities.

 

[wigglethemouse]

There was a zoom today hosted by Solve ME with presenters Dr Lisa Selin from UMass and Dr Kumar from Hifibio.

Dr Selin stated that she was the first to identify T-cell exhaustion in ME/CFS and it was not by gene markers only. Using fresh cells they sorted Tcells by type with magnetic sorting and then measured their function both quiescent and activated vs healthy control. It was this measurement of function that led them to the conclusion that these cells were "exhausted" in their function. The study of this thread builds on that initial work.

When LSHTM did their large immune cell study it was with frozen blood - a few years ago I brought that to the attention of the Selin lab and they said that fresh blood + sorting of Tcells was needed to see the CD4+CD8+ subset.

During the webinar I asked via the Q&A if the Selin lab still needed fresh blood and Rivka the patient representative said they can use frozen. She stated that Dr Selin or Dr Gil should be contacted for the exact details.

All this is over my head. But they did share Dr Selin's email for those that have questions about the work - Selinlab@umassmed.edu . @Jonathan Edwards - you seem to be on the other side of the exhaustion story thinking it is not relevant - perhaps it's time for a "chat" with Dr Selin to see if you can be persuaded?

 

[jnmaciuch]

Just now seeing this thread. I remember skimming the paper when it came out. I believe similar findings are coming up in LC.

But overall, I don’t put much stock in T cell exhaustion as it relates to the etiology of ME/CFS. In the context of cancer survival it makes sense since active immune surveillance is the main thing stopping cancer from spreading. But if it is a relevant phenomenon in ME/CFS, I think it is far more likely to be a downstream consequence, rather than cause, of the disease.

I struggle to see how T cells that aren’t as active as they should be would explain any part of the illness.

The two options would be: 1) there’s some groundbreaking undiscovered function of T cells that is vital for keeping the whole system active and energetic all day long or 2) there’s some aberrant signaling somewhere else and this is one of the many down-the-river echoes of it.

I highly doubt it’s #1. In the case of #2, it’s a useful finding insofar as it’s one more peripheral piece of the puzzle.

 

[wigglethemouse]

I struggle to see how T cells that aren’t as active as they should be would explain any part of the illness.

There are two things I can think off as an armchair enthusiast.

1. The Selin lab has reported increased CD4+CD8+ T-cells in females (fresh blood, T cells sorted into CD8 cells first with magnetic sorting). Could these be Tcells that have failed to mature properly, similar to the Armstrong finding in maturation of B cells? [from the webinar : apparently there are a lot of CD4+CD8+ cells in the Thymus before they mature]

2. If the cytotoxic CD8 cells are less cytotoxic, which I thought was what Dr Selin is reporting, what is the consequence? Are there more "bad" cells in circulation? @DMissa reported higher PBMC cell death rate in ME/CFS vs Controls after a blood draw.

I don’t put much stock in T cell exhaustion as it relates to the etiology of ME/CFS. In the context of cancer survival it makes sense since active immune surveillance is the main thing stopping cancer from spreading.

The Selin lab webinar described that in cancer the Tcell exhaustion is local to the cancer. In ME/CFS they are seeing it in circulating cells which shouldn't be the case. Exhaustion should be local as circulating cells are not doing much.

 

[jnmaciuch]

There are two things I can think off as an armchair enthusiast.
The Selin lab webinar described that in cancer the Tcell exhaustion is local to the cancer. In ME/CFS they are seeing it in circulating cells which shouldn't be the case. Exhaustion should be local as circulating cells are not doing much.

I agree that it's a weird and interesting finding. However, it still doesn't give any role for exhausted T cells in causing the disease, rather than being a consequence of it.

The entire point of an "exhausted" T cell (in its vague definition) is that it does less. It doesn't matter where the doing-less T cells are unless something about the body's functioning requires constant T cell activation for purposes beyond standard immune function. Which we don't have any evidence of.

 

[wigglethemouse]

Am I reading the Hanson/Grimson lab study right that they performed a differential gene analysis following provocation after an exercise challenge. The abstract, body, and methods are rather vague on this for someone that can only skim papers? i.e. differential refers to comparison of genetic markers before and after exercise of T cells in ME/CFS vs sedantary controls.

According to the study CD8 and γδT cells showed increased exhaustion markers and changed genetic landscape but CD4 did not. Why on earth would exercise affect two types of T cells in circulation but not other types? There must be a clue if we can answer that question.

We identified dysregulation across multiple clusters, with the greatest signal in CD8+ T cell subsets and γδT cells (Fig. 1B and Dataset S1). We detected only subtle shifts in the transcriptome of NK and CD4+ T cell subsets, and virtually no differential expression in Treg cells.

From my armchair view : If CD8 T-cells are the ones doing the killing/removal of bad cells and CD4 are not, could increased exhaustion markers in CD8 and not CD4 AFTER exercise indicate that there was a need to remove cells that entered the bloodstream after during/after exercise and after doing this they have a lack of IFN and other stuff they use to do the removal?

 

[wigglethemouse]

I agree that it's a weird and interesting finding. However, it still doesn't give any role for exhausted T cells in causing the disease, rather than being a consequence of it.

Understood. I find the Simmaron report in their ATG13 studies of "impaired ATG13-dependent autophagy, caused the infiltration of inflammatory M1 macrophages" interesting in the CD8 exhaustion context. If autophagy is indeed impaired in ME/CFS would we expect CD8 Tcells to be more "exhausted"?

 

[Jonathan Edwards]

I think the term 'exhaustion' should be binned. It would help if these people just talked about what changes in cell behaviour are observed. I agree with @jnmaciuch that it doesn't make much sense for inactivity of cells to cause ME/CFS or LC symptoms. But then there has been an obsession with 'immunodeficiency' in work on ME/CFS ever since people started comparing it to AIDS.

I would not be surprised if there is a specific abnormality of CD8 T cells. CD8 cells track through muscle and CD4 do not in general. The two have quite different functions and life histories. It seems to me quite likely that whatever markers of function they are calling 'exhaustion' are of interest but just nothing to do with cells being exhausted. Maybe they are already committed to doing something they shouldn't - busy rather than exhausted.

 

[chillier]

There was some talk on the Zhang et al HEAL2 thread about whether epigenetics could be relevant in ME. I don't know that epigenetics has really been looked at in ME but they look at it here in this paper using ATAC-seq on n=7 patient CD8 T memory cells.

I noticed from this volcano pot that the most significantly inaccessible gene region related to TPPP . This gene has been discussed before on this forum: there was a norwegian gwas that nearly had this gene as a hit but didn't quite reach significance. I can't remember what the paper was but I know @forestglip mentioned it recently, can you remember? This gene appears to be involved in cytokeleton organisation in central nervous system glia; it's important in myelination.



The idea with ATAC-seq is that you use enzymes that cut the genomic DNA, and then sequence the resulting fragments. As the enzymes are only able to cut the DNA at points where it is accessible (ie, not wrapped up and bound to proteins like histones), you can infer from the sequencing results that the end of the DNA fragments you sequence must correspond to open and accessible regions on the genome. In order to transcribe and 'use' the genes on the genome, they need to be accessible to RNA polymerases and transcription factors. In the case of TPPP it being inaccessible means it probably wouldn't be able to be transcribed, without first changing the epigenetic state of the cells.

 

[Nightsong]

I remember TPPP appeared as possibly implicated in Hajdarevic et al:

In the Norwegian discovery cohort, the TPPP gene region showed the most significant association (rs115523291, P = 8.5 × 10−7), but we could not replicate the top SNP. However, several other SNPs in the TPPP gene identified in the Norwegian discovery cohort showed modest association signals in the self-reported UK biobank CFS cohort, which was also present in the combined analysis of the Norwegian and UK biobank cohorts, TPPP (rs139264145; P = 0.00004). Interestingly, TPPP is expressed in brain tissues, hence it will be interesting to see whether this association, with time, will be verified in even larger cohorts.

Link | S4ME thread

 

[jnmaciuch]

It would be interesting to see if TPPP is downregulated in neurons as well, though that would probably require a post-mortem sample. My experience with ATAC-seq is that the findings are very rarely consistent between different cell types.

In the context of “T cell exhaustion” I suppose it might most make sense in terms of tubulin meditating cell motility. That would fit with the other top downregulated hits being chemokine-related.

 

[jnmaciuch]

I don't know that epigenetics has really been looked at in ME

I tried to find some studies a few weeks ago and didn’t really see anything noteworthy besides this study. There was one methylation study I believe but no more ATAC-seq.

I’d personally really be interested in ATAC-seq of tissue resident immune cells in ME, but logistically I think it would be borderline impossible to collect those without having your signal dominated by muscle cells.