IIMEC 2023: Maureen Hanson

[butter.]

I've known a few gradual onset pwM.E that took many antibiotics during their young life, they didn't have a known infectious onset but suffer with allergies, MCS and mold for decades. Their immune profile and phenotyping lymphocyte counts were worse than mine.

While that is interesting, they also probably drank a lot of Sprite, that doesn't necesarily mean that's relevant to their later ME.

We should definitely have a look into that though, and maybe even more importantly into why they had to take antibiotics so frequently in the first place.

I am a person with gradual onset, constant infections, and high (insane amounts of) antibiotic intake by the way!

 

[DMissa]

Very compelling ideas. I really can't wait to meet her in a week or so at IACFSME. I think she's at the forefront of the field right now. Very high quality work and intelligent direction.

 

[voner]

That is a very clear and well communicated presentation with wonderful graphics of experimental results that were easy for me to interpret. Some of the data she presents is not yet published. @Hutan, thanks for posting this video.

 

[josepdelafuente]

A great video. I definitely didn't fully understand everything, but I found it encouraging.

 

[Simon M]

This is certainly interesting work, particularly the new, unpublished findings about the “exhausted CD8 T cells signature” of PD-1 and transcription factors. And I like the way that it builds from the early metabolic work into the flow cytometry stuff and the link into the single-cell RNA work.

But I don’t think we should get carried away. Maureen Hansen herself does a good job of not hyping it.

The findings do not point specifically to a chronic viral infection
First, there is no evidence that points specifically to chronic viral infection. CD8 T -cell exhaustion is not specific to viruses, or even pathogens (later in the talk, she talks about T-cell exhaustion in cancer). And as she says, monocyte activation is a sign of an unseen pathogen, but it doesn’t have to be a virus.

Surprisingly small samples
Next, the studies have Surprisingly small sample sizes, particularly given this is one of the biggest ME labs. It’s only 15 patients for the new work, which is pretty much a pilot study. There are only 30 patients for the very interesting single-cell RNA sequencing work. I hope there will be replication studies with larger samples.

It’s surprising that the CD8 T-cells differences don’t stand out in the RNA data
I’m concerned that the (already-published) single-cell RNA sequencing work found the biggest differences between patients and control for monocytes. You would think from the new flow cytometry results that a similar CD8 T-cell signal would shine out like a beaco from the scRNA data, yet that appears not to be the case (I'm fairly sure that substantial CD8 differences were not reported in that study).

The idea of single-cell RNA sequencing is it identifies all the RNA transcripts in a cell and from that it’s straightforward to deduce which proteins are being made (that’s how different immune cells such as monocytes are identified). I would expect the PD-1 marker and the transcription factors to also show up in the data, with corresponding differences between patients and controls.

Can chronic virus infection explain PEM?
At the end of the talk, a patient asks what I think is the key question: how do these findings relate to PEM? Maureen Henson said she didn’t know (I like scientists who are happy to say that).

If the key problem here is chronic infection and T-cell exhaustion, why don’t we see PEM in chronic infections? I’m fairly sure it’s not a feature of hepatitis C infection or AIDS, for instance – though chronic fatigue certainly is.

In short, we have small sample sizes, inconsistent findings, and no sign of PEM in other chronic conditions that are supposed to have a lot of similarities.

I very much hope that Maureen Hansen and her team will pursue this work. These findings may develop into a massive clue about the cause of the illness.

But we should be realistic about the current evidence and how much weight it will bear.

It would be very interesting to hear @Jonathan Edwards's opinion on this work.

 

[Jonathan Edwards]

It would be very interesting to hear @Jonathan Edwards's opinion on this work.

I am tempted to say I don't know.

CD8 exhaustion is an interesting thing to mull over.CD8 cells seem more to be involved in male predominant diseases like ankylosing spondylitis. I once had the idea that ME might be a hidden fourth T cell domain version of the Class I associated syndromes but found the female predominance worrying. On the other hand if this is CD8 exhaustion maybe females would be more susceptible. Perhaps females have less potent CD8 cells so as not to cause trouble in pregnancy.

I don't know.

 

[Sid]

This sounds worth following up on. I’m surprised that this lab is doing N=15 studies considering how well funded they are.

 

[FMMM1]

Really interesting talk by Maureen [I need to re-listen to it] - an excellent scientist & someone with a personal interest in ME/CFS.

Verification of the proposed mechanism i.e. exhaustion of immune cells? I was hoping that someone would ask whether GWAS has a role here e.g. if this is a significant/common cause of ME/CFS then would you expect to see a signal in the DecodeME GWAS study --- immune genes/certain immune genes ---? @Simon
EDIT - wonder if Ron Davis's NIH funded genetic study [HLA genes] would provide a potential way to validate/test the proposed mechanism i.e. exhaustion of immune cells? Ron's study was due to be completed recently (few months ago) but no results published yet.

Also, if the test, re exhaustion of immune cells, is accurate/reproduceable & could be used to identify a large cohort, then would it be possible to look at the genetics in this group/sub-group?

I recall that another researcher was funded to look at exhaustion of MAIT cells - https://www.jax.org/research-and-faculty/research-labs/the-unutmaz-lab

Interesting that if this proposed mechanism i.e. exhaustion of immune cells holds up then there are potential treatments (cancer drugs).

 

[FMMM1]

This sounds worth following up on. I’m surprised that this lab is doing N=15 studies considering how well funded they are.

Yea e.g. if the test, for exhaustion of immune cells, is reliable then looking at a cohort from a biobank, to estimate prevalence etc, would seem to be a logical follow up.

 

[chillier]

It’s surprising that the CD8 T-cells differences don’t stand out in the RNA data

Good point! Just looking back at their scRNA-seq preprint and they do report they see some differences (measured by gene ontology enrichment scores not levels of individual genes) in CD4+ T cells but don't mention CD8+s at all, except to say there is a marginal decrease in counts.

No other proportions of immune cells were significantly altered, except for a marginal decrease in effector/memory CD8+ T cells in patients (0.9-fold, at both timepoints; P=0.04 and 0.09).

I suppose you could give them the benefit of the doubt as three of the genes they look at for CD8 exhaustion with flow cytometry are transcription factors, which are often expressed with very low mRNA copy number that could plausibly be missed with single cell RNA seq with low sequecing depth. But then these transcription factors will all have effector genes whose expression should all change which you'd really think would be picked up.

 

[butter.]

Thank you, Simon!

I see it similarly, mostly.

If the key problem here is chronic infection and T-cell exhaustion, why don’t we see PEM in chronic infections? I’m fairly sure it’s not a feature of hepatitis C infection or AIDS, for instance – though chronic fatigue certainly is.

Can we be sure we are not seeing PEM in later stages of e.g. AIDS and untreated Hepatitis C, there is a good chance people would just call it "feeling bad" instead, such people simply might not have made the connection to exertion, because it's "just the way AIDS is".

PEM could be caused e.g. by a certain kind of mitochondrial damage, or an ion channel issue that some people are more prone to end up with than others when hit by some kind of inflammatory insult. While potentially not "all kinds of possible inflammatory insults" would lead to such damage, "many different types" could do.

In a sense, T-cell exhaustion is probably not causing PEM, but both PEM and T-cell exhaustion are potentially results of chronic damage, that looks similar enough in different people to be considered "one disease entity". At least that is from where we are looking at it, and that is through the "ME/CFS lense".

-----

As you correctly say T-cell exhaustion is seen in many other disease states, this includes degenerative neurological diseases like PD, MS, ALZ, it's not just cancer. In Lupus T-Cell exhaustion is considered helpful and is correlated with better outcomes. All in all, I do not think that using PD1 inhibitor treatments used in cancer will be helpful in ME/CFS, as we probably had "too much activation of T-cells inflicting collateral damage" already. We just haven't find good ways to characterize it.

Irrespective of the root cause of ME/CFS, whether it is a pathogen, auto-immunity or some unknown genetic factor(s), if the CNS is involved (it probably is), immuno-therapies like CAR-T or PD1 inhibitors are of no value.

It might be important to note that long term side- effects of such treatment approaches include "extreme fatigue" and one might be tempted to say that "extreme fatigue" after exertion could be actually PEM.

 

[FMMM1]

Speculation - I'd expect that:

• Ron Davis's NIH funded KIR gene study should turn up a signal i.e. if Maureen Hanson's theory re T-cell exhaustion is correct - the results from DecodeME would also be interesting for this reason (independently testing proposed disease mechanism); and
• Maureen would have sight of the results from Davis's KIR gene study [she's part of OMF].

I'm a little surprised that Prusty's work, re viral activation, hasn't been mentioned in this thread.

This [EDIT - T-cell exhaustion] seems to have wider relevance e.g. to Lyme and long covid - that may/should mean that it's an attractive area:

• to fund i.e. for bodies like NIH & Horizon Europe; and
• for high profile researchers/groups like Akiko Iwasaki.

But as per Simon McGrath (above) -- "I don’t think we should get carried away. Maureen Hansen herself does a good job of not hyping it."

 

[MeSci]

@Simon

I think you mean @Simon M?

 

[Simon M]

RE expecting to see signs of CD8 T-cell exhaustion in the RNA data:

Good point! Just looking back at their scRNA-seq preprint and they do report they see some differences (measured by gene ontology enrichment scores not levels of individual genes) in CD4+ T cells but don't mention CD8+s at all, except to say there is a marginal decrease in counts.

Thanks.

I suppose you could give them the benefit of the doubt as three of the genes they look at for CD8 exhaustion with flow cytometry are transcription factors, which are often expressed with very low mRNA copy number that could plausibly be missed with single cell RNA seq with low sequecing depth. But then these transcription factors will all have effector genes whose expression should all change which you'd really think would be picked up.

This 2019 review says similar
CD8+ T cell exhaustion
Exhausted T cells are characterized by progressive loss of effector functions (cytokine production and killing function), expression of multiple inhibitory receptors (such as PD-1 and LAG3), dysregulated metabolism... These altered functions are closely related with altered transcriptional program ... that clearly distinguish exhausted T cells from normal effector and memory T cells.

 

[Simon M]

Verification of the proposed mechanism i.e. exhaustion of immune cells? I was hoping that someone would ask whether GWAS has a role here e.g. if this is a significant/common cause of ME/CFS then would you expect to see a signal in the DecodeME GWAS study --- immune genes/certain immune genes ---?

With pretty much all hypotheses, a GWAS study is a good place to look for confirmatory data. The unknown is whether or not DecodeME will be big enough to pick up most signals. Firstly, until you've done a GWAS, you won't know how strong the genetic signal is (unless you already have big robust genetic studies that ME lacks). Second is th issue of heterogeneity/subgroups; the more subgroups, the more any signal is diluted.

Also, if the test, re exhaustion of immune cells, is accurate/reproduceable & could be used to identify a large cohort, then would it be possible to look at the genetics in this group/sub-group?

That might help identify a subgroup, but you would still need a lot of people identified as GWAS signals are weak; identifying that many people may not be feasible.

Yea e.g. if the test, for exhaustion of immune cells, is reliable then looking at a cohort from a biobank, to estimate prevalence etc, would seem to be a logical follow up.

That is an excellent idea.

EDIT - wonder if Ron Davis's NIH funded genetic study [HLA genes] would provide a potential way to validate/test the proposed mechanism i.e. exhaustion of immune cells? Ron's study was due to be completed recently (few months ago) but no results published yet.

Not sure. CD8 cells interact with HLA receptors, but it's one step removed, and I think the HLA study is quite small - but I'm out of my depth.

Can we be sure we are not seeing PEM in later stages of e.g. AIDS and untreated Hepatitis C, there is a good chance people would just call it "feeling bad" instead, such people simply might not have made the connection to exertion, because it's "just the way AIDS is".

I don't think so. The term PEM was coined in 1992 specifically for (ME/)CFS precisely because there was no existing term to describe such an unusual symptom. And Nancy Klimas is an immunologist/clinician who sees both ME and HIV/Aids patients. I'm sure she would have commented if Aids patients have PEM.

In the data I've seen, Chronic Hep C is associated with far less fatigue than ME.

 

[chillier]

Interesting that if this proposed mechanism i.e. exhaustion of immune cells holds up then there are potential treatments (cancer drugs).

You might already know this - One of the proteins in this talk PD-1 was associated with a recent nobel prize along with CTLA-4. These genes are supposedly abused by certain advanced cancers to escape the immune system, and targeted inhibition with drugs can improve outcomes in some cases. I imagine these therapies hurt.

 

[chillier]

RE expecting to see signs of CD8 T-cell exhaustion in the RNA data:

Thanks.


This 2019 review says similar
CD8+ T cell exhaustion
Exhausted T cells are characterized by progressive loss of effector functions (cytokine production and killing function), expression of multiple inhibitory receptors (such as PD-1 and LAG3), dysregulated metabolism... These altered functions are closely related with altered transcriptional program ... that clearly distinguish exhausted T cells from normal effector and memory T cells.

My partner thinks it might not be unreasonable to not see things like this if the phenotype is not that strong, as the coverage can be quite low in scRNA-seq as they're looking at many PBMC cell types besides CD8s, and also depending on how many patients they're putting on a chip/ doing on a sequencing run which will make the depth even shallower. 10x scRNA-seq is pretty expensive ( my memory is something like £10k a chip but I could be misremembering ) and they did a lot of samples - I think 30 controls, and 30 patients before and after exercise for a total of 120.

I've worked with scRNA-seq data before and we could see all sorts of things including transcription factors, and this was on cells from disintegrated whole organisms, so many many cell types - but then we'd often integrate data from multiple chips and sequence deeply.

I think the obvious experiment to do would be to FACS sort out CD8 T cells and do RNA-seq on them, or even just qPCR of the relevant genes. I wonder if maybe they've tried this already and didn't see anything.

 

[Simon M]

I think the obvious experiment to do would be to FACS sort out CD8 T cells and do RNA-seq on them, or even just qPCR of the relevant genes. I wonder if maybe they've tried this already and didn't see anything.

Good to hear that it might not be surprising not to see a signal of CD8 exhaustion in the single cell RNA data they already have.

it’s great to have these insights from the lab.

 

[Simon M]

Have you thought of contacting Maureen Hansen to ask if she’s done or considered the studies you suggest? I think you would get a response.

 

[chillier]

Have you thought of contacting Maureen Hansen to ask if she’s done or considered the studies you suggest? I think you would get a response.

I think it's a long shot but I sent her an email to inquire.