The itaconate shunt hypothesis

Re female predominance
Monocytes are the main source of STING-mediated IFN-a production, 2022

Summary
Background
Type I interferon (IFN-I) production by plasmacytoid dendritic cells (pDCs) occurs during viral infec- tion, in response to Toll-like receptor 7 (TLR7) stimulation and is more vigorous in females than in males. Whether this sex bias persists in ageing people is currently unknown. In this study, we investigated the effect of sex and aging on IFN-a production induced by PRR agonist ligands.

Methods
In a large cohort of individuals from 19 to 97 years old, we measured the production of IFN-a and inflam- matory cytokines in whole-blood upon stimulation with either R-848, ODN M362 CpG-C, or cGAMP, which activate the TLR7/8, TLR9 or STING pathways, respectively. We further characterized the cellular sources of IFN-a.

Findings
We observed a female predominance in IFN-a production by pDCs in response to TLR7 or TLR9 ligands. The higher TLR7-driven IFN-a production in females was robustly maintained across ages, including the elderly. The sex-bias in TLR9-driven interferon production was lost after age 60, which correlated with the decline in circu- lating pDCs. By contrast, STING-driven IFN-a production was similar in both sexes, preserved with aging, and cor- related with circulating monocyte numbers. Indeed, monocytes were the primary cellular source of IFN-a in response to cGAMP.

Interpretation
We show that the sex bias in the TLR7-induced IFN-I production is strongly maintained through ages, and identify monocytes as the main source of IFN-I production via STING pathway.


"This is particularly clear for Toll Like Receptor (TLR)-7, a single-stranded RNA (ssRNA) receptor encoded by an X- linked gene. The response of innate immune cells and B cells initiated by the TLR7-mediated sensing of ssRNA is an essential line of defense against exogenous RNA viruses1114 and endogenous retroviruses."
 
This recent paper is very readable, giving background on IFN; there's quite a few interesting points for our purposes:
Importance of Type I and III Interferons at Respiratory and Intestinal Barrier Surfaces

The two most important IFNs that can be produced by virtually all cells in the body during intrinsic innate immune response belong to two distinct families: the type I and type III IFNs. The type I IFN receptor is ubiquitously expressed whereas the type III IFN receptor’s expression is limited to epithelial cells and a subset of immune cells. While originally considered to be redundant, type III IFNs have now been shown to play a unique role in protecting mucosal surfaces against pathogen challenges.
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From what I can see, Type III IFNs can be produced by many cells, but the receptors to Type III IFNs are found on epithelial cells and some immune cells. Type III IFNs do trigger the ISG - the interferon stimulated genes - so can cause uninfected epithelial cells to produce more interferon on that positive feedback loop.


Heterogeneity of Intrinsic Immune Response: Not All Infected Cells Produce IFNs
The textbook view of how PRRs sense pathogens and lead to the production of IFNs (Figure 1) would suggest that all infected cells in a population are equal: All cells will respond to pathogen infection and produce IFNs. However, recent studies have shown that each cell within a homogeneous cell population can respond differently. Work by O’Neal et al.showed that only a fraction of murine fibroblasts infected with West Nile virus produced IFN mRNA regardless of the viral load (42). Similarly, cell-to-cell variability was shown to regulate the ability of mouse fibroblasts infected with Sendai virus to produce IFN-β1 mRNA (43). Further studies have confirmed these observations and have shown that this heterogeneity is of cellular origin and not viral, and is due to intrinsic differences related to the activation and nuclear translocation of IFN regulatory transcription factors NFкB and IRF7
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It seems that among a whole lot of the same sort cells in a person, only some will produce IFNs - so perhaps there are particular conditions that increase the proportion of cells that secrete IFN. I guess also, there might be differences in the number of IFN receptors, so there might be differences in the sensitivity to a given level of IFN.

Probably the most important step in mounting an antiviral response is the ability of cells to turn it off. Failure to arrest IFN signaling in tissues leads to inflammatory disorders in patients and interferonopathies (72). These disorders arise when cellular pathways fail to regulate IFN signaling and are often treated by blocking IFN signaling through the use of JAK inhibitors (73).

The suppressor of cytokine signaling (SOCS) (e.g. SOCS1 and SOCS3) are considered the most potent negative regulators used by cells to control type I IFN signaling as they can directly interact with TYK2 interfering with its activation (74). SOCS1 specifically acts by modulating the activity of IFNAR1 through downregulating TYK2 expression (75). Overexpression of SOCS1 in hepatic cells lines has been shown to also act on type III IFN leading to decreases in ISG production (76). Importantly, in vivo studies using SOCS1 knock-out mice showed increased ISG induction in the liver in response to type III IFNs while the lung and gut were only mildly affected (76). As lung and gut cells have been shown to be TYK2 independent, this suggests that either SOCS1 acts through another method to impact type III IFN signaling or that there are organ-specific differences in the regulation of IFNs.
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Interferonpathies! Of course the molecules that act as brakes on interferon signalling like SOCS are not necessarily straightforward - they may not work in all parts of the body or on all relelvant IFNs.
 
More from that Type I and Type III paper linked in the last post:

There are lots of issues important to be aware of when studying the cells. How close together cells and whether they are polarised are might influence whether the ISG's, the interferon stimulated genes, get turned on by interferon, and so whether they go on to secrete more interferon. The history of the cells might also influence whether they produce interferon. It seems as though there is a lot to learn, and studying the cells in vitro or in mouse models may not give us the right answers.

It is possible that the sensitivity of cells to IFNs is directly or indirectly regulated at the epigenetic level, and that a lack of synchronicity in these regulatory pathways causes delays or insensitivity to either or both type I and III IFNs.

Furthermore, as type III IFNs act on epithelial surfaces it is important to consider their polarization state. Many experiments in laboratory settings use epithelial cells in sparse conditions whereas in the normal tissue environment they are tightly connected and polarized. The state of the cells is critical when evaluating responsiveness to IFNs as mouse intestinal cells have shown to be more sensitive to IFN-λ when reaching a polarized status (Figure 3B) (92) while human intestinal epithelial cells become less responsive to IFNs when polarized (71). Understanding the molecular mechanism of how within a population cell density, polarization status and epigenetic inheritance influence responsiveness to either IFN is a promising research axis that will help us to delineate the differences observed between different tissues and between different species.
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upon influenza infection of respiratory epithelial cells, type III IFNs were produced first, and if the influenza virus load stayed low they were the most important IFNs used to clear the infection. Upon a greater viral load, type I IFNs were required to control the infection (29).
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The intensity of the infection, and possibly even how it enters the body (through the nose or otherwise) might influence which interferons are employed to deal with an infection. The type III's seem to be consistent with a lower level grumbling immune response. I wonder if Robert's team measured type III interferons in the blood. I wonder if they could usefully be measured in the gut.

That review is really information-rich. I recommend it as a way to understand how complex all this is, and how many opportunities there are for something to go wrong, both in the body and in the research.

I do think this 'Itaconate shunt interferon-signalling' hypothesis is worth exploring; thanks to Robert and his collaborators and funders for continuing to do so.
 
Hutan said:
Robert suggests that IFNa might be being produced in blood cells by some people, including the healthy controls. Whereas, the IFNa in people with ME/CFS may be high in tissues. He suggests that it's like trying to measure a pollutant in the sea - you might find low levels that aren't much of a problem by themselves, but the problem might be coming from one particular river where the levels are really toxic.
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Could there be a much simpler explanation for the data outliers (apart from the outliers the data is reasonably well separated)?

Could the high interferon levels in the 2 controls be due to those two fighting a minor infection at the time of sampling?

Could the patient group with low interferon be a subgroup with different underlying pathophysiology? We still can't be sure that everybody diagnosed with ME, even with the strictest criteria, has the same thing going on underneath. We have some interesting "opposite" immune phenotypes going on: pwME who almost never catch a virus versus those who catch everything going, pwME with persistently slightly elevated WBC versus those with persistenly lowish WBC, and pwME who got some brief symptom improvement after the covid vaccine versus those who reacted very badly.

None of which proves anything one way or the other but it does suggest it's not impossible we have a situation similar to type 1 and type 2 diabetes. In diabetes both types end up with too much glucose in the blood but for different reasons. In ME we all end up with PEM but are there different paths to PEM?

Talking of the devil, I'm not sure I understand how this hypothesis accounts for PEM? I can sort of see how physical exercise could lead to translocation of gut bugs into the blood stream and the innate immune system getting upset about that. But orthostatic or cognitive exertion?

And the lowered ATP production would seem to predict a more stable misery than the fluctuating symptom load we actually get? This is a question I have for all the hypotheses centered on low ATP. Sure, a cell without enough ATP to do its job is going to be compromised but how do you get from there to PEM? Depending on the type of exertion the starting point would be different types of compromised cells but all would lead to PEM. Do the affected cells send out a common alarm signal that ultimately leads to PEM? But this particular hypothesis assumes only a small number of cells are dysfunctional so how are they affected by all manner of different types of exertion? Does it have to be a very specific type of cell in the trap. e.g. vagus nerve cells or cells near it, to be able to have such system-wide impact?

In the unlikely event anyone's still reading, you can see I'm thoroughly confusing myself here!
Hutan said:
There are drugs that can block IFNa, but Robert notes that they need to get some proof to support this hypothesis. IFNa is important, and blocking it is not a good plan unless you really know what you are doing and have a good reason to be doing it. I wonder if there are some people with ME/CFS who have been given IFN-blocking treatment.
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You'd think there must be at least a few.

If ME is maintained by a self-sustaining feedback loop that would be good news. Briefly interrupting the loop could reset the system. I doubt it would be as easy as it sounded in the video to work out how exactly to do this but it would be a very concrete target for a pharmaceutical company to get stuck into if existing drugs aren't quite up to the job.

But if ME is maintained by a persistent pathogen continuously reactivating the feedback loop then you'd also have to stop the pathogen and that would be a whole lot more difficult.

Anyway, I'm pleased to see testing of the hypothesis' predictions is taking place :thumbup:
 
Ravn said:
And the lowered ATP production would seem to predict a more stable misery than the fluctuating symptom load we actually get? This is a question I have for all the hypotheses centered on low ATP. Sure, a cell without enough ATP to do its job is going to be compromised but how do you get from there to PEM? Depending on the type of exertion the starting point would be different types of compromised cells but all would lead to PEM. Do the affected cells send out a common alarm signal that ultimately leads to PEM? But this particular hypothesis assumes only a small number of cells are dysfunctional
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Perhaps, if a subset of cells are impaired but are themselves able to compensate just enough to maintain degraded function, then there might be a balancing of energy needs or other functions across the system. If demands increase (eg standing, moving, thinking) maybe the usual compensation mechanism can be out-stripped. This could be detrimental to the affected cell subset, leading to more symptoms relating to functions of those cells; but might also affect the normal cells that are doing the compensating - perhaps they're driven just a little too hard and/or have to use more and less favourable emergency backup mechanisms. In so doing they may develop temporary impairments to their usual functions that takes time to return to baseline?

It could even be that "too much PEM" can lead to a deterioration in disease severity, as the previously normal compensating cells became damaged from doing too much or using unfavourable biochemical mechanisms. That might also be an itaconate shunt or some different biochemical pathway or just generic "mitochondrial damage" from say reactive oxygen species.

Signals showing favouring of eg fatty acids, or other metabolic shifts, might be occurring in the otherwise normal cells, that are contributing to the compensation. I'm thinking of ideas like the paper that described lactate as a universal fuel that allowed the balance of energy needs across the whole system.
 
From the thread we have on the Pariente study of interferon treatment for people with Hepatitis C, some excerpts posted by chrisb from a 1988 study:

chrisb said:
Smith et al (1988)(Smith, Tyrell, Coyle and Higgins. Effects of interferon alpha on performance in man; a preliminary report . Psychopharmacology 96 414-416) injected normal volunteers with alpha interferon and those receiving 1.5Mu of interferon developed symptoms which closely resembled influenza. They also showed identical changes in performance to those shown by people with influenza, with some function being impaired but others remaining intact. Furthermore, after effects of interferon challenge were observed even though the symptoms had disappeared .

Cognitive Changes in Myalgic encephalomyelitis. Andrew Smith in Post viral fatigue syndrome (ME) 1991 eds Jenkins and Mowbray.

Edited to include date and italics
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chrisb said:
It has already been noted that fatigue is a very common feature in interferon therapy. Patients on interferon who suffer from this fatigue find that it is exacerbated by physical exercise. Some patients have to stop working, particularly those whose occupations have a largely physical component, while the majority report that their social functioning is impaired. Despite the agreement on the occurrence of fatigue as a side effect of interferon therapy, there is difficulty in comparing this with that occurring in PVFS because "fatigue" is largely undefined in interferon studies. For example the distinction is rarely made between mental and physical fatigue.

Interferon in viral illness and ME. E McDonald and A Mann. Post viral Fatigue Syndrome (ME) 1991 eds Mowbray and Jenkins

it is interesting that the authors were from the Institute of Psychiatry. In those days the CFQ had probably not got a firm hold and greater judgment on such matters was possible.
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It suggests that the people were experiencing a range symptoms that were like influenza, and that the fatigue was exacerbated by physical exercise. So, it could just possibly be the same thing as ME/CFS. It would be interesting to talk with people who have experienced interferon treatment.

On the question of PEM -
There's the suggestion that cells in the anti-viral state are "burning dirty", producing ammonia as a waste product which is toxic. Maybe when cells are having to work hard, there's a lot of toxic waste products? And maybe cells that run out of energy or are overwhelmed by toxins send out distress signals and/or die an unregulated cell death that might contribute to a systemic 'sickness response'?

I haven't had time to think through that well, it's just a guess.
 
Hutan said:
It suggests that the people were experiencing a range symptoms that were like influenza, and that the fatigue was exacerbated by physical exercise.
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It would be really interesting to compare two cohorts, one with ME and the other on interferon therapy, in a study comprising carefully-designed physical and cognitive tests. Especially as patients who're due to begin interferon therapy could presumably be tested beforehand to see what changes.
 
Some very recent Robert Phair posts on PR

“Chris and I recently had a great Zoom meeting with Bob Naviaux and Bhupesh Prusty and agreed on two important points: 1) our two theories are converging on the innate immune system, and 2) ME/CFS is a cell-autonomous or mosaic-dysfunctional disease.

Questions welcome.”

Not sure what a cell autonomous or mosaic-dysfunctional disease is—would welcome any clarification if anyone has an idea.

https://forums.phoenixrising.me/thr...fa-itaconate-shunt-part-2.89388/#post-2430533

plus two posts in members only threads which s4me prohibits links to but you can find by searching PR for Htester.
 
Jaybee00 said:
Not sure what a cell autonomous or mosaic-dysfunctional disease is—would welcome any clarification if anyone has an idea.
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There are probably better review articles to be found, but Google highlighted this slideshow PDF from Washington University at St Louis with a simple summary —

a) Cell autonomy: where phenotype and genotype of cells are concordant

– a genotypically mutant cell displays a mutant phenotype.

b) Cell [nonautonomy]: when phenotype and genotype of cells are not concordant

- a genotypically mutant cell may cause a genotypically wild-type cell to exhibit a mutant phenotype.
and/or
- a genotypically wild-type cell may rescue a genotypically mutant cell.
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Cell autonomous gene action suggests that the product is involved in signal reception, signal transduction, or does not participate in a process involving cell-cell interactions.

Cell non-autonomous gene action suggests that the product is a signaling molecule or participates in the synthesis of a signaling molecule.
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Braganca said:
So Phair is saying the metabolic trap hypothesis is dead?
“When the experimental data do not consistently corroborate a theory like the IDO metabolic trap, I'm naturally disappointed.”
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That’s what it sounds like. It seems these ‘trap’ hypothesis’s are falling out of favor. Hopefully the speeches coming up in May reveal some findings from the studies that have been done.
 
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