Itaconate modulates immune responses via inhibition of peroxiredoxin 5, 2025, Tomas Paulenda et al

[jnmaciuch]

IRG1 encodes the protein that catalyzes itaconate production--they did an IRG1 [edit: knockout] to see if interferon beta production is dependent on itaconate, I believe.

The theory about itaconate regulating ROS is that most cells have fine tuned mechanisms that kick in when ROS ramp up [e.g. PRDX5] precisely because ROS are generally bad for cell function. However, macrophages kill pathogens via ROS, so they don't want these inhibitory mechanisms ramped up. If TLR4 is stimulated, IRG1 activity facilitates upregulation of itaconate, which has the ability to essentially block the ROS block. Meaning it lets ROS increase beyond what would normally be allowed in other cells so that the macrophages can use it for pathogen clearance

[Edit: the connection with interferon beta is that blocking-the-ROS-block seems to be the thing that enables interferon beta production. Other non-natural itaconate derivatives don't have this block-the-block action, therefore if you administer them to cells, you'll end up with an "anti-inflammatory" anti-ROS effect that is not seen with endogenous itaconate]

 

[wigglethemouse]

I guess one question I have from having looked at public cell expression databases, IRG1/ACOD1 is also highly expressed in Monocyctes. We know from Hanson et al in ME/CFS and Long Covid studies that a subset of monocytes have different genetic expression in patients vs controls. How does IRG1/Itaconate play a role in those cells before they mature into macrophages?

 

[jnmaciuch]

I guess one question I have from having looked at public cell expression databases, IRG1/ACOD1 is also highly expressed in Monocyctes. We know from Hanson et al in ME/CFS and Long Covid studies that a subset of monocytes have different genetic expression in patients vs controls. How does IRG1/Itaconate play a role in those cells?

macrophages come from monocytes! (if they're not self-proliferating tissue-resident macrophages)

 

[Hutan]

On other PRDX's - this from the Sweetman/Tate paper that looked at proteomic expression in PBMCs and found reduced PRDX6:

Many of the identified mitochondrial proteins increased in expression (see Fig. 4) were involved in proper functioning of OXPHOS complex in the inner membrane of the mitochondrion. Of the OXPHOS complexes, Complex I and Complex V (ATP Synthase), had a significant number of their constituent proteins with increased expression compared to controls (NDUFA3, NDUFB3, NDUB11 and NDUB12 in Complex I, and ATP5E, ATP5D, ATP5F1 and USMG5 in Complex V). Enhanced ATP metabolic processes, generation of precursor metabolites and energy, oxidative phosphorylation, redox homeostasis and increased recycling of NAD, were identified by both STRING and DAVID functional association analysis in the ME/CFS PCA cohort.

While primarily increased abundance of mitochondrion-related proteins was seen in the ME/CFS PCA group (Fig. 4), there were several important proteins with decreased relative abundance. These included PRDX6 (whole cell body) and OXR1with roles in redox regulation, and some proteins involved in the assembly of the mitochondrion such as TIMM8A. Mitochondrial IDH2, also relatively decreased in the ME/CFS PCA subgroup, uses NADP(+) as an electron receptor to catalyze its forward oxidative decarboxylation reaction in cellular defense against oxidative damage [39].

PRDX6, or peroxiredoxin 6, is a bifunctional enzyme with two key roles: acting as an antioxidant by reducing hydroperoxides and as a phospholipase A2 (PLA2) involved in phospholipid metabolism. It helps protect cells from oxidative stress and plays a role in maintaining the integrity of cell membranes.

 

[Hutan]

Itaconate is not a very potent inhibitor of SDH. Hence, quite large concentrations are required for it's action. These are concentrations that are reached in activated macrophages. But, after export/import to another cell, they don't reach necessary levels in my opinion. I'm planning experiments to verify this. I haven't seen for example an experiment where supernatant (media) from activated WT/Irg1-KO (unable to produce itaconate) macrophages would induce SDH inhibition in any cell of choice.

That's a very interesting investigation.

It also would be great to know about the effect of itaconate on the other PRDXs. Sweetman's paper (last post) suggests there is less PRDX6 expression in ME/CFS, which might result in the same sort of mechanism as suggested for PRDX5 - more H2O2, more interferon.

A pilot study on the immune cell proteome of long COVID patients shows changes to physiological pathways similar to those in myalgic encephalomyelitis/chronic fatigue syndrome
This is another paper from the Tate lab that found PRDX2 was upregulated.

Peroxiredoxin-2 (PRDX2) is a mitochondrial antioxidant enzyme upregulated in both LC and ME/CFS datasets. PRDX2 reduces reactive oxygen species (ROS) by hydrolysing H2O2. Elevated levels of PRDX2 in our studies suggests there is increased ROS generation in both LC and ME/CFS immune cells. PRDX2 has been implicated in neurological disease due to aberrant management of ROS54. Peroxisomes are an independent organelle that metabolically interact with mitochondria but also play a role in ROS production and scavenging, and dysfunctional effects on mitochondria can affect peroxisomal physiology55. Peroxisomal dysfunction is linked with decreased levels of plasmalogens (a class of glycerophospholipids in cell membranes) that have been reported in ME/CFS56.

 

[SNT Gatchaman]

I've tagged some other papers with peroxiredoxin.

 

[paulendat]

Please allow me to adjust some of the points.

Thanks to Professor Maxim Artyomov for the nice talk. I haven't caught up with the conversation on this thread that happened over my night yet.

A lot was covered and I don't have the background to take on some of the points quickly enough. Some of the things I took away from this (which may be wrong), beyond what this paper covers:

1. How easy it is to come to a wrong conclusion. People thought the non-natural itaconate versions would work the same as the natural version, but they don't. It can be worth revisiting findings, poking into the details of the chemistry.

2. IRG1 inhibition is the key thing in the mechanism. Other (non-natural) substances inhibit IRG1 (e.g. 2 Methylsuccinate acid) and have the same effect of increasing interferon production.

3. Question about the sustained effect. The sustained high peroxide levels might be useful for dealing with engulfed pathogens. (But there is also the sustained effect of the interferon production).

4. Natural itaconate is membrane permeable. It is only produced by immune cells. There was a question about whether itaconate is secreted or leaks out of immune cells, in order to prime neighbouring cells (immune cells, other cells?). Professor Artyomov seemed to indicate that some leakage is possible but, if so, the level must be at a very low level. Perhaps some cells could be very sensitive to exogenous itaconate.

Professor Artyomov talked about how itaconate potentially could have this effect in any cell, but most cells don't want ROS production getting out of hand, so he thinks the endogenous production in immune cells only is an adaptation to enable those cells to carry out their function.
(Presumably, if you have high levels of interferons being secreted, interferons can do the job of signalling a pathogen problem?)

4. Fungal cells produce itaconate.

5. Itaconate has an inhibitory effect on PRDX5. It also seems to affect PRDX1. It is possibly affecting multiple PRDX's (2, 3, 4, 6). It would be interesting to see what the function of those other molecules is, and if they have any relevance to us.

1. You are absolutely correct. The problem arises especially when people use derivatives of itaconate and simply call it itaconate.

2. 2-Methyl succinct acid is not Irg1 inhibitor. Just like itaconate, it inhibits PRDX5, boosts IFNb production and inhibits inflammasome activation.

4. Natural itaconate by nature is not at all or poorly membrane permeable. But there are transporters that allow it to enter cells without the need of membrane-permeable derivatives.

 

[Hutan]

Thanks very much @paulendat. I've edited my notes in the post above.

Re point 2, I mixed up PRDX5 with IRG1.


So, the cycle is (I think?)

• Pathogen or damage associated molecular patterns (PAMPs and DAMPs) increase IRG1 expression
• That increases itaconate levels in the immune cell
• That reduces levels of PRDX5 (which would normally be mopping up ROS including H2O2)
• So, there is more H2O2
• That results in more interferon being released by the cell
• Interferons can increase itaconate in other immune cells

 

[paulendat]

That's a very interesting investigation.

It also would be great to know about the effect of itaconate on the other PRDXs. Sweetman's paper (last post) suggests there is less PRDX6 expression, which might result in the same sort of mechanism as suggested for PRDX5 - more H2O2, more interferon.

A pilot study on the immune cell proteome of long COVID patients shows changes to physiological pathways similar to those in myalgic encephalomyelitis/chronic fatigue syndrome
This is another paper from the Tate lab that found PRDX2 was upregulated.

This all is ongoing and experiments are running. I have reason to believe (I have experimental proof that is not yet perfect) Prdx3 is not affected. This opens huge avenue of novel research on multiple fronts. It remains to be seen, whether it is also in ME/CFS. I hope it does. But we need a hard proof. Otherwise it's just talking .

 

[paulendat]

To paulendat's earlier point, I've found this paper:
https://www.nature.com/articles/s41598-020-80933-7

Which shows that endogenous itaconate does not seem to stimulate interferon gamma in cytotoxic T cells. Inhibition of SDH by another exogenous agent, however, did enhance interferon gamma production in pre-activated T cells. Which really makes me want to see what if anything is bound to SDH in ME/CFS T cells...

You don't want to use SDH inhibitors as therapeutics. They can be helpful in some cases. But one of the side effects is Alzheimers.

 

[paulendat]

IRG1 encodes the protein that catalyzes itaconate production--they did an IRG1 knockdown to see if interferon beta production is dependent on itaconate, I believe.

The theory about itaconate regulating ROS is that most cells have fine tuned mechanisms that kick in when ROS ramp up [e.g. PRDX5] precisely because ROS are generally bad for cell function. However, macrophages kill pathogens via ROS, so they don't want these inhibitory mechanisms ramped up. If TLR4 is stimulated, IRG1 activity facilitates upregulation of itaconate, which has the ability to essentially block the ROS block. Meaning it lets ROS increase beyond what would normally be allowed in other cells so that the macrophages can use it for pathogen clearance

[Edit: the connection with interferon beta is that blocking-the-ROS-block seems to be the thing that enables interferon beta production. Other non-natural itaconate derivatives don't have this block-the-block action, therefore if you administer them to cells, you'll end up with an "anti-inflammatory" anti-ROS effect that is not seen with endogenous itaconate]

We did Irg1 knock-out. This is different from knock-down. In case of knock-down, you are decreasing protein expression by targeting mRNA. Usually efficiency around 50-90% decrease.

In the case of knock-out, you delete the gene encoding your protein in the animal. Resulting in a complete loss of protein expression in the animal or primary ccells.This is step above knock-down.

For the edit, derivatives of itaconate like DI or 4-OI induce NRF2. On one hand NRF2 is a pathway that induces antioxidant response. It gets triggered in presence of large quantities of ROS. It literally evolved after emergence of oxygen in the atmosphere and oceans. It is also known to inhibit IFNb. This is why there is inhibition in DI treated macrophages. And it is not only IFNb but also IL1b and IL6, that are inhibited by DI/NRF2.

 

[jnmaciuch]

We did Irg1 knock-out. This is different from knock-down. In case of knock-down, you are decreasing protein expression by targeting mRNA. Usually efficiency around 50-90% decrease.

Ah thank you, I misspoke.

For the edit, derivatives of itaconate like DI or 4-OI induce NRF2. On one hand NRF2 is a pathway that induces antioxidant response. It gets triggered in presence of large quantities of ROS. It literally evolved after emergence of oxygen in the atmosphere and oceans. It is also known to inhibit IFNb. This is why there is inhibition in DI treated macrophages. And it is not only IFNb but also IL1b and IL6, that are inhibited by DI/NRF2.

Yes I'm familiar with the pathway from a rotation professor that was interested in CRISPR screens of homeostatic pathways. I've been looking into NRF2 since proteasome findings seem to come up repeatedly in ME/CFS. Initially I did not hold much confidence in those findings since, as a GO pathway, it tends to come up very often in the absence of other strong signals (at least in my work). However, since NRF2 is regulated by constant ubiquination, I'm now thinking that pre-existing differences in proteasome degradation may be related in some way as a triggering event. I am still trying to work out a testable hypothesis though, I'm just noting the possible connection

[Edit: glutathione was also found to be predictive pre-ME/CFS in a longitudinal study done by Leonard Jason's group when I was interning there, possibly pointing to something about ROS regulation as a common thread]

 

[paulendat]

I guess one question I have from having looked at public cell expression databases, IRG1/ACOD1 is also highly expressed in Monocyctes. We know from Hanson et al in ME/CFS and Long Covid studies that a subset of monocytes have different genetic expression in patients vs controls. How does IRG1/Itaconate play a role in those cells before they mature into macrophages?

Yes, Irg1 is expressed in monocytes, macrophages, neutrophils and to some extent in dendritic cells.

My assumption is that the effect of itaconate we observe in macrophages will also work in monocytes. I don't doubt that Prdx5 and SDH will be inhibited by itaconate. If it will translate into immunoregulation as observed in macrophages has to be investigated.

 

[jnmaciuch]

You don't want to use SDH inhibitors as therapeutics. They can be helpful in some cases. But one of the side effects is Alzheimers.

Was not suggesting using it as a therapeutic! Just wondering aloud about potentially using co-IP or another method to determine if there is something differentially bound to SDH in ME/CFS vs control

 

[paulendat]

Was not suggesting using it as a therapeutic! Just wondering aloud about potentially using co-IP or another method to determine if there is something differentially bound to SDH in ME/CFS vs control

I apologize, I misunderstood. How do you envision a role of adaptive immune system in the disease? Do you expect autoimmunity targeting neurons (cytotoxic T cells or autoantibodies)? If I'm not wrong that doesn't seem to be the case. Or something more like dysfunctional Treg cells leading to inappropriate reaction to a pathogen?

 

[jnmaciuch]

I apologize, I misunderstood. How do you envision a role of adoptive immune system in the disease? Do you expect autoimmunity targeting neurons (cytotoxic T cells or autoantibodies)? If I'm not wrong that doesn't seem to be the case. Or something more like dysfunctional Treg cells leading to inappropriate reaction to a pathogen?

At the moment I only have speculation with a lot of unknowns. My suspicion does not rely on autoimmunity. Rather, I'm tossing around the idea of a feedback loop of metabolic reprogramming between adaptive and innate immune cells, in which interferon gamma release (or maybe another signal) would "prime" macrophages to some stimulus released during activity similar to your itaconic acid pretreatment, and some metabolite released by activated macrophages perpetuates metabolic reprogramming in lymphocytes to produce higher than normal levels of interferon gamma.

What I see in the literature is potential indirect evidence of malate-aspartate shuttle impairment, so I am thinking that the same metabolite released by macrophages would affect most neighboring cells, and potentially be present in low levels in the circulation to also affect lymphocytes.

Since a shift towards aerobic glycolysis seems to be required for interferon gamma production, I am wondering if a signal which continuously alters the TCA cycle (such as SDH impairment) in lymphocytes might be sufficient on its own to cause continued interferon gamma production in the absence of a de novo stimulus (or perhaps hyperreaction to normal stimuli). Obviously that would be a feedback loop that also exists in healthy people, so if such a loop exists, the question is whether there is something that normally blocks it after infection resolves so that healthy people aren't developing ME/CFS.

I do not currently have the resources to test this out myself and am just starting to formulate the idea, so I'd be happy to hear your insight if you have any.

 

[Stuart79]

=5. Itaconate has an inhibitory effect on PRDX5. It also seems to affect PRDX1. It is possibly affecting multiple PRDX's (2, 3, 4, 6). It would be interesting to see what the function of those other molecules is, and if they have any relevance to us.

Could inhibition of PRDX be the cause of red blood deformability problems observed in ME/CFS? Per Grok, PRDX2 seems to be important for maintaining RBC deformability.

 

[Hutan]

@Stuart79

This is another paper from the Tate lab that found PRDX2 was upregulated.

There may be problems with the Tate lab's paper (including with Long Covid participant selection ) but it suggested that PRDX2 was increased.
(as opposed to PRDX6 that was found to be low)

 

[hotblack]

I’m a bit late to this discussion and can’t access the full paper but from the “how did we get here” overview and ideas about crossovers with other theories people like @jnmaciuch have it sounds really interesting.

Look forward to the talk being available somewhere. Happy to help extracting and sharing the audio from the video it if that helps.

 

[Jonathan Edwards]

By knock down data do you mean like the knock your socks of eureka moment data? Or something else.

Also are you saying that the particular pathway step in your theory involving b cells is likely wrong or the entire thing?

I meant knock down in the sense of a knock down argument to which there is no rebuttal. Not a knock-down or out mouse! Hopefully knocking your socks off too.

It is the step involving B cells (i.e. antibody) that I think may well be wrong; the rest of it looks to me a fairly good bet - but that draws in lots of ideas we have all been playing with for a while. In a way the hypothesis is an attempt to see if all the pieces can be drawn together with one extra step. That may turn out to be the lime slice in the Corona that you never actually ingest. The solution may turn out to be possible without it but the extra step adds a bit of extra zing to the theorising.