I think we need to understand exactly what's going on in the WASF3 paper, before we can propose what the goal is. A lot of drugs/supplements ME/CFS patients have tried can "reduce ER stress" by general (e.g. upstream, high-level) mechanisms, but these don't yield impressive results over the long-term.
Normal Unfolded Protein Response (UPR)
Overview from:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8146082/
The unfolded protein response (UPR) is the cells’ way of maintaining the balance of protein folding in the endoplasmic reticulum, which is the section of the cell designated for folding proteins with specific destinations such as other organelles or to be secreted by the cell. The UPR is activated when unfolded proteins accumulate in the endoplasmic reticulum. This accumulation puts a greater load on the molecules in charge of folding the proteins, and therefore the UPR works to balance this by lowering the number of unfolded proteins present in the cell. This is done in multiple ways, such as lowering the number of proteins that need to be folded; increasing the folding ability of the endoplasmic reticulum and by removing some of the unfolded proteins which take longer to fold. If the UPR is successful at reducing the number of unfolded proteins, the UPR is inactivated and the cells protein folding balance is returned to normal. However, if the UPR is unsuccessful, then this can lead to cell death.
Now, what does that process look like in terms of the protein kinases? I found a good excerpt from:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3578356/:
PERK’s lumenal stress-sensing domain is structurally and functionally related to Ire1’s, though the sequence identity is low, and PERK also contains a cytosolic kinase domain that undergoes trans-autophosphorylation in response to ER stress. Unlike Ire1, however, PERK also phosphorylates the eukaryotic translation initiation factor eIF2α. Phosphorylation of eIF2α results in a reduction of general protein synthesis and thus a decrease in the load of proteins entering the ER (Harding et al. 1999). Under such conditions, mRNAs containing inhibitory upstream open reading frames in their 5′-untranslated region are preferentially translated (Jackson et al. 2010). One such mRNA encodes the transcription factor ATF4 that activates downstream UPR target genes, including GADD34 (growth arrest and DNA damage-inducible 34) and CHOP (transcription factor C/EBP homologous protein) (Harding et al. 2000; Scheuner et al. 2001). GADD34 encodes the regulatory subunit of the protein phosphatase PP1C complex that dephosphorylates eIF2α (Novoa et al. 2001), comprising a negative feedback loop to reverse the translational attenuation mediated by PERK. The downstream transcription factor CHOP activates genes involved in apoptosis (Wang et al. 1998; Zinszner et al. 1998). Thus, the PERK branch first mediates a prosurvival response, which switches into a proapoptotic response on prolonged ER stress (Walter and Ron 2011).
Takeaways of the stress response:
- PERK is a sensor of ER stress (e.g. of unfolded protein accumulation in the ER)
- When activated by stress, PERK's job is to deactivate (by phosphorylation) eIF2α
- eIF2α positively regulates protein synthesis
- Decreasing the total number of proteins that need to be folded is one method to reduce accumulation of unfolded proteins in the ER, which are the cause of ER stress
Now, what happens when there is no more ER stress? PERK should automatically become disabled, because it is a direct sensor of ER stress (or almost direct). So, PERK will stop phosphorylating eIF2α, but something still needs to
dephosphorylate eIF2α to bring protein synthesis back to normal. That 'something' is PP1 and GADD34: (
https://www.pnas.org/doi/10.1073/pnas.1501557112)
Following relief of the stress, the growth arrest and DNA damage-inducible protein GADD34 associates with the broadly acting serine/threonine protein phosphatase 1 (PP1) to dephosphorylate eIF2α.
Known Pathological UPR
Now the dual nature of eIF2α becomes more apparent: turning down total protein synthesis, while helpful during ER stress, is probably not ideal long-term: (
https://www.cell.com/trends/cell-biology/fulltext/S0962-8924(20)30101):
Although activation of UPR aims to restore cellular function, prolonged ER stress response can activate apoptotic signals, leading to the robust expression of downstream signaling, which damage the target cells (Figure 1A ). Indeed, increasing evidence demonstrates that metabolic disorders, such as obesity, type 2 diabetes, and age-associated pathogenesis, are associated with chronic ER stress.
But,
the most important point is that the cell's high-level goal of activating the ER stress response was not necessarily the problem:
However, the ER stress response or sensing failure also contributes to the progression of metabolic diseases where the downstream molecules involved in ER stress responses fail to be fully activated despite the activation of the upstream ER stress sensors
This last bolded sentence is the crux of the WASF3 paper's hypothesis. But, it has also been observed in other diseases, such as in diabetic/obese mice:
Similarly, the tendency of the phosphorylated ER stress sensor PERK (protein kinase R-like ER kinase) is high, while the downstream target phosphorylation of eIF2α (eukaryotic initiation factor 2-α-subunit) and DDIT3 (DNA damage-inducible transcript 3)/GADD153 (growth arrest- and DNA damage-inducible protein 153), or CHOP [CCAAT/enhancer-binding protein (C/EBP) homologous protein], are decreased
It's like the thermostat (PERK) is set to cool things down, but the furnace (eIF2α) never turns off fully. So, the thermostat stays pathologically activated, forever.
Pathological UPR in ME/CFS
Now the significance of the WASF3 paper are clear: it's essentially the same state as the diabetic/obese mouse model:
Increased ER stress would normally be expected to turn down protein translation, but intriguingly, the inhibitory phosphorylation of protein translation factor eIF2α, a target of PERK kinase activity, was unexpectedly lower (i.e.,
activated) in patient S1 cells (Fig. 6A, lane 2 vs. 1).
And they found that inhibiting PP1, which I explain in the beginning of this post, was effective
by directly intervening with the downstream molecules (namely eIF2α):
While the effect of TUDCA was less apparent as expected of a relatively nonspecific drug, the inhibitor of protein phosphatase 1 (PP1) salubrinal, which prevents the dephosphorylation of eIF2α thereby inhibiting protein translation, was more effective in decreasing the levels of both PERK and WASF3 in S1 cells (Fig. 6A, lanes 3-6 vs. 2).
Relation to ATG 13 paper (@SlamDancin 's question)
I don't pretend to understand the depths of this stuff well enough to give a confident answer here. But, here's what I found after googling some stuff.
(
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849280/):
Inhibition of mTORC1 by rapamycin actually induces stress responses, including reduction in protein synthesis and induction of autophagy, which are protective mechanisms for the cells to survive under stress conditions
(
https://academic.oup.com/nar/article/41/16/7683/2411270?login=false)
[...] recent data suggest that, analogous to yeast, the suppression of mTORC1 activity permits ULK1 to form an autophagy initiation complex with ATG13 (2). The phosphorylation of eIF2α, which also occurs with amino acid deprivation as well as with endoplasmic reticulum (ER) and other cellular stresses, similarly attenuates global protein synthesis (reviewed in (3)). However, eIF2α phosphorylation also paradoxically increases the translation of select mRNAs, including the transcription factor ATF-4 which transactivates the autophagy genes LC3B and ATG5
If I were to force a conclusion, maybe the upregulated ATG13 found in the ME/CFS paper (
https://www.sciencedirect.com/science/article/abs/pii/S1044743122000379?via=ihub) could represent a parallel effort to attenuate protein synthesis. And, it would stay pathologically activated for the same reason that PERK remains pathologically activated: the downstream molecules aren't cooperating to get the job done.
Next Steps in Understanding
There are a lot of other proteins and "chaperones" mentioned in the WASF3 paper, like BiP, that I don't fully understand yet. I think some of these chaperones are intended to help with protein folding, which sort of addresses the "root" of the problem more than reducing global protein synthesis, which might be seen as more of a "workaround". But I'm not sure if this interpretation is quite right.
