Monday, March 30, 2020

Look after your lysosomes

I was a little cautious about the efficacy vs toxicity of chloroquine and its derivatives in my last post.

George Henderson just retweeted this snippet;

Sadly the narrow line between the degree of raising lysosomal pH to blunt viral replication and that which might release sufficient cysteine to strip the FeS clusters out from complex I can be crossed quite easily, so it appears.

Worryingly Dr Barman appears to have been one of those people with some degree of metabolic syndrome and who might have been someone most likely to benefit from prophylaxis against coronavirus replication.

My own observation during my very rare trips to our local hospital is that medical professionals are far from immune to metabolic syndrome. Couple that with extreme stress, high viral load exposure, severe sleep deprivation and the sort of food/snacks available in hospitals and you have to worry for the health of these people.

None of them want to have metabolic syndrome, a problem which is built in to our public health guidelines. These people are laying their lives on the line to support the lipid hypothesis. Most of their patients are in hospital secondary to the lipid hypothesis. Those developing ARDS in the ITU do so in a large part as a result of the lipid hypothesis.

Just my rather sad view from the sidelines.


Wednesday, March 25, 2020

From Yeasts to Chloroquine

This paper is from Hughes and Gottschling

An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast

It got a mention in the blog back in 2012 when it was freshly published. The group have gone on to study yeasts, ageing and the lysosome-like vacuole of yeasts. Their core finding is that vacuolar pH controls mitochondrial "health" which controls ageing, at least in their model.

The group has been very busy and earlier this year this paper was published from Hughes' lab:

Cysteine Toxicity Drives Age-Related Mitochondrial Decline by Altering Iron Homeostasis

The paper describes a very long series (way too many to detail here) of experiments aimed at adjusting vacuolar pH upwards and downwards and observing the effect on the survival of mother yeast cells through repeated cell divisions (replicative age rather than chronological age, there are arguments about which matters most).

Bottom line: Acidifying vacuolar pH extends lifespan, reducing its acidity shortens it.

Why should that be?

Their next series of experiments demonstrated that cysteine toxicity was the driver of early mitochondrial functional decline secondary to loss of vacuolar acidity. Cysteine is normally harmless and essential for life. Your cells love it, just so long as it is within the vacuole (or lysosome in humans), not in the cytoplasm. It's kept there by a vacuolar amino acid transporter driven by the vacuole proton gradient. The pH gradient is generated using a vacuolar vATP-ase to pump protons from the cytoplasm in to the vacuole, using ATP. It's related to the mitochondrial ATP synthase but normally runs in reverse.

If, on a long term basis, vacuolar pH rises (ie the vATP-ase fails), cysteine is released from the vacuole in to the cytoplasm where it auto-oxidises, generating much too much hydrogen peroxide. This reacts with the iron-sulphur clusters of complex I and many other crucial enzymes in the mitochondria. In old age cysteine becomes toxic through vacuolar failure.

I've been interested in this for some time because Barja and Sinclair have both intimated that they are tending to avoid animal proteins in favour of low cysteine/methionine plant proteins. Cysteine is the cellular executioner when vacuole pH rises during the old age of yeasts or lysosomal pH rises in ageing mammalian cells. It's interesting because methionine restriction (which reduces cysteine levels) appears to core to the longevity promotion seen with caloric restriction or protein restriction in mice fed on crapinabag.

You have to wonder whether we are looking at this the wrong way round. What if crapinanbag, based on starch and sucrose, causes early onset lysosomal failure which can be ameliorated by removing the cysteine, which is the cellular execution mechanism?

This would make methionine restriction's longevity extension rather specific to glucose based metabolism. My biases would tend to favour this point of view. There are no data, yet.

As an aside:

Now, I have speculated that both influenza and corona viruses need anabolic processes generated by mTOR activation. This requires acute acidification of the lysosome. Blocking acute lysosomal acidification is one technique currently being investigated for treating the life threatening pneumonia which develops in susceptible individuals during the current COVID-19 pandemic. There are suggestions that chloroquine, a suppressor of lysosomal acidification, might be an effective treatment. My guess is because it blocks anabolism.

There is probably a fine line between suppressing anabolism and releasing a mitochondrial-executing concentration of cysteine.

Neither Hughes nor Gottschling were considering therapeutic inhibition of vacuolar acidification as a stratagem for anything. They were more interested in avoiding long term loss of vacuolar acidity to delay mitochondrial function decline. But blunting anabolism without causing catastrophic cysteine release is a current anti-viral/anti-neoplastic therapeutic target.

You can see that the drug chloroquine a) might work and b) might be very toxic in overdose.

It does currently appear that it might work but we should never forget that "clinical experience is no guarantee of therapeutic efficacy".

However it would be great if it really did work.


Tuesday, March 17, 2020

ARDS and linoleic acid

Adult/Acute Respiratory Distress Syndrome is topical at the moment. In the comments to the last post I wondered whether omega six fatty acids, especially linoleic acid, might be a driver of ARDS, which is one of the most intractable ITU problems in response to major infection/trauma/inflammatory insults.

Tucker came up with this abstract

Plasma fatty acid changes and increased lipid peroxidation in patients with adult respiratory distress syndrome

and I peeked at the related papers to find this gem:

An increase in serum C18 unsaturated free fatty acids as a predictor of the development of acute respiratory distress syndrome

Again, only an abstract and mostly describing a pilot study. But here is the critical statement:

"Increases in unsaturated serum acyl chain ratios differentiate between healthy and seriously iII patients, and identify those patients likely to develop ARDS".

That is, the more linoleic (and oleic) acid you have as FFAs in your bloodstream, relative to my beloved palmitic acid, the more likely you are to develop ARDS. Which carries a high risk of death.

That was 1996.  The work will have been done before that, so we have known that linoileic acid is bad news for well over 20 years.

If you are a Standard American on the Standard American Diet, or anyone else in the world poisoned by a cardiologist-promoted PUFA based diet, any weight loss through illness will release significant amounts of linoleic acid from your adipocytes. That might just trigger ARDS in the aftermath of a viral pneumonia.

There's a lot of it about.


BTW Steve Cooksey has a rather nice post up citing a lot of the refs featuring how to maintain an effective innate immune system, so as to avoid the viral pneumonia in the first place. It's a good read.

Saturday, March 07, 2020

Cell surface oxygen consumption (4) Influenza

This press release, from 2013, surfaced on twitter (embarrassingly I have again lost the tweeter due a hat tip for this. Mea culpa. Found him, it was resurfaced/retweeted by Guðmundur Jóhannsson).

Glucose: Potential new target for combating annual seasonal flu

which summarises this paper:

Glycolytic control of vacuolar-type ATPase activity: a mechanism to regulate influenza viral infection.

Over the last few weeks I happen to have been immersed in vacuoles/lysosomes, cysteine toxicity, longevity and yeasts. Oh, and mTORC1, which is deeply associated with lysosomes. So I'm in a mindset of how lysosomes/mTOR control longevity/anabolism.

Anyhoo. Influenza A virus uses lysosomes to maximise its survival. My prediction is that it activates mTOR to induce a marked anabolic state and hijacks that anabolic state to generate lots and lots of influenza A virus particles. It will do that, much as a cancer cell might, by aerobic glycolysis working on the basis that glycolysis, while inefficient, is very, very fast at generating ATP compared to OxPhos. This would suggest that the free availability of glucose secondary to hyperglycaemia (or increased access of glucose to the cytoplasm secondary to hyperinsulinaemia) will increase the success of the influenza virus, as found in Kohio's paper.

Which brings us to anabolism and glycolysis. Not only does aerobic glycolysis supply ATP for anabolism faster than OxPhos can but it also supplies phosphoenolpyruvate for amino acid synthesis, plus other anabolic substrates come from glucose via assorted pathways.

However for every glucose molecule which generates a pair of 1-3 bisphosphoglycerate molecules two NAD+ are consumed. If these glycerate molecules are used for anabolism via phosphoenolpyruvate they will not restore the NAD+ balance by converting to lactate. The basic story is in

Cell surface oxygen consumption (2)


Cell surface oxygen consumption (3)

with an introduction to the concept in

Cell surface oxygen consumption (1)

The glycerophosphate shuttle won't do the job because this too is limited to the speed of OxPhos. Cell surface oxygen consumption does fit the bill for rapid restoration of NAD+.

So. Does influenza virus drive cell surface oxygen consumption to facilitate anabolism at a speed fast enough to keep it one step ahead of the innate immune system?

I don't know.

But another standard (primarily rodent) model RNA virus certainly does.

Oxygen uptake associated with Sendai-virus-stimulated chemiluminescence in rat thymocytes contains a significant non-mitochondrial component

I think this will be a basic feature of rapid anabolism, be that viral or neoplasia related.

Will hyperglycaemia and/or hyperinsulinaemia facilitate viral directed anabolism under infection by another, more topical novel human RNA virus?

Personally, I'm not planning on finding out the hard way when I get around to catching the current bug.