Why me, O Lord, Why me?

It was very hard for my multiple sclerosis (MS) patients to understand why they were singled out for MS, given the publicity given to theories of viral causation, popular at least since I started getting seriously interested in neurology as a 3rd year medical student in 1964.  Herpes simplex (fever blisters) was a popular culprit, but we all know lots of people who’ve had them without coming down with MS.

The best explanation I could give them was of my med school classmate Marty, a Jewish kid from Pittsburgh.  Graduating in 1966 at the height of American involvement in Vietnam, all my classmates entered the service within a few years.  Marty was sent to Vietnam  as a GMO (General Medical Officer).  He was quickly sent back stateside as he developed a severe anemia.  Why?

Well malaria was endemic in Vietnam, and anyone going over received an antiMalarial as prophylaxis.  The malarial parasite does its damage by infecting red blood cells.  The antiMalarial drug he received inhibited a red cell enzyme Glucose 6 Phosphate Dehydrogenase (G6PD), essentially starving the parasites.  Marty had a partial deficiency of this enzyme.  Such deficiencies are relatively common in areas endemic for Malaria, as it is protective, just as the sickle cell trait is protective against Malaria in Africa.  A variety of other mutations in different red cell proteins arising in endemic areas are also protective (example Thalassemia in Greece, etc. etc.)

So if Marty had never been sent to Vietnam he would never have become anemic.  I’d tell my patients that they had some biochemical difference (totally unknown back then) that made them susceptible to complications of infection with a common organism.  Not very satisfying, but it was the best I could do.

In the case of another virus Epstein Barr Virus (EBV) which causes infectious mononucleosis, this explanation (50+ years later) turned out to be exactly correct.    Not only that it shows the extreme subtlety of what ‘causation’ in medicine actually means.

Not only must the unlucky people getting MS after EBV infection be different biochemically, they must be infected with a particular variant of EBV (not all EBV is the same, just as not all people or SARS-CoV-2 are the same).

That’s the view from 30,000 feet.  You can stop here but the full explanation is unsparingly technical.  It is to be found in Cell vol. 186 pp. 5675 – 5676, 5708 – 5718 ’23 ]

Here goes.

Long term control of Epstein Barr Virus is mediated by cytotoxic T lymphocytes which recognize parts of EBV proteins.  One such protein is EBNA1, and antibodies to amino acids #386 – #405 of EBNA1 cross react with amino acids #370 – #389 of a human protein called GlialCAM (for Glial Cell Adhesion Molecule) which is important in maintaining the myelin sheath around axons in the brain (MS is basically a destructive immune attack on myelin).

Such an antibody is called autoreactive, in the sense that it is reacting to a normal human protein.  Cells producing autoreactive antibodies (autoreactive cells) are normally eliminated by cytotoxic natural killer cells.  In the case of EBV specific T cells they are eliminated by natural killer cells expressing proteins NKG2C and NKG2D.  They target the autoreactive GlialCAM specific autoreactive B cells.  Some people have deletion of the gene coding for NKG2C rendering them more susceptible to MS after EBV infection.

But wait, there’s more. There are many EBV variants and some of them upregulate another human protein HLA-E by containing another protein (LMP1) which stabilizes HLA-E.  HLA-E blunts the natural killer cell attack on autoreactive GlialCAM cells.

So it’s a delicate dance of unfortunate events ‘causing’ MS.  A mild genetic defect in the human, and a genetic variant in the virus, both of which must occur for causation.

Who knew that medical causation could be so subtle.

We had to destroy the village to save it

I never thought I’d quote Karl Marx but here he is “history repeats itself, first as tragedy than as farce.”  Most readers of this post weren’t born when the following statement became part of the public consciousness during the Vietnam war — “It became necessary to destroy the town to save it.” This quote has often been paraphrased as “We had to destroy the village in order to save it.”  Whether or not it was actually said to Peter Arnett, a critic of the war, is forever unknown and quite contentious. It was said during the Tet offensive about the battle of Ben Tre, a Vietnam provincial capital in January 1968, the year I became an Air Force MD.  It was definitely a tragic time.

Now we have the farce of the Colorado Supreme Court removing a candidate (Trump) from the ballot to save democracy.

Addendum 23 December — https://www.bbc.com/news/world-europe-67810463  — “A former TV journalist who announced she would challenge President Putin in Russia’s spring election has been barred from standing.Independent politician Yekaterina Duntsova wanted to run on a platform to end the war with Ukraine.But the electoral commission voted unanimously to reject her candidacy three days after her application, citing 100 “mistakes” on her form.Ms Duntsova said she would appeal the decision at the Supreme Court.”

Isn’t it nice to have company?

Well, you can’t say you weren’t warned — from a post of two weeks ago

Efforts to Disqualify Trump Uphold Democracy

No, the Onion hasn’t taken over the opinion page of the New York Times.   Nor was this written by the ghost of George Orwell, or Ali Khamenei the current  ‘supreme leader’ of Iran who chooses who may run for office and who may not.  It was written by Mark A. Graber, a constitutional scholar and university professor in Maryland, proving yet again that only someone of high intelligence could defend something so stupid.  But as Marshall McLuhan said ‘the medium is the message’, and the fact that the Times chose to publish it is significant. Nothing published by the Times happens by chance.  It is the American Pravda after all — https://luysii.wordpress.com/2023/11/21/reading-americas-pravda/

At last a Science article about Alzheimer Rx that doesn’t trash Cassava Sciences

An article “Immunotherapies for Alzheimer’s Disease”  (Science vol. 382 pp. 1242 – 1244 ’23) avoids hype about these therapies and doesn’t trash Cassava Sciences or Simufilam (by ignoring it).   They note that “aducanumab, lecanemab, and donanemab are far from curative, but they all slow cognitive decline by ~25 to 30% over 18 months.   Continuing to avoid hype they say “reduction of brain Aβ in early symptomatic AD has a positive, but modest, clinical effect.”

They don’t ignore side effects. “ARIA-E (edema in the brain parenchyma or sulcal effusion—i.e., extravasated fluid in the leptomeninges along the sulcal spaces) and ARIA-H (hemosiderin deposits resulting from red blood cell breakdown products—i.e., microhemorrhages) (9). Although the incidence of ARIAs is increased by antibody treatment and is observed in roughly one-third of treated participants, in most individuals, it is asymptomatic.

This is similar to the rationale put out for the ‘asymptomatic hemorrhages’ seen after intravenous tissue plasminogen activator (TPA) for stroke.

Ask yourself, would you want any of them (ARIA-E, ARIA-H, asymptomatic hemorrhage) ?  I wouldn’t and the long term effects of such things are unknown.

They also deal with the cost of immunotherapy. “In the US, aducanumab, lecanemab, and donanemab each have an annual cost of $26,500, but associated imaging and monitoring means that costs for a year of treatment may exceed $75,000. ”

All in all, a very fair minded article.

But what really caught my eye was the following statement. “In cancer, many drugs are approved with modest effects on overall survival, but over time, data emerge showing exceptional responses in select individuals who are cured or are in very-long-term remission.”

This is exactly what I saw in my examination of Cassava’s data on the first 50 patients to complete 9 months of treatment on Simufilam.  Basically 5/50 had a greater than 50% improvement in their ADAS-Cog11.   This is why I’m so excited about the drug.  No antimicrobial cures all infections (because they are different).  Similarly, there is no compelling evidence that all Alzheimer’s disease is the same.

Now I am a retired clinical neurologist after 33 years of training and practice.  You never see results like this in Alzheimers disease.  I likely saw 1 demented patient a week during this time.  Although the 9 month results were not double blinded and open label, long clinical experience tells me that these results are spectacular and unprecedented (even if they only occur in 10% of patients getting Simufilam).

Here is a link to a post analyzing these results in far greater detail https://luysii.wordpress.com/2021/08/25/cassava-sciences-9-month-data-is-probably-better-than-they-realize/

A brand new theory of traumatic cerebral edema

I saw and tried to treat traumatic cerebral edema (brain swelling) in the 3 and half years I worked with 2 very busy neurosurgeons.  A paper this month in Nature (volume 623 pp. 992 – 1000 ’23) argues that we’ve had  its cause  all wrong.

Neurologists are well aware of brain swelling around a stroke because of damage to blood vessels by the stroke.  Such swelling is localized, but can get worse and worse (e. g. larger and larger) and kill the patient by compressing the brain stem.  Similarly brain swelling around tumors is (initially) local to them.  Both are thought to be due to leaky abnormal blood vessels

The Nature paper argues that acute post-traumatic brain edema is to due to suppression of glymphatic and lymphatic flow.  Since the glymphatic system was only described 10 years it’s time for some background.

First — a bit of history. The tissue of the brain is so tightly packed that it is impossible to see the cells that make it up with the usual stains used by light microscopists. People saw nuclei all right but they thought the brain was a mass of tissue with nuclei embedded in it (like a slime mold). Muscle is like that — long fibers with hundreds of nuclei here and there. It wasn’t until that late 1800′s that Camillo Golgi developed a stain which would now and then outline a neuron with all its processes. Another anatomist (Ramon Santiago y Cajal) used Golgi’s technique and argued with Golgi that yes the brain was made of cells. Fascinating that Golgi, the man responsible for showing nerve cells, didn’t buy it. This was a very hot issue at the time, and the two received a joint Nobel prize in 1906 (only 5 years after the prizes began).

How tightly packed are the cells in the brain? The shortest wavelength of visible light is 4000 Angstroms. Cells in the brain are packed far more tightly. To see the space between the brain cell external membranes you need an electron microscope (EM). Just preparing a sample for EM really fries the tissue. Neurons are packed together with less than 1000 Angstroms between them. So how much of this is artifact of preparation for electron microscopy has never been clear to me. One study injected a series of quantum dots of known diameter into the cerebral spinal fluid (CSF) to see the smallest sized dot that could insinuate itself between neurons [ Proc. Natl. Acad. Sci. vol. 103 pp. 5567 – 5572 ’06 ]. The upper limit was around 350 Angstroms. No wonder the issue was contentious when all they had was light microscopy.

Surprisingly, the PNAS paper comes up with an estimate that brain extracellular space comprises 20% of brain volume. I find this hard to accept given the above. So how does the brain get rid of waste products? It turns out that there is a circulation of cerebrospinal fluid (CSF) of sorts. Inject a tracer that you can follow into the CSF. After a period of time the tracer enters the brain along arteries (not veins) and after still more time it leaves the brain along the  horribly named glymphatic system which drains into the cervical lymphatic vessels.

Rather than leaky vessels the Nature paper above says that traumatic brain swelling is due to a suppression of glymphatic flow which gets out of the brain through lymphatic vessels.  This is held to be a response to excessive systemic release of norepinephrine, a well known response to trauma of any sort.  That’s pretty far out, except the the authors were able to back up their idea by attenuating (not cure) traumatic cerebral edema (in experimental animals) by blocking the sympathetic nervous system.  Norepinephrine binds to a variety of receptors in the body (called adrenergic receptors), so the authors used 3 different drugs

propranolol (Inderal) which blocks beta adrenergic receptors

prazosin (Minipress) which blocks alpha1 adrenergic receptors

atipamezole which blocks alpha2 adrenergic receptors.

I’m sure some plucky neurosurgeon will try it out, as the therapy we used (high dose corticosteroids) back then  didn’t always work for traumatic brain edema, but it usually worked beautifully for the edema around tumors.

The higher drivel revisited

Only 3 potentates of the academy could have said opprobrium of genocide depends on context. The exchange between the 3 and Congresswoman Stefanik has been viewed over a billion times and it’s only been a few days.  For most viewers it was like turning over a rock and seeing what crawls out.

So it’s time to republish an old post on the higher drivel and its happy home in the higher reaches of academe.  Not much has changed since 2011

The higher drivel – II

From the obituary of a leading philosopher at an Ivy League institution. He proposed the following thought experiment to resolve the question of whether objects and relationship exist in the world independently of how we perceive them. This is what bothered Einstein about quantum mechanics, and he is said to have asked Bohr (I think) ” do you think the moon is not there if we don’t look at it”. The thought experiment is a brain placed in a vat by a mad scientist (I’m not making this up). So the brain in the vat — call him Oscar –could not formulate the sentence of “I am a brain in vat” because Oscar has no experience of a real brain or a real vat.

For this they’re currently paying 60K+ a year? It’s the higher drivel. (note this was written in 2011)

I read a book by another philosopher (Nozick) with similar impossible situations he worried about after a rave review in the New York Times book review a few years ago. It had questions of the order ‘would bubblegum taste the same on the surface of the sun’.

“The predicament of any tropological analysis of narrative always lies in its own effaced and circuitous recourse to a metaphoric mode of apprehending its object; the rigidity and insistence of its taxonomies and the facility with which it relegates each vagabond utterance to a strict regimen of possible enunciative formations testifies to a constitutive faith that its own interpretive meta-language will approximate or comply with the linguistic form it examines.”

From p. 35 of the NYTimes book review 16 October’11

You could actually major in this stuff (Semiotics) at an Ivy League university (Brown) in the 80’s. According to the article, Semiotics was the third most popular humanities major there at the time.  One son got in in ’86, but (fortunately) didn’t go there.  Nonetheless he was quite interested in Semiotics, hence the name of this blog.  Fortunately the author of the above quote recovered and notes “I now spend more time learning from the insights of science than deconstructing its truth claims.”

What a gigantic waste of time.  Think what Brown could have done by abolishing the department and using the funds for chemistry or mathematics.  The writer tries to salvage something from the experience noting that ‘a striking number of semiotics students have gone on to influential careers in the media and the creative arts.’  Unfortunately this explains a lot about the current media and ‘the creative arts’.

Students were being conned then, and they’re being conned now.  It might not have mattered what you majored in 50+ years ago at an Ivy League university, the world seemed to want us regardless.   A friend majored in Near Eastern studies, was hired by a bank, never saw the MidEast and did quite well.  Not so today.  The waitress serving us last Wednesday at a local bar was a graduate of one of the seven sisters in 2010.  She majored in Sociology and Psychology, is in debt for > 20K for the experience and is unable to find better work.   It isn’t clear what such a major prepares you for other than what she’s doing.  Finding out the distribution of majors of the jobless 20 somethings participating in occupy Wall Street would be interesting

For a taste of the semiotics world of the 80’s, Google Alan Sokal and read about the fun he had with such a journal — “Social Text”.  Should you  still have the stomach for such things read “The Higher Superstition” by Gross and Levitt, which goes into more detail about Derrida, Foucault and a host of (mostly French) philosophes and what they tried to pull off.

Tags: Alan Sokal, brain in a vat, Higher drivel, Semiotics, The Higher Superstition.

Why studying the cell is like the blind men and the elephant

I’ve been reading about stress granules for over 20 years.  My notes on them contain over 60,000 characters and have my summaries of the information in over 50 papers.  They go by a lot of names — processing body, P body etc.  They are an example of phase separation in the cell, similar to other better known players such as the nucleolus.  They are formed by the cellular response to a variety of stresses — starvation, lack of oxygen, reactive oxygen species, changes in cellular pH, problems with mRNA translation into protein, etc. etc.

One protein called G3BP1 is constantly found in them, but like a lot of phase separated bodies their composition isn’t fixed and they contain lots of different proteins and RNAs which come and go from the body.  Heraclitus would have loved the stress granule, you never step into (study) the same stress granule twice. They may be a new form of matter — https://luysii.wordpress.com/2015/12/06/a-new-form-of-matter/.  They are fascinating to the chemist as their composition (stoichiometry) isn’t constant — https://luysii.wordpress.com/2022/07/20/bye-bye-stoichiometry-2/  and chemists, particularly physical chemists have spent a lot of time studying them.

Most of their components (mostly proteins and RNAs) are characterized by having multiple areas which can bind to other areas.  Protein sequences able to bind to RNA are common in them, as are areas of proteins which never settle down to a single structure, and areas of proteins with a very simple amino acid composition (low complexity domains).  So phase separated bodies are a fascinating field of study for cell biologists, molecular biologists, protein chemists, physical chemists, physicists and (not so much) organic chemists, all busily studying away about their chemical properties.

Into this mix comes a completely different way of looking at stress granules, e.g. as molecular plugs for holes arising in the cellular membranes found in lysosomes and endosomes.  This is an entirely new (and very important) function for stress granules, which hadn’t even been considered (until now).  Here, their physicality rather than their chemical nature is what matters, allowing another set of blind men to study the stress granule elephant in a completely different way.  For details please see Nature vol. 923 pp. 919 – 920, 1062 – 1069 ’23.  Given the subject matter, I find it fascinating that one Alex S. Holehouse is of the authors of 919 – 920

Efforts to Disqualify Trump Uphold Democracy

No, the Onion hasn’t taken over the opinion page of the New York Times.   Nor was this written by the ghost of George Orwell, or Ali Khamenei the current  ‘supreme leader’ of Iran who chooses who may run for office and who may not.  It was written by Mark A. Graber, a constitutional scholar and university professor in Maryland, proving yet again that only someone of high intelligence could defend something so stupid.  But as Marshall McLuhan said ‘the medium is the message’, and the fact that the Times chose to publish it is significant. Nothing published by the Times happens by chance.  It is the American Pravda after all — https://luysii.wordpress.com/2023/11/21/reading-americas-pravda/

On to how deal with the students harassing others at Harvard, Penn, MIT etc., the answer goes back over 30 years ago to something called charm school.

After serving as an army doc for two years in ’68 – ’70, a time when we had 500,000 men in Vietnam, I left with little respect for its leadership. I was stateside at one of the Army’s premier hospitals, which was a plum assignment (because the army was very short of neurologists). This meant that 2 year docs who’d served their first year in Vietnam got their choice of assignment when returning stateside. So I saw plenty of them. NOT ONE thought we were winning over there, despite what the top brass said to the press and the president.

So who would have thought that 33 years later I’d be friendly with a retired Major General, George Baker. Never say never. He was a very intelligent man, an orthopedic surgeon, who’d been chief at Walter Reed and found retirement boring, so he practiced at my hospital. He told me about something he called charm school. It was where officers newly promoted to  General  rank were sent for training. They were told to toe the straight and narrow sexually and in other matters, and that if a planeload of them went down, the army would have no trouble at all filling their shoes.

So it is with the harassers, defacers, threateners etc. at the above schools.   Their shoes can easily be filled.  Throw them out.  There are innumerable similarly qualified candidates for admission who did not get in, who would doubtless love to transfer in with no loss to Harvard, Penn and MIT and a general improvement in comity.

Reality has intruded.  I had intended to write a post showing how closely our study of cellular physiology resembles the blind men and the elephant.  Hopefully tomorrow.  Stay tuned.  It’s fascinating.

What you can measure isn’t always what’s important

Back in the bad old days some residents would make sure that dying patients were in electrolyte (sodium, potassium, chloride CO2) balance, even though they were irrelevant to why the patient was dying (cancer, stroke, cardiac failure, etc. etc.).  Severe electrolyte imbalance can kill.  It was basically CYA.  While ‘lytes could easily be measured they were not what was important.

Similarly, the economy is great — inflation is no longer so bad and is decreasing, unemployment is low and the gross national product is increasing.  Tell that (Bidenomics) to the 60%+ of Americans living paycheck to paycheck according to three different polls conducted this year.  Inflation rate, unemployment rate, GNP are just irrelevant numbers to them.  They see diminished purchasing power every time they buy groceries (not included in inflation), buy gas, or try to eat out.

Similarly the controversy over protein electrophoretic patterns of Simufilam and whether they have been fudged is irrelevant to the far more important question of whether it helps people with Alzheimer’s disease think.  Here the important number is their scores on cognitive tests and their functioning on the activities of daily living.  I think it does.  For an elaboration please see — https://luysii.wordpress.com/2021/08/25/cassava-sciences-9-month-data-is-probably-better-than-they-realize/

Res Ipsa Loquitur

The first sequencing of the human genome was ‘completed’  in April 2003 taking 13 years and costing over a billion dollars.

It really wasn’t complete, and even by 2022 10 megaBases (of the 3.2 gigaBases) hadn’t been sequenced

Science vol. 382 1 December p. 980 ’23 The UK biobank just released the WHOLE genome sequences of 500,000 people.

Imagine what we’d know if our understanding of the results had similarly accelerated.

 

 

Opiate receptors 51 years on

It seems like only yesterday that Candace Pert found the morphine receptor  as a graduate student at Johns Hopkins 2 years after graduating BrynMawr at 24 and getting (academically) screwed by Solomon Snyder, who may have a department named after him at Hopkins but who will never get the Nobel prize.

Things seemed so simple back then, and the route to the nonaddicting opiate seemed clear.  Well its 51 years and counting since 1972 and things have become incredibly complicated as we learn more and more about our opiate receptors (there are 4).

A marvelous review is available (if you have a subscription) replete with multiple cryoEM structures of multiple receptors with multiple ligands at  resolution approaching amino acid size (better than 3.5 Angstroms).  Cell vol. 186 pp. 5203 – 5219 ’23.

Just in terms of combinatorial size, the possibilities are quite large.

There are 4 types of G Protein Coupled Receptors (GPCRs) binding opiate peptides — mu, delta, kappa and nociceptive.  Although we have all sorts of small molecule drugs binding to them (morphine, heroin, fentanyl and worse), their natural ligands in our brains are protein fragments (of which there are 20) derived from 4 precursor proteins) — so that’s 80 possibilities there.

To get anything done inside the brain, each of the 4 GPCRs binds to G proteins of the G(i/o) class of which there are 7.

But wait, there’s more.  All good things come to an end, and to stop signaling the intracellular part of the GPCR is phosphorylated by the awfully named GRKs (G receptor kinases) of which there are 7.

Once the G proteins are phosphorylated, they leave the intracellular part of the GPCR, and another protein (arrestin) binds to the same area of the GPCR.  There are 4 known arrestins.

The possibilities are multiplicative since they’re independent — so its

20 x 4 x 7 x 7 x 4 = 15,680 different possible interactions.

For a long time it was thought that arrestins terminated opiate peptide signaling, dragging the receptor inside the cell and schlepping it to either the lysosome or the proteasome where it was then destroyed by proteolysis.

Not so.  After arrestin binding, the opiate receptors can be found in endosomes where they can continue to signal, so we’re not really sure just what the effects of the arrestins are on opiate signaling.

Now let’s hear it for the biochemical ingenuity of plants.  Even the smallest opiate peptide (met-enkephalin) has 5 amino acids, far too large to insert itself in the 7 alpha helices of the GPCR crossing the cell membrane.  So they bind to the extracellular surface of the GPCR, particularly extracellular loop 2 (ICL2) which contains 21 amino acids.  Yet plants have figured out how to make small molecules like morphine which bind to the parts of the GPCR in the cell membrane.  It’s hard for me to see an evolutionary push (selection pressure) for them to do this.

Well that’s a rather broad overview of what’s in the paper, but there is much much more.  Reading it is like eating intellectual fruitcake — it is far too dense to be ingested and digested at one sitting.

Two further tidbits to whet your interest.  The paper contains a detailed discussion (with pictures of the structures) of why fentanyl is so much more potent than morphine.  But of course such things require as knowledge of organic chemistry.  The benzene ring of Fentanyl engages in direct pi pi electron interactions with the toggle switch amino acids tryptophans #295 and #328 (W295 and W328).  Benzene doesn’t contain an isolated benzene moiety.  Also the phenylethyl group of Fentanyl interacts hydrophobically with a minor binding pocket of morphine found between transmembrane 2 (TM2) and TM3.     Meat and drink for an old organic chemist such as yours truly.

Tidbit #2.  On activation of the opiate GPCR, there is inward movement of TM5 and outward movement of TM6 along with clockwise rotations of TM6.  This is initiated by ligand reconstruction of the polar network in the binding pocket, the collapse of the sodium pocket and rearrangement of the proline, isoleucine and phenylalanine triad (all 3 found on 3 different transmembrane segments (TMs).

Put the multiple structures shown in the paper are thousands of times more instructive than the previous two paragraphs, confirming yet again the old adage.