Category Archives: Neurology & Psychiatry

Non-patent trolling

A conversation with a son who is in high tech brought up what a blister on the body politic patent trolling is https://en.wikipedia.org/wiki/Patent_troll.  I told him that I’m having trouble simply trying to give an idea away.  The idea is basically that some cases of chronic fatigue syndrome are due to senescent cells.  There is a simple way to look for this — measure a master transcription factor for cellular senescence (p16INK^4a) in blood cells.  If correct, a rational therapy for CFS (senolytics) is immediately at hand.  I’ve shopped this around, and someone at Stanford involved with CFS claims that he will test it.  I’ve heard nothing so far.  The idea is free for the taking.  Therapy for CFS essentially  helps patients live their symptoms rather than diminishing them or attacking the underlying problem.

Since I”m going to Venice for 2 weeks to celebrate my wife’s birthday, there won’t be any new posts for a while — so here is the idea as presented in two posts from my blog — take it and run with it.  The patients are waiting.

Not a great way to end 2017

Not a great way to end 2017

2017 ended with a rejection of the following letter to PNAS.

As a clinical neurologist with a long standing interest in muscular dystrophy(1), I was referred many patients who turned out to have chronic fatigue syndrome (CFS) . Medicine, then and now, has no effective treatment for CFS.

A paper (2) cited In an excellent review of cellular senescence (3) was able to correlate an intracellular marker of senescence (p16^INK4a) with the degree of fatigue experienced by patients undergoing chemotherapy for breast cancer. Chemotherapy induces cellular senescence, and the fatigue was thought to come from the various cytokines secreted by senescent cells (Senescence Associated Secretory Phenotype—SASP) It seems logical to me to test CFS patients for p16^INK4a (4).
I suggested this to the senior author; however, he was nominated as head of the National Cancer Institute just 9 days later. There the matter rested until the paper of Montoya et al. (5) appeared in July. I looked up the 74 individual elements of the SASP and found that 9 were among the 17 cytokines whose levels correlated with the degree of fatigue in CFS. However, this is not statistically significant as Montoya looked at 51 cytokines altogether.

In October, an article(6) on the possibility of killing senescent cells to prevent aging contained a statement that Judith Campisi’s group (which has done much of the work on SASP) had identified “hundreds of proteins involved in SASPs”. (These results have not yet been published.) It is certainly possible that many more of Montoya’s 17 cytokines are among them.

If this is the case, a rational therapy for CFS is immediately apparent; namely, the senolytics, a class of drugs which kills senescent cells. A few senolytics are currently available clinically and many more are under development as a way to attack the aging process (6).

If Montoya still has cells from the patients in the study, measuring p16^INK4a could prove or disprove the idea. However, any oncology service could do the test. If the idea proves correct, then there would be a way to treat the debilitating fatigue of both chemotherapy and CFS—not to mention the many more medical conditions in which severe fatigue is found.
Chemotherapy is a systemic process, producing senescent cells everywhere, which is why DeMaria (2) was able to use circulating blood cells to measure p16^INK4a. It is possible that the senescent cells producing SASP in CFS are confined to one tissue; in which case testing blood for p16^INK4a would fail. (That would be similar to pheochromocytoma cells, in which a few localized cells produce major systemic effects.)

Although senolytics might provide symptomatic treatment (something worthwhile having since medicine presently has nothing for the CFS patient), we’d still be in the dark about what initially caused the cells to become senescent. But this would be research well worth pursuing.

Anyone intrigued by the idea should feel free to go ahead and test it. I am a retired neurologist with no academic affiliation, lacking the means to test it.
References

1 Robinson, L (1979) Split genes and musclar dystrophy. Muscle Nerve 2: 458 – 464

2. He S, Sharpless N (2017) Senescence in Health and Disease. Cell 170: 1000 – 1011

3. Demaria M, et al. (2014) Cellular senescence promotes adverse effects of chemotherapy and cancer relapse. Cancer Discov. 7: 165 – 176

4. https://luysii.wordpress.com/2017/09/04/is-the-era-of-precision-medicine-for-chronic-fatigue-syndrome-at-hand/

5. Montoya JG, et al., (2017) Cytokine signature associated with disease severity in chronic fatigue syndrome patients, Proc Natl Acad Sci USA 114: E7150-E7158

6. Scudellari M, (2017) To stay young, kill zombie cells Nature 551: 448 – 450

Is a rational treatment for chronic fatigue syndrome at hand?

If an idea of mine is correct, it is possible that some patients with chronic fatigue syndrome (CFS) can be treated with specific medications based on the results of a few blood tests. This is precision medicine at its finest.  The data to test this idea has already been acquired, and nothing further needs to be done except to analyze it.

Athough the initial impetus for the idea happened only 3 months ago, there have been enough twists and turns that the best way explanation is by a timeline.

First some background:

As a neurologist I saw a lot of people who were chronically tired and fatigued, because neurologists deal with muscle weakness and diseases like myasthenia gravis which are associated with fatigue.  Once I ruled out neuromuscular disease as a cause, I had nothing to offer then (nor did medicine).  Some of these patients were undoubtedly neurotic, but there was little question in my mind that many others had something wrong that medicine just hadn’t figured out yet — not that it hasn’t been trying.

Infections of almost any sort are associated with fatigue, most probably caused by components of the inflammatory response.  Anyone who’s gone through mononucleosis knows this.    The long search for an infectious cause of chronic fatigue syndrome (CFS) has had its ups and downs — particularly downs — see https://luysii.wordpress.com/2011/03/25/evil-scientists-create-virus-causing-chronic-fatigue-syndrome-in-lab/

At worst many people with these symptoms are written off as crazy; at best, diagnosed as depressed  and given antidepressants.  The fact that many of those given antidepressants feel better is far from conclusive, since most patients with chronic illnesses are somewhat depressed.

The 1 June 2017 Cell had a long and interesting review of cellular senescence by Norman Sharpless [ vol. 169 pp. 1000 – 1011 ].  Here is some background about the entity.  If you are familiar with senescent cell biology skip to the paragraph marked **** below

Cells die in a variety of ways.  Some are killed (by infections, heat, toxins).  This is called necrosis. Others voluntarily commit suicide (this is called apoptosis).   Sometimes a cell under stress undergoes cellular senescence, a state in which it doesn’t die, but doesn’t reproduce either.  Such cells have a variety of biochemical characteristics — they are resistant to apoptosis, they express molecules which prevent them from proliferating and — most importantly — they secrete a variety of proinflammatory molecules collectively called the Senescence Associated Secretory Phenotype — SASP).

At first the very existence of the senescent state was questioned, but exist it does.  What is it good for?  Theories abound, one being that mutation is one cause of stress, and stopping mutated cells from proliferating prevents cancer. However, senescent cells are found during fetal life; and they are almost certainly important in wound healing.  They are known to accumulate the older you get and some think they cause aging.

Many stresses induce cellular senescence of which mutation is but one.  The one of interest to us is chemotherapy for cancer, something obviously good as a cancer cell turned senescent has stopped proliferating.   If you know anyone who has undergone chemotherapy, you know that fatigue is almost invariable.

****

One biochemical characteristic of the senescent cell is increased levels of a protein called p16^INK4a, which helps stop cellular proliferation.  While p16^INK4a can easily be measured in tissue biopsies, tissue biopsies are inherently invasive. Fortunately, p16^INK4a can also be measured in circulating blood cells.

What caught my eye in the Cell paper was a reference to a paper about cancer [ Cancer Discov. vol. 7 pp. 165 – 176 ’17 ] by M. Demaria, in which the levels of p16^INK4a correlated with the degree of fatigue after chemotherapy.  The more p16^INK4a in the blood cells the greater the fatigue.

I may have been the only reader of both papers with clinical experience wth chronic fatigue syndrome.  It is extremely difficult to objectively measure a subjective complaint such as fatigue.

As an example of the difficulty in correlating subjective complaints with objective findings, consider the nearly uniform complaint of difficulty thinking in depression, with how such patients actually perform on cognitive tests — e. g. there is  little if any correlation between complaints and actual performance — here’s a current reference — Scientific Reports 7, Article number: 3901(2017) —  doi:10.1038/s41598-017-04353.

If the results of the Cancer paper could be replicated, p16^INK4 would be the first objective measure of a patient’s individual sense of fatigue.

So I wrote both authors, suggesting that the p16^INK4a test be run on a collection of chronic fatigue syndrome (CFS) patients. Both authors replied quickly, but thought the problem would be acquiring patients.  Demaria said that Sharpless had a lab all set up to do the test.

Then fate (in the form of Donald Trump) supervened.  A mere 9 days after the Cell issue appeared, Sharpless was nominated to be the head of the National Cancer Institute by President Trump.  This meant Dr. Sharpless had far bigger fish to fry, and he would have to sever all connection with his lab because of conflict of interest considerations.

I also contacted a patient organization for chronic fatigue syndrome without much success.  Their science advisor never responded.

There matters stood until 22 August when a paper and an editorial about it came out [ Proc. Natl. Acad. Sci. vol. 114 pp. 8914 – 8916, E7150 – E7158 ’17 ].  The paper represented a tremendous amount of data (and work).  The blood levels of 51 cytokines (measures of inflammation) and adipokines (hormones released by fat) were measured in both 192 patients with CFS (which can only be defined by symptoms) and 293 healthy controls matched for age and gender.

In this paper, levels of 17 of the 51 cytokines correlated with severity of CFS. This is a striking similarity with the way the p16^INK4 levels correlated with the degree of fatigue after chemotherapy).  So I looked up the individual elements of the SASP (which can be found in Annu Rev Pathol. 21010; 5: 99–118.)  There are 74 of them. I wondered how many of the 51 cytokines measured in the PNAS paper were in the SASP.  This is trickier than it sounds as many cytokines have far more than one name.  The bottom line is that 20 SASPs are in the 51 cytokines measured in the paper.

If the fatigue of CFS is due to senescent cells and the SASPs  they release, then they should be over-represented in the 17 of the 51 cytokines correlating with symptom severity.  Well they are; 9 out of the 17 are SASP.  However although suggestive, this increase is not statistically significant (according to my consultants on Math Stack Exchange).

After wrote I him about the new work, Dr. Sharpless noted that CFS is almost certainly a heterogeneous condition. As a clinician with decades of experience, I’ve certainly did see some of the more larcenous members of our society who used any subjective diagnosis to be compensated, as well as a variety of individuals who just wanted to withdraw from society, for whatever reason. They are undoubtedly contaminating the sample in the paper. Dr. Sharpless thought the idea, while interesting, would be very difficult to test.

But it wouldn’t at all.  Not with the immense amount of data in the PNAS paper.

Here’s how. Take each of the 9 SASPs and see how their levels correlate with the other 16 (in each of the 192 CSF patients). If they correlate better with SASPs than with nonSASPs, than this would be evidence for senescent cells being the cause some cases of CFS. In particular, patients with a high level of any of the 9 SASPs should be studied for such correlations.  Doing so should weed out some of the heterogeneity of the 192 patients in the sample.

This is why the idea is testable and, even better, falsifiable, making it a scientific hypothesis (a la Karl Popper).  The data to refute it is in the possession of the authors of the paper.

Suppose the idea turns out to be correct and that some patients with CFS are in fact that way because, for whatever reason, they have a lot of senescent cells releasing SASPs.

This would mean that it would be time to start trials of senolyic drugs which destroy senescent cells on the group with elevated SASPs. Fortunately, a few senolytics are currently inc linical use.  This would be precision medicine at its finest.

Being able to alleviate the symptoms of CFS would be worthwhile in itself, but SASP levels could also be run on all sorts of conditions associated with fatigue, most notably infection. This might lead to symptomatic treatment at least.  Having gone through mono in med school, I would have loved to have been able to take something to keep me from falling asleep all the time.

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Will acyclovir be a treatment for Alzheimer’s ?

When I was a first year medical student my aunt died of probable acute herpes simplex encephalitis at Columbia University Hospital in New York City.  That was 55 years ago and her daughters (teenagers at the time) still bear the scars.  Later, as a neurologist I treated it, and after 1977, when acyclovir, which effectively treats herpes encephalitis came out, I would always wonder if acyclovir would have saved her.

The drug is simplicity itself.  It’s just guanosine (https://en.wikipedia.org/wiki/Guanosine) with two of the carbons of the ribose missing.  Herpesviruses have an enzyme which forms the triphosphate incorporating it into its DNA killing the virus.  Well, actually we have the same enzyme, but the virus’s enzyme is 3,000,000 times more efficient than ours, so acyclovir is relatively nontoxic to us.  People with compromised renal function shouldn’t take it.

What does this have to do with Alzheimer’s disease?  The senile plaque of Alzheimers is mostly the aBeta peptide (39 – 43 amino acids) from the amyloid precursor protein (APP).  This has been known for years, and my notes on various papers about over the years contain 150,000 characters or so.

Even so, there’s a lot we don’t understand about APP and the abeta peptide — e.g. what are they doing for us?  You can knockout the APP gene in mice and they appear normal and fertile.  The paper cited below notes that APP has been present in various species for the past 400,000,000 years of evolutionary time remaining pretty much unchanged throughout, so it is probably doing something useful

A recent paper in Neuron (vol. 99 pp. 56 – 63 ’18) noted that aBeta is actually an antimicrobial peptide.  When exposed to herpes simplex it binds to glycoproteins on its surface and then  oligomerizes forming amyloid (just like in the senile plaque) trapping the virus.  Abeta will protect mice against herpes simplex 1 (HSV1) encephalitis.  Even more important — infection of the mice with HSV1 induced abeta production in their brains.

People have been claiming infections as the cause of just about every neurodegeneration since I’ve been a neurologist, and papers have been written about HSV1 and Alzheimer’s.

Which brings me to the second paper (ibid. pp. 64 – 82) that looked for the viral RNAs and DNAs in over 900 or so brains, some with and some without Alzheimer’s.  They didn’t find HSV but they found two other herpes viruses known to infect man (HHV6, HHV7 — which cause roseola infantum).  Humans are subject to infection with 8 different herpes virus (Epstein Barr — mononucleosis, H. Zoster — chickenpox etc. etc.).   Just about everyone of us has herpes virus in latent form in the trigeminal ganglion — which gets sensory information from our faces.

So could some sort of indolent herpesvirus infection be triggering abeta peptide production as a defense with the senile plaque as a byproduct?  That being the case, given the minimal benefits of any therapy we have for Alzheimer’s disease so far, why not try acyclovir (Zovirax) on Alzheimer’s.

I find it remarkable that neither paper mentioned this possibility, or even discussed any of the antivirals active against herpesviruses.

An incredible way to look at the brain

http://www.pnas.org/content/115/27/6940 [ Proc. Natl. Acad. Sci. vol. 115 pp. 6940 – 6945 ’18 ] demonstrates an incredible new way to visualize brain structures.  I don’t think the paper is behind a paywall, so follow the link and look at the movies.

The technique can be used on paraffin embedded brain.  Not to be tried at home unless you have a microCT with a liquid jet anode source, and a high resolution synchrotron instrument with special Xray waveguide optic.

No staining was involved, and they used electron contrast to show purkinje cells, granule cells, and the ramified dendritic tree of the Purkinje cells in a 1 cubic millimeter punch ‘biopsy’ of paraffin embedded cerebellum.

The moves are incredible, as unlike the standard CT or MRI, you can move a plane through the images (the movies show this), stop it at leisure.  Visualization of a plane moving through the material shows what the brain looks like in 3 d.  Then there are a few 3 d reconstructions (presented as 2 dimensional projective drawings we’re used to seeing), but even these can be moved around.

Words are inadequate.  Go to the link and look at the movies.  Let me know if you have trouble reaching it.

The Gambler’s fallacy is actually based on our experience

We don’t understand randomness very well. When asked to produce a random sequence we never produce enough repeating patterns thinking that they are less probable. This is the Gambler’s fallacy.  If heads come up 3 times in a row, the Gambler will bet on tails on the next throw   Why?  This reasoning is actually based on experience.

The following comes from a very interesting paper of a few years ago  [ Proc. Natl. Acad. Sci. vol. 112 pp. 3788 – 3792 ’15 ].  There is a surprising amount of systematic structure lurking within random sequences. For example, in the classic case of tossing a fair coin, where the probability of each outcome (heads or tails) is exactly 0.5 on every single trial, one would naturally assume that there is no possibility for some kind of interesting structure to emerge, given such a simple form of randomness.

However if you record the average amount of time for a pattern to first occur in a sequence (i.e., the waiting time statistic), it is longer for a repetition (head–head HH or tail–tail TT  (an average of six tosses is needrequired) than for an alternation (HT or TH, only four tosses is needed). This is despite the fact that on average, repetitions and alternations are equally probable (occurring once in every four tosses, i.e., the same mean time statistic).

For both of these facts to be true, it must be that repetitions are more bunched together over time—they come in bursts, with greater spacing between, compared with alternations (which is why they appear less frequent to us). Intuitively, this difference comes from the fact that repetitions can build upon each other (e.g., sequence HHH contains two instances of HH), whereas alternations cannot.

Statistically, the mean time and waiting time delineate the mean and variance in the distribution of the interarrival times of patterns (respectively). Despite the same frequency of occurrence (i.e., the same mean), alternations are more evenly distributed over time than repetitions (they have different variances) — which is exactly why they appear less frequent, hence less likely.

Then the authors go on to develop a model of the way we think about these things.

“Is this latent structure of waiting time just a strange mathematical curiosity or could it possibly have deep implications for our cognitive level perceptions of randomness? It has been speculated that the systematic bias in human randomness perception such as the gambler’s fallacy might be due to the greater variance in the interarrival times or the “delayed” waiting time for repetition patterns. Here, we show that a neural model based on a detailed biological understanding of the way the neocortex integrates information over time when processing sequences of events is naturally sensitive to both the mean time and waiting time statistics. Indeed, its behavior is explained by a simple averaging of the influences of both of these statistics, and this behavior emerges in the model over a wide range of parameters. Furthermore, this averaging dynamic directly produces the best-fitting bias-gain parameter for an existing Bayesian model of randomness judgments, which was previously an unexplained free parameter and obtained only through parameter fitting. We show that we can extend this Bayesian model to better fit the full range of human data by including a higher-order pattern statistic, and the neurally derived bias-gain parameter still provides the best fit to the human data in the augmented model. Overall, our model provides a neural grounding for the pervasive gambler’s fallacy bias in human judgments of random processes, where people systematically discount repetitions and emphasize alternations.”

Fascinating stuff

Omar Khayyam and the embryology of the cerebral cortex

“The moving finger writes; and, having writ, moves on”.  Did Omar Khayyam realize he was talking about the embryology of the human cerebral cortex?  Although apparently far removed from chemistry, embryology most certainly is not.  The moving finger in this case is an enzyme modifying histone proteins.

In the last post (https://luysii.wordpress.com/2018/06/04/marshall-mcluhan-rides-again/) I discussed how one site in the genome modified  the expression of a protein important in cancer (myc) even though it was 53,000 positions (nucleotides) away.  When stretched out into the usual B-form DNA shown in the text books this would stretch 1.7 microns or 17% of the way across the diameter of the usual spherical nucleus.  If our 3,200,000 nucleotide genome were chopped up into pieces this size some 60,000 segments would have to be crammed in.  Clearly DNA must be bent and wrapped around something, and that something is the nucleosome which is shaped like a fat disk.  Some 160 or so nucleotides are wrapped (twice) around the circumference of the nucleosome, giving a 10fold compaction in length.

The nucleosome is made of histone proteins, and here is where the moving finger comes in.  There are all sorts of chemical modifications of histones (some 130 different chemical modifications of histones are known).  Some are well known to most protein chemists, methylation of the amino groups of lysine, and the guanido groups of arginine, phosphorylation and acetylation  of serine and threonine.  Then there are the obscure small modifications –crotonylation, succinylation and malonylations.  Then there are the protein modifications, ubiquitination, sumoylation, rastafarination etc. etc.

What’s the point?  All these modifications determine what proteins and enzymes can and can’t react with a given stretch of DNA.  It goes by the name of histone code, and has little to do with the ordering of the nucleotides in DNA (the genetic code).  The particular set of histone modifications is heritable when cells divide.

Before going on, it’s worth considering just how miraculous our cerebral cortex is.  The latest estimate is that we have 80 billion neurons connected by 150 trillion synapses between them.  That’s far too much for 3.2 nucleotides to explicitly code for.

It turns out that almost all neurons in the cerebral cortex are born in a small area lining the ventricles.  They then migrate peripherally to form the 6 layered cerebral cortex.  The stem cell of the embryonic cortex is something called a radial glial cell which divides and divides each division producing 1 radial glial cell and 1 neuron which then goes on its merry way up to the cortex.

Which brings us (at last) to the moving finger, an enzyme called PRDM16 which puts a methyl group on two particular lysines  (#4 and #9) of histone H3.  PRDM16 is highly enriched in radial glia and nearly absent in mature neurons.  Knock PRDM16a out in radial glia, and the cortex is disorganized due to deficient neuronal migration.  Knock it out in newly formed neurons and the cortex is formed normally.  The moving finger having writ (in radial glia) moves on and is no longer needed (by mature neurons). “nor all thy Piety nor Wit shall lure it back to cancel half a line.  Nor all thy tears wash out a word of it”.

You may read more about this fascinating work in Neuron vol. 98 pp. 867 – 869, 945 – 962 ’18

The other uses of amyloid (not all bad)

Neurologists and drug chemists pretty much view amyloid as a bad thing.  It is the major component of the senile plaque of Alzheimer’s disease, and when deposited in nerve causes amyloidotic polyneuropathy.  A recent paper and editorial casts amyloid in a different light [ Cell vol. 173 pp. 1068 – 1070, 1244 – 2253 ’18 ].  However if amyloid is so bad why do cytomegalovirus, herpes simplex viruses and E. Coli make proteins to prevent a type of amyloid from forming.

Cell death isn’t what it used to be.  Back in the day, they just died when things didn’t go well.  Now we know there are a variety of ways that cells die, and all of them have rather specific mechanisms.  Apoptosis (aka programmed cell death) is a mechanism of cell death used widely during embryonic development.  It allows the cell to die very quietly without causing inflammation.  Necroptosis is entirely different, it is another type of programmed cell death, designed to cause inflammation — bringing the immune system in to attack invading pathogens.

Two proteins (Receptor Interacting Protein Kinase 1 — RIPK1, and RIPK3) bind to each other forming amyloid, that looks for all the world like typical amyloid –it binds Congo Red, shows crossBeta diffraction and has a filamentous appearance.  Fascinating chemistry aside, the amyloid formed is crucial for necroptosis to occur, which is why various bugs try to prevent it.

The paper above describes the structure of the amyloid formed — unusual in itself, because until now amyloid was thought to involve the aggregation of a single protein.

The proteins are large: RIPK1 contains 671 amino acids, and RIPK3 contains 518.  They  both contain RHIMs (Receptor interacting protein Homotypic Interaction Motifs) which are fairly large themselves (amino acids 496 – 583 of RIPK1 and 388 – 518 of RIPK3).  Yet the amyloid the two proteins form use a very small stretches (amino acids 532 – 543 from RIPK1 and 451 – 462 from RIPK3).  How the rest of these large proteins pack around the beta strands of the 11 amino acid stretches isn’t discussed in the paper.  Even within these stretches, it is two consensus tetrapeptides (IQIG from RIPK1, and VQVG from RIPK3) that do most of the binding.

Even if you assume that I (Isoleucine) Q (glutamine) G (glycine) V (valine) occur at a frequency of 5%, in our proteome of 20,000 proteins assuming a length of amino acids IQIG and VQVG should occur 10 times each.  This may explain why 300/20,000 of our proteins contain a 100 amino acid  segment called BRICHOS which acts as a chaperone preventing amyloid formation. For details see — https://luysii.wordpress.com/2018/04/01/a-research-idea-yours-for-the-taking/.

Just another reason to take up the research idea in the link and find out just what other things amyloid is doing within our cells in the course of their normal functioning.

 

Cultural appropriation, neuroscience division

If Deng Xiaoping can have Socialism with Chinese Characteristics, I can have a Chinese saying with neuroscientific characteristics — “The axon and the dendrite are long and the nucleus is far away” mimicking “The mountains are high and the Emperor is far away”. The professionally offended will react to the latest offense du jour — cultural appropriation  — of course.  But I’m entitled and I spoke to my Chinese daughter in law, and people over there found it flattering and admiring of Chinese culture that the girl in Utah wore a Chinese cheongsam dress to her prom.

Back to the quote.  “The axon and the dendrite are long and the nucleus is far away”.  Well, neuronal ends are far away from the cell body — the best example are axons from the sacral spinal cord which in an NBA player can be a yard long.  But forget that, lets talk about the ends of dendrites which are much closer to the cell body than that.

Presumably neurons have different types of dendrites so they can respond to different types of inputs. Why should dendrites respond identically if their inputs are different? They don’t.    A dendrite responding to acetyl choline will express neurotransmitter receptors distinct from another dendrite on the same neuron distinct from a dendrite responding to dopamine.  The protein cohorts of axons and dendrites are different.  How does this come about?  Because the untranslated part of mRNA on the 3′ end (3’UTR) contains a sequence called a zipcode which binds to specific proteins which then move the mRNA to a specific location in the neuron (axon or dendrite).  Presumably all dendrites initially had the same complement of mRNA.

So depending on what’s happening at a particular dendrite on a neuron, more or less of a given protein is made.   This is way too abstract.  Suppose you want to strengthen a synapse.  You’d make more of a neurotransmitter receptor or an ion channel for whatever transmitter that dendrite is getting.

It is well established that axons and dendrites store mRNAs and make proteins from them far from the nucleus (aka the emperor).  If you think about it, just how a receptor for dopamine gets to a dendrite receiving dopamine and not to a dendrite (on the same neuron) getting glutamic acid as a transmitter, is far from clear.  There are zipcodes distinguishing axons from dendrites, but I’m unaware that there are zipcodes for dopamine dendrites distinct from other types of dendrites.

If that weren’t enough consider [ Neuron vol. 98 pp. 495 – 511 ’18 ].  Even for an mRNA coding for the same protein (presumably transcribed from just one gene), there can be more than one type of 3’UTR (and this in the same cell).  Note also that 3’UTRs are longer in neurons than in other tissues.

So the authors looked at the mRNAs in dendrites — they did this by choosing a tissue (the hippocampus) where rows of cell bodies are well separated from their dendrites.  They found that for a given dendritic mRNA there was more than one 3’UTR, and that the mRNAs with longer 3’UTRs had longer halflives.  Even more exquisitly neuronal activity altered the proportion of the different 3’UTR isoforms. The phenomenon is quite general — over 50% of all genes and over 70% of genes enriched in neurons showed multiple 3′ UTRs.

So there is a whole control system built into the dendritic system, and it varies with what is happening locally.

The emperor emits directives (mRNAs) but what happens locally is anyone’s guess

A pile of spent bullets — take II

I can tell you after being in neurology for 50 years that back in the day every microscopic inclusion found in neurologic disease was thought to be causative.  This was certainly true for the senile plaque of Alzheimer’s disease and the Lewy body of Parkinsonism.  Interestingly, the protein inclusions in ALS weren’t noticed for decades.

However there are 3 possible explanations for any microscopic change seen in any disease.  The first is that they are causative (the initial assumption).  The second is that they are a pile of spent bullets, which the neuron uses to defend itself against the real killer.  The third is they are tombstones, the final emanations of a dying cell, a marker for the cause of death rather than the cause itself.

An earlier post concerned work that implied that the visible aggregates of alpha-synuclein in Parkinson’s disease were protective rather than destructive — https://luysii.wordpress.com/2018/01/07/are-the-inclusions-found-in-neurologic-disease-attempts-at-defense-rather-then-the-cause/.

Comes now Proc. Natl. Acad. Sci. vol. 115 pp. 4661 – 4665 ’18 on Superoxide Dismutase 1 (SOD1) and ALS. Familial ALS is fortunately less common than the sporadic form (under 10% in my experience).  Mutations in SOD1 are found in the familial form.  The protein contains 153 amino acids, and as 6/16 160 different mutations in SOD1 have been found.  Since each codon can contain only 3 mutations from the wild type, this implies that, at a minimum,  53/153 codons of the protein have been mutated causing the disease.  Sadly, there is no general agreement on what the mutations actually do — impair SOD1 function, produce a new SOD1 function, cause SOD1 to bind to something else modifying that function etc. etc.  A search on Google Scholar for SOD1 and ALS produced 28,000 hits.

SOD1 exists as a soluble trimer of proteins or the fibrillar aggregate.   Knowing the structure of the trimer, the authors produced mutants which stabilized the trimer (Glycine 147 –> Proline) making aggregate formation less likely and two mutations (Asparagine 53 –> Isoleucine, and Aspartic acid 101 –> Isoleucine) which destabilized the trimer making aggregate formation more likely.  Then they threw the various mutant proteins at neuroblastoma cells and looked for toxicity.

The trimer stabilizing mutant  (Glycine 147 –> Proline) was toxic and the destabilizing mutants  (Asparagine 53 –> Isoleucine, and Aspartic acid 101 –> Isoleucine)  actually improved survival of the cells.  The trimer stabilizing mutant was actually more toxic to the cells than two naturally occurring SOD1 mutants which cause ALS in people (Alanine 4 –> Valine, Glycine 93 –> Alanine).  Clearly with these two something steric is going on.

So, in this experimental system at least, the aggregate is protective and what you can’t see (microscopically) is what kills cells.

A research idea yours for the taking

Why would the gene for a protein contain a part which could form amyloid (the major component of the senile plaque of Alzheimer’s disease) and another part to prevent its formation. Therein lies a research idea, requiring no grant money, and free for you to pursue since I’ll be 80 this month and have no academic affiliation.

Bri2 (aka Integral TransMembrane protein 2B — ITM2B) is such a protein.  It is described in [ Proc. Natl. Acad. Sci. vol. 115 pp. E2752 – E2761 ’18 ] http://www.pnas.org/content/pnas/115/12/E2752.full.pdf.

As a former neurologist I was interested in the paper because two different mutations in the stop codon for Bri2 cause 2 familial forms of Alzheimer’s disease  Familial British Dementia (FBD) and Familial Danish Dementia (FDD).   So the mutated protein is longer at the carboxy terminal end.  And it is the extra amino acids which form the amyloid.

Lots of our proteins form amyloid when mutated, mutations in transthyretin cause familial amyloidotic polyneuropathy.  Amylin (Islet Amyloid Polypeptide — IAPP) is one of the most proficient amyloid formers.  Yet amylin is a protein found in the beta cell of the pancreas which releases insulin (actually in the same secretory granule containing insulin).

This is where Bri2 is thought to come in. It is also found in the pancreas.   Bri2 contains a 100 amino acid motif called BRICHOS  in its 266 amino acids which acts as a chaperone to prevent IAPP from forming amyloid (as it does in the pancreas of 90% of type II diabetics).

Even more interesting is the fact that the BRICHOS domain is found in 300 human genes, grouped into 12 distinct protein families.

Do these proteins also have segments which can form amyloid?  Are they like the amyloid in Bri2, in segments of the gene which can only be expressed if a stop codon is read through.  Nothing in the cell is perfect and how often readthrough occurs at stop codons isn’t known completely, but work is being done — Nucleic Acids Res. 2014 Aug 18; 42(14): 8928–8938.

I find it remarkable that the cause and the cure of a disease is found in the same protein.

Here’s the research proposal for you.  Look at the other 300 human genes containing the BRICHOS motif (itself just a beta sheet with alpha helices on either side) and see how many have sequences which can form amyloid.  There should be programs which predict the likelihood of an amino acid sequence forming amyloid.

It’s very hard to avoid teleology when thinking about cellular biochemistry and physiology.  It’s back to Aristotle where everything has a purpose and a design.  Clearly BRICHOS is being used for something or evolution/nature/natural selection/the creator would have long ago gotten rid of it.  Things that aren’t used tend to disappear in evolutionary time — witness the blind fish living in caves in Mexico that have essentially lost their eyes. The BRICHOS domain clearly hasn’t disappeared being present in over 1% of our proteins.

Suppose that many of the BRICHOS containing proteins have potential amyloid segments.  That would imply (to me at least) that the amyloid isn’t just junk that causes disease, but something with a cellular function. Finding out just what the function is would occupy several research groups for a long time.   This is also where you come in.  It may not pan out, but pathbreaking research is always a gamble when it isn’t stamp collecting.

 

Amyloid again, again . . .

Big pharma has spent (and lost) several fortunes trying to attack the amyloid deposits of Alzheimer’s.  But like my late med school classmate’s book — “Why God Won’t Go Away” ==https://www.amazon.com/Why-God-Wont-Go-Away/dp/034544034X, amyloid won’t go away either.   It’s a bit oblique but some 300 of our proteins contain a 100 amino acid stretch called BRICHOS.  Why? Because it acts as a chaperone protein preventing proteins with a tendency to form amyloid from aggregating into fibrils.   The amino acids form a beta sheet surrounded front and back by a single alpha helix.

[ Proc. Natl. Acad. Sci. vol. 115 pp. E2752 – E2761 ’18 ] Discusses Bri2 (aka Integral Transmembrane protein 2B (ITM2B), a 266 amino acid type II transmembrane protein. Bri2 contains a carboxy terminal domain Bri23 released by proteolytic processing between amino acids #243 #244 by furinlike proteases. Different missense mutations at the stop codon of Bri2 cause extended carboxy terminal peptides called  Abri or Adan to be released by the proteases. Abri produces Familial British Dementia (FBD) and Adan produces Familial Danish Dementia (FDD). Both are associated with amyloid deposition in blood vessels, and amyloid plaques throughout the brain along with neurofibrillary tangles.

What is fascinating (to me) is that the cause and cure are both present in the same molecule Bri2 also contains a BRICHOS domain.  This implies (to me) that possibly the segment possibly forming amyloid is being used by the cell in some other fashion.

Bri2 is found in the beta cell of the pancreas (produces insulin).  The beta cell also produces Islet Amyloid PolyPeptide (IAPP  aka amylin ) one of the most potent amyloid forming proteins known.  Nonetheless the pancreas makes tons of it, and like insulin, is secreted by the beta cell in response to elevated blood glucose.  The present work shows that Bri2 is what keeps IAPP from forming amyloid.  The BRICHOS segment (amino acids #130 – #231) is released from Bri2 by ADAM10 (you don’t want to know what the acronym stands for).

How many of the 300 or so human proteins containing the BRICHOS domain also have amyloid forming segments.  If they do, this implies that the amyloid forming segments are doing something physiologically useful.