The staggering implications of one axon synapsing on another

It isn’t often that a single paper can change the way we think the brain works.  But such is the case for the paper described in the previous post (full copy below *** ) if the implications I draw from it are correct.

Unfortunately this post requires a deep dive into neuroanatomy, neurophysiology, neuropharmacology and cellular molecular biology.  I hope to put in enough background to make some of it comprehensible, but it is really written for the cognoscenti in these fields.

I’m pretty sure that some of these thoughts are both original and unique

Briefly, the paper provided excellent evidence for one axon causing another to fire an impulse (an action potential).   The fireror was from a neuron using acetyl choline as a neurotransmitter, and the fireree was a dopamine axon going to the striatum.

Dopamine axons are special.  They go all over the brain. The cell body of the parent neuron of the axon to be synapsed on uses dopamine as a neurotransmitter.  It sits in the pars compacta of the substantia nigra a fair piece away from the target they studied (the striatum). “Individual neurons of the pars compacta are calculated to give rise to 4.5 meters of axons once all the branches are summed”  — [ Neuron vol. 96 p. 651 ’17 ].”  These axons release dopamine all over the brain.  There aren’t many dopamine neurons to begin with just 80,000 which is 1 millionth of the current (probably unreliable) estimate of the number of neurons in the brain 80,000,000,000.

Now synapses between neurons are easy to spot using electron microscopy.  The presynaptic terminal contains a bunch of small vesicles and is closely apposed (300 Angstroms — way below anything the our eyes can see) to the post synaptic neuron which also looks different, usually having a density just under the membrane (called, logically enough, post-synaptic density).  Embedded in the postsynaptic membrane are proteins which conduct ions such as Na+, K+, Cl- into the postsynaptic neuron triggering an action potential.

But the dopamine axons going all over the brain have a lot of presynaptic specialization, but in many of the cases the post-synaptic neuron and its postsynaptic density is nowhere to be found (or the receptors for dopamine aren’t near the presynaptic specialization).  This is called volume neurotransmission.

However, in the nuclei studied (the striatum) dopamine synapses on dendrites of the major cell type (the medium spiny neuron) are well described and the 5 receptors for dopamine (called G Protein Coupled Receptors — GPCRs) are found there.  None of the GPCRs conduct ions or trigger action potentials (immediately anyway).  Instead, they produce their effects much more slowly and change the metabolism of the interior of the cell.  This is true for all GPCRs, regardless of the ligand activating them — and humans have 826 GPCR genes.

Note also that volume neurotransmission means that dopamine reaches nonNeuronal tissue — and there is good evidence that dopamine receptors are present on glial cells, pericytes and blood vessels.

The story doesn’t end with dopamine.  There are 3 other similar systems of small numbers of neurons collected into nuclei, using different neurotransmitters, but whose axons branch and branch so they go all over the brain.

These are the locus coeruleus which uses norepinephrine as a neurotransmitter, the dorsal raphe nucleus which uses serotonin and the basal nucleus of Meynert which uses acetyl choline.  There is excellent evidence that the first two (norepinephrine and serotonin) use volume neurotransmission. I’m not sure about those of the basal nucleus of Meynert.

What is so remarkable about the paper, that it allows the receiving neurons to (partially) control what dopamine input it gets.

All norepinephrine receptors are GPCRs, while only one of the 16 or so serotonin receptors conducts ions, the rest being GPCRs.

Acetyl choline does have one class of receptors (nicotinic) which conducts ions, and which the paper shows is what is triggering the axon on axon synapse.  The other class (muscarinic) of acetyl choline receptor is a GPCR.

Addendum 29 September — it goes without saying (although I didn’t say it) that any molecule released by volume neurotransmission doesn’t confine itself to finding targets on neurons.  Especially with norepinephrine, it could bind to receptors for it on the vasculature causing circulatory effects.  They could also bind to GPCRs on pericytes and glia.

Now the paper tested axon to axon firing in one of the four systems (dopamine) in one of the places its axons goes (the striatum).  There is no question that the axons of all 4 systems ramify widely.

Suppose axon to axon firing is general, so a given region can control in someway how much dopamine/serotonin/norepinephrine/acetyl choline it is getting.

Does this remind you of any system you are familiar with?  Perhaps because my wife went to architecture school, it reminds me of an old apartment building, with separate systems to distribute electricity, plumbing, steam heat and water to each apartment, which controls how much of each it gets.

Perhaps these four systems are basically neurological utilities, necessary for  the function of the brain, but possibly irrelevant to the computations it is carrying out, like a mother heating a bottle for her baby in water on a gas stove on a cold winter night.  The nature of steam heat, electricity, water and gas tell you very little about what is going on in her apartment.

The paper is so new (the Neuron issue of 21 September) that more implications are sure to present themselves.

Quibbles are sure to arise.  One is that fact that the gray matter of our brain doesn’t contain much in the way of neurons using acetyl choline as a neurotransmitter.  What it does have is lots of neurons using GABA which we know can act on axons, inhibiting axon potential generation.  This has been well worked out with synapses where the axon emerges from the neuron cell body (the initial segment).  However the different ionic composition of axons in the developing brain results in GABA having an excitatory effect.  Perhaps ionic composition varies in different parts of the neuron.

The work was done in living animals, so the paper contains no electron micrographs.  Such work is sure to be done.  No classical presynaptic apparatus may be present, just two naked axons touching each other and interacting by ephaptic transmission (the term does not appear in the paper).

So a lot of work should be done, the first of which should be replication. As the late Carl Sagan said “extraordinary claims require extraordinary evidence”.

Finally:

As Mark Twain said ” There is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact.”

 

Biden is in early dementia — the evidence

As a neurologist I am often asked about Biden’s mental capacity.  My first post on the subject occurred after the first debate with Trump.  I thought he was intact — you can read about it here.

https://luysii.wordpress.com/wp-admin/post.php?post=5200&action=edit&calypsoify=1

Then I was asked to comment on the possibility that his previous operation for aneurysm could be causing trouble. I didn’t think this was likely as so much time had passed.  Interestingly, I knew the neurosurgeon as a Penn undergraduate when I was a neurology resident.  You can read the post at the end — Biden’s cerebral aneurysm.

That was written last December.

I changed my opinion after his press conference. of 14 June ’21 https://www.youtube.com/watch?v=PAWRHM4i3Dg
I strongly suggest you look at the segment at 15 minutes where his response makes little sense, and then he shuts down completely for 7 seconds, apparently quite confused. That’s my reading of the video. Form your own opinion.

Then on June 23rd I was sent another clip where he was confused

— https://www.c-span.org/video/?512595-1/president-biden-attends-us-eu-summit-brussels

It is an 8 minute speech, and the clip can be found at 2 minutes, again showing an episode of confusion.

 

But first a story:

As a third year medical student on psychiatry rotation,  I interviewed a Bryn Mawr student who was on the psych ward (my wife was also an undergraduate at the time).  I well knew the intensity of the place, and how much pressure the girls (see the end of the post) put on themselves.  So I talked and talked and commiserated with her.  After a pleasant enough time the I concluded the interview and left.   The teaching psychiatrist asked me what I thought, and I told him how frigtening I found it given what I knew about Bryn Mawr. He asked me if I found out that she thought the television was talking to her.  Basically by yapping when she went off track, I kept her sane.

So I learned to shut up, and let people tell me what was wrong with them.  This is why Biden likely did well during the debates. The short time given to answer and the barrage of questions and interruptions kept him focused.

It really came home as I looked at the whole 8 minutes of the second clip trying to find the brief period of confusion.  Please look at the whole clip yourself and draw your own conclusions.  I see a pleasant,  rambling, slow thinking,  occasionally confused old man.

 

This is what early dementia looks like.

I was severely criticized by a follower after the first post.  Here it is,  “Issuing alarmist statements about his mental health is reprehensible. You are not his physician. Moreover, armchair diagnosis is frowned upon by the American Psychiatric Association.I’ve been following your blog for several years and also have been reading you comments on the “in the pipeline” blog. On the basis of that experience I had not expected to stoop that low.”

In my defense, I was defeated by the new WordPress editor which wouldn’t let me bring in the evidence shown here.  Apparently it was a (still extant) incompatibility of Safari with the editor.   I was still impressed enough by how confused Biden looked that I posted it anyway.

As the late Carl Sagan said “extraordinary claims require extraordinary evidence”. So here is the evidence (finally).  Apologies for the delay.

As children, our least favorite explanation was ‘because I say so’.

Essentially that’s part of what I’m offering here.  I was involved in clinical neurology from ’67 to ’00, and at a minimum saw at least 1 demented patient a week during that time.  That’s an underestimate, as I’d make rounds on other neurologists patients when covering weekends.  I doubt that anyone reading this has similar extensive experience.

So Biden just looks like all the early dementia patients I saw during that time.  Given my experience, I think that should carry some weight.

The fact that Biden appears sharp at times is typical of early stage dementia.  I’ve certainly seen it in family and friends, with such things being excused as ‘it must have been the heat’ or ‘they must not have been feeling well’.

Why is this important?  Khrushchev’s estimate of President Kennedy’s weakness lead to the Cuban Missile Crisis of 1962. Khrushchev’s son confirmed this when he spoke at the Kennedy Center at Harvard.   Kennedy was receiving narcotics for his back.  The side effects of what little medicines we had back then weren’t appreciated.  Example: thyroid and amphetamines were used to help people lose weight.

Biden does not appear mentally strong to Putin or Xi (or me).

• Yes women undergraduates at Bryn Mawr and other members of the seven sisters called themselves girls (or at least were called that by males wishing to date them).  According my wife, who just corrected me,  Bryn Mawr undergraduates called themselves women, in contrast to a nearby educational institution which advertised “Are you a Harcum Girl?”  Similarly, 10 years later Native Americans in Montana called themselves Indians, not having the benefit of the linguistic and moral improvements to which we have currently ascended.

 

 

Biden’s cerebral aneurysm

A bombshell that wasn’t

Yesterday, a friend sent me the following

” Chinese Coronavirus Is a Man Made Virus According to Luc Montagnier the Man Who Discovered HIV

Contrary to the narrative that is being pushed by the mainstream that the COVID 19 virus was the result of a natural mutation and that it was transmitted to humans from bats via pangolins, Dr Luc Montagnier the man who discovered the HIV virus back in 1983 disagrees and is saying that the virus was man made.”

Pretty impressive isn’t it?  Montagnier says that in the 30,000 nucleotide sequence of the new coronovirus SARS-CoV-2 he found sequences of the AIDS virus (HIV1).  Worse, the biolab in Wuhan was working both on HIV1 and coronaviruses.  It seems remote that a human could have been simultaneously infected with both, but these things happen all the time in the lab, intentionally or not.

It really wouldn’t take much to prove Montagnier’s point.  Matching 20 straight nucleotides from HIV1 to the Wuhan coronavirus is duck soup now that we have the sequences of both.  HIV1 has a genome with around 10,000 nucleotides, and the Wuhan coronavirus has a genome of around 30,000.  Recall that each nucleotide can be one of 4 things: A, U, G, C.  In the genome the nucleotides are ordered, and differences in the order mean different things — consider the two words united and untied.

Suppose Montagnier found a 20 nucleotide sequence from HIV1 in the new coronavirus genome. How many possibilities are there for such a sequence?  Well for a 2 nucleotide sequence there are 4 x 4 == 4^2 = 16,  for a 3 nucleotide sequence 4 x 4 x 4 == 4^3 = 64.  So for 20 nucleotides there are 4^20 possible sequences == 1,099,511,622,776 different possibilities.  So out of the HIV1 genome there are 10,000 – 20 such sequences, and in the coronavirus sequence there are 30,000 -20  such sequences so there are 10,000 times 30,000 ways for a 20 nucleotide sequence to match up between the two genomes.  That 300,000,000 ways for a match to occur by chance — or less than .1%.  If you’re unsatisfied with those odds than make the match larger.  25 nucleotides should satisfy the most skeptical.

But there’s a rub — as Carl Sagan has said  “Extraordinary claims require extraordinary evidence.”  Apparently Montagnier hasn’t published the sequence of HIV1 he claims to have found in the coronavirus.   If anyone knows what it is please write a comment.

Then there’s the fact that Montagnier appears to have gone off his rocker. In 2009 he published a  paper (in a journal he apparently built) which concludes that diluted DNA from pathogenic bacterial and viral species is able to emit specific radio waves” and that “these radio waves [are] associated with ‘nanostructures’ in the solution that might be able to recreate the pathogen”.

Sad.  Just as one of the greatest chemists of the 20th century will be remembered for his crackpot ideas about vitamin C (Linus Pauling), Montagnier may be remembered for this.

On second thought, there is no reason to need Montagnier and his putative sequence at all. The sequences of both genomes are known.     Matching any 20 nucleotide sequence from HIV1 to any of the 30,000 – 20 20 nucleotide sequences from the Wuhan flu is a problem right out of Programming 101.  It’s a matter of a few loops, if thens and go to’s.  . If you’re ambitious  you could start with smaller sequences say 5 – 10 nucleotides, find a match, move to the next largest size sequence and repeat until you find the largest contiguous sequence of nucleotides in HIV1 to be found in the coronavirus.

You can read about the Wuhan lab in an article from Nature in 2017 — https://www.nature.com/news/inside-the-chinese-lab-poised-to-study-world-s-most-dangerous-pathogens-1.21487

Cytocapsular tubes

“Extraordinary claims require extraordinary evidence”  Carl Sagan.  That goes in spades for a recent PNAS article vol. 115 pp. E1137 – E1146 2018 — http://www.pnas.org/content/115/6/E1137.

Start by looking at the following 3 videos

pnas.1717910115.sm01-3.avi

pnas.1717910115.sm02-2.avi

pnas.1717910115.sm03-2.avi

Unfortunately, to get to them, it appears that you must be a PNAS subscriber, so I’ll tell you what they show.

First, some background. Cell culture usually involves putting them into a Petri dish, something inherently two dimensional, but most cells in our body live in a 3 dimensional environment. So this work implanted Human Mammary Epithelial Cells (HMECs) into a 3 dimensional matrix of Matrigel (an extracellular matrix surrogate secreted by mouse sarcoma cells, containing, laminin, nidogen, collagen and heparan sulfate proteoglycans) Matrigel also contains the growth factors Transforming Growth Factor Beta (TGFbeta) and Epidermal Growth Factor (EGF), both of which prevent differentiation and promote proliferation. The 3d Matrigel matrix is softer and spongier than the hard surface of a Petri dish.

The behavior of these cells in the Matrigel is completely different than that usually seen. In fact no one has ever seen anything like it before, which is why, if possible you must look at the 3 movies the paper supplies in the supplementary material (referenced above).

The cells move around, but nowhere to be seen are the lamellipodia or the filopodia seen in 2 dimensional cell culture.

In the first movie a small cell repeatedly generates and retracts multiple membranous protrusions called cytocapsues (some larger than the cell itself) which the cell sometimes enters.

The second has multiple cells within the tubes formed by the cytocapsules (cytocapsular tubes) migrating within them. The cells drag the tubes through the matrix, without breaking the tube or allowing another tube to merge with it.

If replicated, this work has bearing on embryology, normal organ function and cancer metastasis.

No one has ever seen anything like this. Why not? The authors say that ‘only when the polymerization, density and viscoelasticity of the Matrigel is tightly controlled are the tubes seen. Unlike secreted extracellular vesicles, cells get inside the cytocapsular tubes. The tubes themselves interconnect and form networks. The tubes degrade and decompose without cells inside them.

They note that polymerized actin (microfilaments) are present under the tube membranes.

Even though the membranes are mostly lipids, proteins are required, and eIF4E levels are elevated. Inhibiting it suppresses cytocapsular tube generation.

It’s worth repeating Sagan – “Extraordinary claims require extraordinary evidence” Stay tuned

Maybe there is something to it after all

Nearly 8 years ago I wrote a post (see below) about a rather fantastic paper, that said that in order to turn on gene transcription, the DNA had to be damaged first. This caused all sorts of repair enzymes to rush to the damaged site, opening up the chromatin there and allowing RNA polymerase II (which is large) to get to the DNA and transcription to proceed. I wrote the original author who was Italian, who said he was ill, but nothing further appeared about the idea (as far as I know). Remember what Carl Sagan said “Extraordinary claims require extraordinary evidence.”

Now Science (vol. 351 p. 147 ’16 ) has an abstract of an article in Nat. Commun. 6, 10191 (2015). “Curiously, DNA repair factors have been found associated with tran- scriptionally paused, inducible genes. Bunch et al. show that the activation of paused and inducible genes in human tissue culture cells triggers DNA breaks at the RNA polymerase pause site. The subsequent recruitment and signaling activity of DNA repair factors is critical for DNA repair, release of the RNA polymerase, and the transition to the transcrip- tion elongation phase of gene expression.”

Here’s the relevant portion of the post from 2/08. How about that ! ! ! DNA breaks are even more spectacular than 8 oxo-guanine

An incredible article appeared last month in the journal Science. (see below for the abstract). If it can be verified and if it applies generally, our conception of just how genes coding for protein are turned on will be radically changed (yes, there are many other kinds of genes other than those coding for proteins). If DNA compaction, nucleosomes, histones, lysine methylation and demethylation, the histone code, nuclear hormone receptors (particularly the estrogen receptor), DNA glycosylase and topoisomerase aren’t old friends have a look at the first comment on this post for the background you need (it’s back on the Skeptical Chymist). Don’t worry, there is plenty of chemistry to follow.

Some histone code modifications are reversible, particularly acetylation of the epsilon amino group of lysine. Enzymes acetylating histone lysines are called histone acetylases, those removing it are called histone deacetylatases (HDACs). However, lysine methylation was thought to be permanent until ’04 when several enzymes able to demethylate lysine were found. One such enzyme is called LSD1 (it has nothing to do with the hallucinogen). It removes the two methyl groups from lysine #9 of histone #3 (H3K9me2). If this modification is present on a nucleosome near a gene, the gene is silenced, so the methyls must be removed so the protein it codes for can be made.

The estrogen receptor + estrogen complex bound to the ERE (the estrogen response element – a 15 nucleotide DNA sequence) triggers H3K9me2 removal. The process of demethylation is oxidative (how else would you split a nitrogen to hydrocarbon bond?). Hydrogen peroxide is produced, a loose cannon which oxidizes the juicy electron-rich bases of DNA nearby, forming in particular 8 oxo-guanine, as guanine is the most easily oxidized DNA base. Since 21% of the DNA bases in our genome are guanine, H2O2 doesn’t have far to look. This calls in some fairly heavy artillery (DNA glycosylase to remove the 8 oxo-guanine, topoisomerase IIbeta to unwind the DNA so it can be repaired, the repair enzymes, etc, etc…). Naturally this opens up the compacted DNA structure around the gene allowing RNA polymerase II to do its work transcribing the estrogen responsive gene into mRNA (once the damage is repaired).

So according to this paper, estrogen turns on gene transcription by damaging DNA. This is fantastic (if true). There’s more. The estrogen receptor is but one member of a group of proteins called nuclear hormone receptors. The name comes from the fact that other hormones (progesterone, androgen, thyroid, glucocorticoids, mineralocorticoids) have their own proteins that turn on (or turn off) genes the same way. Subsequently it was found that some vitamin metabolites (vitamin D3, vitamin A) have similar receptors even though they aren’t hormones. The human genome contains 48 such proteins. Less than half of them have known ligands. Those with known ligands have their finger in just about every metabolic pie in the cell.

One final point. It has been estimated that 8-oxoguanine is formed 100,000 times each day in every cell. Perhaps its formation is physiologic rather than pathologic. Where does that leave antioxidant therapy, which has been touted to do everything but cure hemorrhoids? Well, one such trial was done on 29,000 Finnish men at high risk for lung cancer (they were smokers) [New England J. Med. vol. 330 pp. 1029-1035 (1994)] Alpha tocopherol (one antioxidant used in the study) didn’t decrease the incidence of lung cancer, and there was an 18% higher incidence of lung cancer among the men receiving beta carotene (another antioxidant). In medicine, theory is great but data trumps it every time.

Science vol. 301 pp. 202 – 206 ’08, B. Perillo et. al.

Modifications at the N-terminal tails of nucleosomal histones are required for efficient transcription in vivo. We analyzed how H3 histone methylation and demethylation control expression of estrogen-responsive genes and show that a DNA-bound estrogen receptor directs transcription by participating in bending chromatin to contact the RNA polymerase II recruited to the promoter. This process is driven by receptor-targeted demethylation of H3 lysine 9 at both enhancer and promoter sites and is achieved by activation of resident LSD1 demethylase. Localized demethylation produces hydrogen peroxide, which modifies the surrounding DNA and recruits 8-oxoguanine–DNA glycosylase 1 and topoisomeraseIIβ, triggering chromatin and DNA conformational changes that are essential for estrogen-induced transcription. Our data show a strategy that uses controlled DNA damage and repair to guide productive transcription.

The old year goes out with a bang

A huge amount of cellular genomics will have to be redone if the following paper is replicated. Remember “Extraordinary claims require extraordinary evidence.” Carl Sagan.

What’s all the shouting about? Normally when you think about messenger RNA (mRNA) as it exists in the cytoplasm after the initial transcript is significantly massaged in the nucleus, you think about the part that codes for amino acids. This ‘coding region’ is the part that is translated into amino acids by the ribosome. But mRNA is invariably larger having nucleotides at each end (3′ and 5′) which have other uses. These are called the 3′ Untranslated Region (3′ UTR) and 5′ Untranslated Region (5′ UTR).

So if you do single cell RNA sequencing (which we can do now) it shouldn’t matter what nucleotide sequence you search for (5′ UTR, 3′ UTR or the coding region) as all mRNA contains one of each.

Not so says this paper [ Neuron vol. 88 pp. 1149 – 1156 ’15 ].

Given the mRNA for a given protein in a single cell, using a probe for the 3’UTR and a probe for the coding sequence should give you the same abundance for both. That’s not what they found at all for single neurons from the brain. In some cases there was much more RNA coding for the 3’UTR than for the coding segment of a given mRNA for a protein. In others there was much less. Even more impressively is that the 3’UTR/(3’UTR + coding) ratio for a given protein varies between different parts of the brain. Obviously this ratio should be .5 given what we knew about mRNA in the past. The ratio has to be between 0 and 1.

Well they looked at a lot of proteins. The did find around 1,400 genes with a ratio of .5 (as expected), but they found 700 showing a ratio of .2 (lots more 3’UTR than coding sequence), and 1,100 showing a ratio of .8. Overall plotting the ratio vs. number of genes with that ratio gives something looking like a bell curve (Gaussian distribution).

It’s long been known that mRNA levels don’t exactly correlate with the levels of proteins made from them. If there’s lots of 3’UTRs around the authors found that there was relatively little protein made from the gene.

A variety of brain atlases have published mRNA abundances for various regions of the brain. If they just used one probe (as they probably did) this is clearly not enough.

The 3’UTRs may be acting as ceRNAs (competitive endogenous RNAs). These have been known for years — I’ve included a post of 3 years ago on the subject (at the end).

So this work (if replicated) throws everything we thought we knew about mRNA into a cocked hat. It’s why I love science, there’s always something really new to think about. Happy New Year !!!

Chemiotics II
Lotsa stuff, basically scientific — molecular biology, organic chemistry, medicine (neurology), math — and music
Why drug discovery is so hard: reason #20 — competitive endogenous RNAs

The chemist will appreciate le Chatelier’s principle in action in what follows. We are far from knowing all the players controlling cellular behavior. So how in the world will we find drugs to change cellular behavior when we don’t know all the things affecting it. The latest previously unknown cellular player to enter the lists are competitive endogenous RNAs (ceRNAs). For details see Cell vol. 147 pp. 344 – 357, 382 – 395 ’11. The background the pure chemist needs for what follows can all be found in the category “Molecular Biology Survival Guide.

Recall that microRNAs are short (20 something) polynucleotides which bind to the 3′ untranslated region (3′ UTR) of mRNA, and either (1) inhibit its translation into protein (2) cause its degradation. In each case, less of the corresponding protein is made. The microRNA and the appropriate sequence in the 3′ UTR of the mRNA form an RNA-RNA double helix (G on one strand binding to C on the other, etc.). Visualizing such helices is duck soup for a chemist.

Molecular biology is full of such semantic cherry bombs as nonCoding DNA (which meant DNA which didn’t cord for protein), a subset of Junk DNA. Another is the pseudogene — these are genes that look like they should code for protein, except that they don’t because of lack of an initiation codon or a premature termination codon. Except for these differences, they have the nucleotide sequence to code for a known protein. It is estimated that the human genome contains as many pseudogenes (20,000) as it contains true protein coding genes [ Genome Res. vol. 12 pp. 272 – 280 ’02 ]. We now know that well over half the genome is transcribed into mRNA, including the pseudogenes.

PTEN (you don’t want to know what it stands for) is a 403 amino acid protein which is one of the most commonly mutated proteins in human cancer. Our genome also contains a pseudogene for it (called PTENP). Interestingly deletion of PTENP (not PTEN) is found in some cancers. However PTENP deletion is associated with decreased amounts of the PTEN protein itself, something you don’t want as PTEN is a tumor suppressor. How PTEN accomplishes this appears to be fairly well known, but is irrelevant here.

Why should loss of PTENP decrease PTEN itself? The reason is because the mRNA made from PTENP, even though it has a premature termination codon, and can’t be made into protein, is just as long, so it also contains the 3’UTR of PTEN. This means PTENP is sopping up microRNAs which would otherwise decrease the level of PTEN. Think of PTENP mRNA as a sponge.

Subtle isn’t it? But there’s far more. At least PTENP mRNA closely resembles the PTEN mRNA. However other mRNAs coding for completely different proteins, also have binding sites in their 3’UTR for the microRNA which binds to the 3UTR of PTEN, resulting in its destruction. So transcription of a completely different gene (the example of ZEB2 is given) can control the abundance of another protein. Essentially its mRNA is acting as a sponge, sopping up the killer microRNA.

It gets worse. Most microRNAs have binding sites on the mRNAs of many different proteins, and PTEN itself has a 3’UTR which binds to 10 different microRNAs.

So here is a completely unexpected mechanism of control of protein levels in the cell. The general term for this is competitive endogenous RNA (ceRNA). Two years ago the number of human microRNAs was thought to be around 1,000. Unlike protein coding genes, it’s far from obvious how to find them by looking at the sequence of our genome, so there may be quite a few more.

So most microRNAs bind the 3’UTR of more than one protein (the average number is unclear at this point), and most proteins have binding sites for microRNAs in their 3’UTR (again the average number is unclear). What a mess. What subtlety. What an opportunity for the regulation of cellular function. Who is going to be smart enough to figure out a drug which will change this in a way that we want. Absence of evidence of a regulatory mechanism is not evidence of its absence. A little humility is in order.