Technology marches on — or does it?

Technology marches on — perhaps.  But it certainly did in the following Alzheimer’s research [ Neuron vol. 104 pp. 256 – 270 ’19 ] .  The work used (1) CRISPR (2) iPSCs (3) transcriptomics (4) translatomics to study Alzheimer’s.  Almost none of this would have been possible 10 years ago.

Presently over 200 mutations are known in (1) the amyloid precursor protein — APP (2) presenilin1 (3) presenilin2.  The presenilins are components of the gamma secretase complex which cleaves APP on the way to the way to the major components of the senile plaque, Abeta40 and Abeta42.

There’s a lot of nomenclature, so here’s a brief review.  The amyloid precursor protein (APP) comes in 3 isoforms containing 770, 751 and 695 amino acids.  APP is embedded in the plasma membrane with most of the amino acids extracellular.  The crucial enzyme for breaking APP down is gamma secretase, which cleaves APP inside the membrane.  Gamma secretase is made of 4 proteins, 2 of which are the presenilins.  Cleavage results in a small carboxy terminal fragment (which the paper calls beta-CTF) and a large amino terminal fragment. If beta secretase (another enzyme) cleaves the amino terminal fragment Abeta40 and Abeta42 are formed.  If alpha secretase (a third enzyme) cleaves the amino terminal fragment — Abeta42 is not formed.   Got all that?

Where do CRISPR and iPSCs come in?  iPSC stands for induced pluripotent stem cells, which can be made from cells in your skin (but not easily).  Subsequently adding the appropriate witches brew can cause them to differentiate into a variety of cells — cortical neurons in this case.

CRISPR was then used to introduce mutations characteristic of familial Alzheimer’s disease into either APP or presenilin1.  Some 16 cell lines each containing a different familial Alzheimer disease mutation were formed.

Then the iPSCs were differentiated into cortical neurons, and the mRNAs (transcriptomics) and proteins made from them (translatomics) were studied.

Certainly a technological tour de force.

What did they find?  Well for the APP and the presenilin1 mutations had effects on Abeta peptide production (but they differered).  Both however increased the accumulation of beta-CTF.  This could be ‘rescued’ by inhibition of beta-secretase — but unfortunately clinical trials have not shown beta-secretase inhibitors to be helpful.

What did increased beta-CTF actually do — there was enlargement of early endosomes in all the cell lines.   How this produces Alzheimer’s disease is anyone’s guess.

Also quite interesting, is the fact that translatomics and transcriptomics of all 16 cell lines showed ‘dysregulation’ of genes which have been associated with Alzheimer’s disease risk — these include APOE, CLU and SORL1.

Certainly a masterpiece of technological virtuosity.

So technology gives us bigger and better results

Or does it?

There was a very interesting paper on the effect of sleep on cerebrospinal fluid and blood flow in the brain [ Science vol. 366 pp. 372 – 373 ’19 ] It contained the following statement –”

During slow wave sleep, the cerebral blood flow is reduced by 25%, which lowers cerebral blood volume  by ~10%.  The reference for this statement was work done in 1991.

I thought this was a bit outre, so I wrote one of the authors.

Dr. X “Isn’t there something more current (and presumably more accurate) than reference #3 on cerebral blood flow in sleep?  If there isn’t, the work should be repeated”

I got the following back “The old studies are very precise, more precise than current studies.”

Go figure.

Does gamma-secretase have sex with its substrates?

This is a family blog (for the most part), so discretion is advised in reading further.   Billions have been spent trying to inhibit gamma-secretase.  Over 150 different mutations have been associated with familial Alzheimer’s disease.  The more we know about the way it works, the better.

A recent very impressive paper from China did just that [ Science vol. 363 pp. 690- 691, 701 eaaw0930 pp. 1 –> 8 ’19 ].

Gamma secretase is actually a combination of 4 proteins (presenilin1, nicastrin, APH1 (anterior pharynx defect) and PEN-2 (presenilin enhancer 2). It is embedded in membranes and has at least 19 transmembrane segments.  It cleaves a variety of proteins spanning membranes (e.g it hydrolyzes a peptide bond — which is just an amide).  The big deal is that cleavage occurs in the hydrophobic interior of the membrane rather than in the cytoplasm where there is plenty of water around.

Gamma secretase cleaves at least 20 different proteins this way, not just the amyloid precursor protein, one of whose cleavage products is the Abeta peptide making up a large component of the senile plaque of Alzheimer’s disease.

To get near gamma secretase, another enzyme must first cleave APP in another place so one extramembrane fragment is short.  Why so the rest of the protein can fit under a loop between two transmembrane helices of nicastrin.  This is elegance itself, so the gamma secretase doesn’t go around chopping up the myriad of extracellular proteins we have.

The 19 or so transmembrane helices of the 4 gamma secretase proteins form a horseshoe, into which migrates the transmembrane segment of the protein to be cleaved (once it can fit under the nicastrin loop).

So why is discretion advised before reading further?  Because the actual mechanism of cleavage involves intimate coupling of the proteins.    One of the transmembrane helices of presenilin1 unfolds to form two beta strands, and the transmembrane helix of the target protein unfolds to form one beta strand, the two strands pair up forming a beta sheet, and then the aspartic acid at the active site of gamma secretase cleaves the target (deflowers it if you will).  Is this sexual or what?

All in all another tribute to ingenuity (and possibly the prurience) of the blind watchmaker. What an elegant mechanism.

Have a look at the pictures in the Science article, but I think it is under a paywall.

Nicastrin the gatekeeper of gamma secretase

Once a year some hapless trucker from out of town gets stuck trying to drive under a nearby railroad bridge with a low clearance. This is exactly the function of nicastrin in the gamma secretase complex which produces the main component of the senile plaque, the aBeta peptide.

Gamma secretase is a 4 protein complex which functions as an enzyme which can cut the transmembrane segment of proteins embedded in the cell membrane. This was not understood for years, as cutting a protein here means hydrolyzing the amide bond of the protein, (e.g. adding water) and there is precious little water in the cell membrane which is nearly all lipid.

Big pharma has been attacking gamma secretase for years, as inhibiting it should stop production of the Abeta peptide and (hopefully) help Alzheimer’s disease. However the paper to be discussed [ Proc. Natl. Acad. Sci. vol. 113 p.n E509 – E518 ’16 ] notes that gamma secretase processes ‘scores’ of cell membrane proteins, so blanket inhibition might be dangerous.

The idea that Nicastrin is the gatekeeper for gamma secretase is at least a decade old [ Cell vol. 122 pp. 318 – 320 ’05 ], but back then people were looking for specific binding of nicastrin to gamma secretase targets.

The new paper provides a much simpler explanation. It won’t let any transmembrane segment of a protein near the active site of gamma secretase unless the extracellular part is lopped off. The answer is simple mechanics. Nicastrin is large (709 amino acids) but with just one transmembrane domain. Most of it is extracellular forming a blob extending out 25 Angstroms from the membrane, directly over the substrate binding pocket of gamma secretase. Only substrates with small portions outside the membrane (ectodomains) can pass through it. It’s the railroad bridge mentioned above. Take a look at the picture — https://en.wikipedia.org/wiki/Nicastrin

This is why a preliminary cleavage of the Amyloid Precursor Peptide (APP) is required for gamma secretase to work.

So all you had to do was write down the wavefunction for Nicastrin (all 709 amino acids) and solve it (assuming you even write it down) and you’d have the same answer — NOT. Only the totally macroscopic world explanation (railroad bridge) is of any use. What keeps proteins from moving through each other? Van der Waals forces. What help explain them. The Pauli exclusion principle, as pure quantum mechanics as it gets.

A new kid on the Alzheimer’s block

There’s a new kid on the Alzheimer’s block, and it may explain why the huge sums thrown at beta-secretase inhibitors by big pharma has been such an abject failure. First, a lot of technical background.

The APP (for amyloid precursor protein) contains anywhere from 563 to 770 amino acids in 5 distinct transcripts made by alternate splicing of the single gene. The 3 main forms contain 695, 751 and 770 amino acids. The 695 amino acid form is found only in brain and peripheral nerve where it predominates, while the transcripts containing 751 and 770 amino acids are found everywhere but predominate in other tissues. The A4 peptides (Abeta peptides) which are the major components of the Alzheimer senile plaque are derived from from the carboxy terminal end of APP (beginning at amino acid #597 ) and contain only 39 – 43 amino acids. About 1/3 of the 39 – 43 amino acid amyloid beta peptide (A beta peptide) is found within the transmembrane segment of APP the other two thirds being found just outside the membrane.  So to get A beta peptides the APP must be cut (more than once) at its carboy terminal end.

For Abetaxx (xx between 39 and 43) to be formed, cleavage must occur outside the membrane in which APP is embedded by beta secretase. This produces a soluble extracellular fragment, with the rest embedded in the membrane (this is called C99). Then gamma secretase (another enzyme) cleaves C99 within the membrane forming the Abeta peptides, which constitute much of the senile plaque of Alzheimer’s disease.

Alpha secretase (yet another enzyme) also cleaves the APP in its carboxy terminal extramembranous part, but does so closer to the membrane, so that part of the protein which would form the aBeta peptide is removed.

R. Scheckman personal communication (2012) — The Abeta peptide is appears to be cleaved by gamma secretase from the fragment generated by beta secretase. However, this happens well inside the cell in the last station of the Golgi apparatus. Then Abeta is swept out of the cell by the secretory pathway. So all this happens INSIDE the cell, rather than at the neuron’s extracellular membrane (which is what I thought).

Remarkably it is very difficult (for me at least) to find out just at what amino acids of the amyloid precursor protein(s) the 3 secretases (alpha, beta, gamma) cleave.

[ Nature vol. 526 pp. 443 – 447 ’15 ] describes a totally new kid on the block, which (if replicated) should make us rethink everything we thought we knew about the amyloid precursor protein and the Abeta peptide. Another set of carboxy terminal fragments (CTFs) called CTFneta is formed from the amyloid precurosr protein (APP). Formation is mediated (in part) by MT5-MMP, a matrix metalloprotease. (In grad school neta is how we pronounced the Greek letter eta, which looks like a script N). The authors call the enzymatic activity forming them neta-secretase (clearly not all the enzymes which do this have been identified at this point). At least the authors tell you where the neta secretases cleave APP695 (between amino acids #504 – #505) . This is amino terminal to the beta and alpha sites (which are at higher amino acid numbers and the gamma site which is at a higher number still).  Alpha and beta secretase then work on CTFneta to produce shorter peptides, called Aneta-alpha, and Aneta-beta.

This isn’t idle chatter as Aneta-alpha, and Aneta-beta are found in the dystrophic neurites in an Alzheimer mouse model (human work is sure to follow). Inhibition of beta secretase activity results in accumulation of CTFneta and Aneta-alpha.

Aneta-alpha itself lowers long term potentiation (LTP) in hippocampal slices (LTP is considered by most to be the best molecular and physiological model we have of learning). As judged by intracellular calcium levels, hippocampal neuronal activity is also inhibited by Aneta-alpha.

What’s fascinating about all this, is that the work possibly explains why the huge amount of money big pharma has spend on beta secretase inhibitors has been such a failure.