Tag Archives: Nonsense mediated decay

Duchenne muscular dystrophy — a novel genetic treatment

Could the innumerable genetic defects underlying Duchenne muscular dystrophy all be treated the same way?  Possibly.  Paradoxically, the treatment involves actually making the gene  even worse.

Understanding how and why this might work involves a very deep dive into molecular biology.  You might start by looking at the series of five background articles I wrote — start at https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/ and follow the links.

I have a personal interest in Duchenne muscular dystrophy because I ran such a clinic from ’72 to ’87 watching young boys and adolescents die from it.  The major advance during that time, was NOT medical or anything I did, but lighter braces, so the boys could stay ambulatory longer.  Things have improved as survival has improved by a decade so they die in their late 20s.

So lets start.  Duchenne muscular dystrophy is caused by a mutation in the gene coding for dystrophin, a large (3,685 amino acids) protein which ties the contractile apparatus of the muscle cell (actin and myosin) to the cell membrane. Although it isn’t the largest protein we have — titin, another muscle protein with 34,350 amino acids is, the gene for dystrophin is the largest we have, weighing in at 2,220,233 nucleotides.  This is why Duchenne is one of the most common diseases due to a defect in a single gene, the gene is so large that lots of things can (and do) go wrong with it.

The gene comes in 79 pieces (exons) which account for under 1/200 of the nucleotides of the gene.  The rest must be spliced out and discarded.  Have a look at http://www.dmd.nl.  to see what can go wrong — the commonest is deletion of parts of the gene (60 – 70% of cases), followed by duplication of other parts (10% of cases) with the rest being mutations that change one amino acid to another.

Duchenne isn’t like cystic fibrosis where some 600 different mutations in the causative CFTR gene were known by 2003 but with 90% of cases due to just one.  So any genetic treatment for that young boy sitting in front of you had better be personalized to his particular mutation.

Or should it?

Possibly not.  We’ll need to discuss 3 things first

l. Nonsense Mediated Decay (NMD)

2. Nonsense Induced Transcriptional Compensation (NITC).

3. The MDX mouse model of Duchenne muscular dystrophy

Nonsense mediated decay.  Nonsense is a poor term, because the 3 nonSense codons (out of 64 possible) tell the ribosome to stop translating mRNA into protein and drop off the mRNA.  That isn’t nonsense.  I prefer stop codon, or termination codon

An an incredibly clever piece of business tells the ribosome (which is after all an inanimate object) when a stop codon occurs too early in the mRNA when there are a bunch of codons afterwards needed to make up the whole protein.

Lets go back to dystrophin and its 79 exons, and the fact that 99.5% of the gene is made of introns which are spliced out.   Remember the mRNA starts at the 5′ end and ends at the 3′ end.  The ribosome reads and translates it from 5′ to 3′. When an intron is spliced out, a protein complex of several proteins is placed on the mRNA some 20 – 24 basepairs 5′ to the splice site (this happens in the nucleus way before the mRNA gets near a ribosome in the cytoplasm).  The complex is called the Exon Junction Complex (EJC). The ribosome then happily munches along the mRNA from 5′ to 3′ knocking off the EJCs as it moves, until it hits a termination codon and drops off.

Over 95% of  genes do not have introns after the termination codon.  What happens if it does? Well then it is called a premature termination codon (PTC) and there is usually an EJC 3′ (downstream) to it.  If a termination codon is present 50 -55 nucleotides 5′ (upstream) to an EJC then NMD occurs.

Whenever any termination codon is reached, release protein factors (eRF1, eRF3, SMG1) bind to the mRNA.  It there is an EJC around (which there shouldn’t be) the interaction between the two complexes triggers phosphorylation of one of EJC proteins, triggering NMD.

So that’s how NMD happens, when there is a PTC.  Clever no?

Nonsense Induced Transcriptional Compensation (NITC).  I realize that this is a lot to throw at you, but a treatment for Duchenne is worth the effort (not to mention other genetic diseases in which the mechanism to be described also applies).

NITC is something I never heard about until two papers appearing in the 13 April Nature (vol. 568 pp. 179 – 180 (editorial), 193 – 197, 259 – 263).  Ever since we could knock out by placing a PTC early (near the 5′ end) of the gene we’ve been surprised by some of the results –e.g. knocking out some genes thought to be crucial had little or no effect.  Other technologies which didn’t affect the gene, but which decreased the expression of the mRNA (such as RNA interference, aka Post-Transcriptional gene silencing — PTGS) did have big phenotypic effects.

This turns out to be due NITC, which turns out to be due to increased transcription of genes which are ancestrally related to the mutant. Gene.  Hard to believe.

Time to go back to NMD.  It doesn’t break mRNA down nucleotide by nucleotide, but fragments it.  These fragments get into the nucleus, and bind to complementary genomic sequences of the PTC gene, and also to genes ancestrally related to the mutant gene (so they’ll have similar nucleotide sequences). Then epigenetics takes over because the fragments recruit the COMPASS complex which catalyzes the formation of H3K4Me3 which is part of the histone code which helps turn on transcription of the gene.  The sequence similarity of ancestrally related genes, allows them and only them to be turned on by NITC.  Even cleverer than finding a PTC by the ribosome.

Something so incredible needs evidence.  Well heterozygotic zebrafish can bemade to have one normal gene and one with a PTC. What do you think happens?  The normal gene is upregulated (e.g. more is made).  Pretty good.

Finally the Mdx mouse.  I’ve been reading about it for years.  It has a PTC in exon 23 of the dystrophin gene, resulting in a protein only 27% as long as it should be.  All sorts of therapeutic maneuvers have been tried on it.  Now any drug development chemist will tell you that animal models are lousy, but they’re all we’ve got.

The remarkable thing about the mdx mouse, is that they don’t get weak.  They do have muscle pathology.  All the verbiage above probably explains why.

So to treat ALL forms of Duchenne put in a premature termination codon (PTC) in exon #23 of the human gene. It should work as there are  4 dystrophin related proteins scattered around the genome — their names are — utrophin, dystrophin related protein 2 (DRP2), alpha dystrobrevin, and beta dystrobrevin

There is an even better way to look for a place to put a PTC in the dystrophin gene.  Our genomes are filled with errors — for details see — https://luysii.wordpress.com/2018/05/01/how-badly-are-thy-genomes-oh-humanity-take-ii/.

There are lots of very normal people around with supposedly lethal mutations (including PTCs) in their genomes.  Probably scattered about various labs are at least 1,000,000 exome sequences in presumably normal people.  I’m not sure how much clinical information about them is available (other than that they are normal).  Hopeful their sex is.  Look at the dystrophin gene of normal males (females can be perfectly healthy carrying a mutant dystrophin gene as it is found on the X chromosome and they have 2) and see if PTCs are to be found.  You can’t have a better animal model than that.

At over 1,000 words this is the longest post I’ve written, and hopefully the most useful.

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Why drug discovery is so hard (particularly in the brain): Reason #28: The brain processes its introns very differently

Useful drug discovery for neurologic and psychiatric disease is nearly at a standstill. It isn’t for want of trying by basic researchers and big and small pharma. A recent excellent review [ Neuron vol. 87 pp. 14 – 27 ’15 ] helps explain why. In short, the brain processes its protein coding genes rather differently.

This post assumes you know what introns, exons and alternate splicing are. For pretty much all the needed background see the following.

First: https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/
Second:https://luysii.wordpress.com/2010/07/11/molecular-biology-survival-guide-for-chemists-ii-what-dna-is-transcribed-into/

When splicing first came out I started making a list of proteins which were alternatively spliced. It is now safe to assume that any gene containing introns (95% of all protein coding genes [ Proc. Natl. Acad. Sci. vol. 112 pp. 17985 – 17990 ’08 ]) results in several protein products due to alternative splicing. The products produced vary from tissue to tissue, probably because most tissues express different splicing regulators.

Here are a few. A2BP1 (aka Rbfox1, aka FOX1) is a brain specific RNA splicing factor found only in postmitotic terminally differentiated neurons. It is deleted in 10% of glioblastomas. Another is nSR100 (neural Specific Related protein of 100 kiloDaltons) — see later.

To show how crucial alternative splicing is for the every existence of the brain, consider this. The neuronal splicing regulator PTBP2 is barely expressed in most tissues. It is upregulated in neurons. Both PTBP1 and PTBP2 are repressors of neural alternative splicing (but some genes are actually enhanced). In a given region of the brain either PTPB1 or PTBP2 is expressed (but not both). PTBP1 promotes skiping of a neural specific exon (exon #10) in PTBP2 transcripts. This exposes a premature termination codon in PTBP2 leading to nonsense mediated decay (NMD). PTPB1 is expressed in most nonNeural tissues and neural precursor cells, but is silenced in developing neurons by the microRNA miR-124. The mRNA for PTBP2 contains an alternative exon which triggers nonsense mediated decay (NMD) when skipped. Inclusion of the exon requires positive transacting factors such as nSR100 in neurons. Repression is mediated by PTBP1 in undifferentiation. microRNAs (which ones?) downregulate PTBP1 during neuronal differentiation, relieving the negative regulation of PTBP2. Depletion of PTBP1 in fibroblasts is enough for PTBP2 induction and neuronal transdifferentiation.

It gets more complicated still. PTBP1 inhibits splicing of introns at the 3′ end of some genes involved in presynaptic function. This results in nuclear retention and turnover via components of the nuclear RNA surveillance machinery. As PTBP1 is downregulated during neuronal differentiation, the target introns are spliced out and the mature mRNAs are found.

Now we get to microExons, something unknown until 2014. For more details see — https://luysii.wordpress.com/2015/01/04/microexons-great-new-drugable-targets/.
Briefly, microexons are defined as exons containing 50 nucleotides or less (the paper says 3 – 27 nucleotides). They have been overlooked, partially because their short length makes them computationally difficult to find. Also few bothered to look for them as they were thought to be unfavorable for splicing because they were too short to contain exonic splicing enhancers. They are so short that it was thought that the splicing machinery (which is huge) couldn’t physically assemble at both the 3′ and 5′ splice sites. So much for theory, they’re out there.

The inclusion in the final transcript of most identified neural microExons is regulated by a brain specific factor nSR100 (neural specific SR related protein of 100 kiloDaltons)/SRRM4 which binds to intronic enhancer UGC motifs close to the 3′ splice sites, resulting in their inclusion. They are ‘enhanced’ by tissue specific RBFox proteins. nSR100 is said to be reduced in Autism Spectrum Disorder (really? all? some?). nSR100 is strongly coexpressed in the developing human brain in a gene network module M2 which is enriched for rare de novo ASD assciated mutations.

MicroExons are enriched for lengths which are multiples of 3 nucleotides. Recall that every 3 nucleotides in mRNA codes for an amino acid. This implies strong selection pressure was used to preserve reading frames as 3n+1 and 3n+2 produce a frameshift. The microExons are enriched in charged amino acids. Most microExons show high inclusion at late stages of neuronal differentiation in genes associated with axon formation and synapse function. A neural specific microExon in Protrudin/Zfyve27 increases its interation with Vessicale Associated membrane protein associated Protein VAP) and to promote neurite outgrowth.

[ Proc. Natl. Acad. Sci. vol. 112 pp. 3445 – 3450 ’15 ] Deep mRNA sequencing of mouse cerebral cortex expanded the list of alternative splicing events TENfold and showed that 72% of multiexon genes express multiple splice variants. Among the newly discovered alternatively spliced exon are 1,104 exons involved in nonsense mediated decay (NMD). THey are enriched in RNA binding proteins including splicing factors. Another set of alternatively spliced NMD exons is found in genes coding for chromatin regulators. Conservation of NMD exons is found in lower vertebrates, but those involving chromatin regulators are found later into the mammalian lineage. So the transcriptome in the brain is even more complicated.

A bit more about the actual effects on protein structure of alternate splicing. The sites chosen for this aren’t random. Cell and tissue differentially regulated alternative splicing events are significantly UNDERrepresented in functionally defined folded domains in proteins, they are enriched in regions of protein disorder that typically are surface accessible and embed short linear interaction motifs (with other proteins and ligands). Among a set of analyzed neural specific exons enriched in disordered regions, 1/3 promoted or disrupted interactions with partner proteins. So regulated exon splicing might specify tissue and cell type specific protein interaction networks. They regard their inclusion/exclusion as protein surface microsurgery.

How much can a little microexon do to protein function? Here’s an example of a 6 nucleotide microexon (two amino acids). Insertion of the microExon in the nuclear adaptor protein Apbb1 enhances its interaction with Kat5/Tip60 a histone deacetylase. The microExon adds Arginine and Glutamic acid to a phosphotyrosine binding domain (PTB domain) which binds Kat4. This enhances binding.

Had enough? The complexity is staggering and I haven’t even talked about recursive splicing — that’s for another post, but here’s a reference if you can’t wait — [ Nature vol. 521 pp. 300 – 301, 371 – 375, 376 – 379 ’15 ]. Pity the drug chemist figuring out which alternatively spliced form of a brain protein to attack (particularly if it hasn’t been studied for microExons).