I have heard some confusion around patients with Dravet syndrome who have missense mutations in SCN1A: are they candidate for the genetic therapies currently in trials or are they excluded from the trials?
The short answer is “Patients with Dravet syndrome caused by missense mutations in SCN1A are candidates for the clinical trials with ASOs and gene therapies to increase SCN1A expression, and will be candidate for this therapies after approval”. The rest of this entry is the longer answer.
What is a haploinsufficiency
If you have a child with Dravet syndrome with a mutation in SCN1A, as most cases have, you might have heard the word “haploinsufficiency”. Haplo means “single” in greek, as opposed to couple or two, so haplo-insufficiency applied to genetics means that they have insufficient copies of that gene because they have a single one, as opposed to two functional copies which is the default for most genes.
In the case of Dravet syndrome caused by mutations in SCN1A, the person has one good gene copy and one bad copy (due to mutations), which leads to no functional protein being produced from that back copy. That leaves them with 50% of the number of good sodium channels Nav1.1 that their neurons need. They have only half of what is sufficient.
The reason I am writing this entry is that we often describe Dravet syndrome as a protein haploinsufficiency, as if patients only had 50% of the sodium channels. But this is a simplification that can worry families of patients with missense mutations who actually have 100% of the sodium channels…. But half of those don´t work.
We also often use mouse models for the disease where indeed only 50% of protein is produced because they have one good copy of SCN1A and one copy that makes no protein. So we think that this is what always happens, they produce only half of the numbers of sodium channels that they need. The consequence, by the way, is less sodium then running through the neuron membrane and less neuron firing. And it is very intuitive to understand that the gene therapies and other genetic treatments will try to bring expression “back to 100%” to help neurons function well.
We often explain Dravet syndrome as only having 50% of the Nav1.1 sodium channels
But what about missense mutations then?
There are many patients with Dravet syndrome that have a mutation of a type called “missense”, the one that doesn’t break the gene, but instead gives you a mistake in the sequence for the sodium channel protein, so that it will have one wrong letter. So you still probably produce 100% of the sodium channels, but only half of them works. The consequence is exactly the same as if the non-functional channels were not even there, it results in less sodium running through the neuron membrane and less neuron firing. But families and even some scientists worry that these patients cannot get the genetic treatments that increase expression of the gene because it will increase both the good and the bad copies. But it doesn’t matter in Dravet syndrome. The bad copies are not “bad” as in doing something bad, they are just useless. In science we call them “loss of function”, they really don’t work, they have lost their function.
I call these cases “functional haploinsufficiencies”. Yes they still produce channels from the bad copy, but these are no longer functional, so when it comes to functional sodium channels they still have half of the ones they needed.
I always understand better if it is in visual form. So I will adapt one of my old cartoons where I pictured the sodium channel as a door in the membrane that lets sodium come in. I am also guilty of only drawing the 50% of protein being produced scenario, which is true for mutations that break the gene and make no protein. But I never draw the missense scenario, where the number of doors for sodium is still fine but half of them are closed. The result is functionally the same: the neuron only has half of the doors that it needs to get enough sodium in. It doesn’t matter if the other half of the doors are missing or closed. It really doesn’t matter.
Missense mutations still result in only half of the sodium channels (the sodium doors) being functional
For me the door visual makes it much easier to understand why the different types of mutation result in the same biological protein. It is like everyone trying to leave a concert at once and having only half of the doors that could handle that many people. It doesn’t matter if the other half of the doors don’t exit or are shut, the result is the same, not enough usable doors.
By the way years ago we made a Dravet mouse model with a missense mutation that has been seen in several patients. And we then looked at what happened to that channel: it is produce and nicely sits in the neuron membrane as it should, but it remains closed at voltages where the good channels open to let sodium in. In door terms, there is no problem in the number of doors, the mutant ones are just closed all the time, and therefore as useless as if they were missing.
Why is this important for clinical trials?
There are currently two therapies in clinical trials for Dravet syndrome that are designed to increase expression of the sodium channel Nav1.1 by increasing the production of protein (the channel) from the SCN1A gene.
The most advanced therapy does this by using a small piece of RNA called an “antisense oligonucleotide” or ASO for short. It is the drug zorevunersen from Stoke Therapeutics (also known as STK-001). The second one is a gene therapy that uses a virus to bring to neurons the instructions to read the SCN1A gene more. It is called ETX101, from Encoded Therapeutics. I won’t get into the science details, you just need to know that both are currently in clinical trials for patients with Dravet syndrome caused by mutations in SCN1A, and both work by ending up in an increase of good sodium channels (opened doors at the concert).
Both clinical trials accept patients with the two types of loss of function mutations in SCN1A, including the missense. They are not only for patients that have mutations that break the SCN1A gene (nonsense, frameshift, gene deletions). That is a misunderstanding that worries families and the reason for this post.
ETX101 trials asks for “Participant must have a predicted loss of function pathogenic or likely pathogenic SCN1A variant.”
Zorevunersen trials asks for “Documented pathogenic, likely pathogenic variant, or variant of uncertain significance in the SCN1A gene associated with DS”. By the way this trial is not currently enrolling, they finished their Phase 2 trials and are preparing for the Phase 3.
Also VERY important, the large Phase 1/2 trial with zorevunersen is completed, showed safety and efficacy in the patients treated with the genetic drug, and the company has publicly explained that even though they don’t have enough patients to mathematically compare missense versus the other mutations, there doesn’t seem to be any signal that the missense patients don’t respond to this treatment. In this trial they had 45% of patients with missense mutations, and 55% with truncating mutations which are the ones that make no protein from that gene copy.
So it is not true that clinical trials to upregulate expression of SCN1A are only for patients with truncation mutations. But what about safety?
Another worry by scientists has been that the brain won’t handle having 200% of sodium channels (of doors), that it will be dangerous. But the science to support this belief is not there, and in fact both companies had to evaluate their genetic therapies in healthy non-human primates (monkeys) who don’t have Dravet syndrome and therefore have their two GOOD copies of SCN1A, and to show that their therapies increase the production of sodium channels and the monkeys are still fine. Companies need to prove this before getting permission to run trials in patients. So monkeys are fine with 150-200% or more of open doors (letting more sodium in!), which means that we don’t have worries for patients going from 50% of open doors to hopefully 100% of open doors. The extra closed doors, if they have missense mutations of the type that results in protein being made but not functional, are really not a problem.
Gene therapies and ASOs that increase expression from the SCN1A gene or mRNA are also in trials for patients with missense mutations in SCN1A
IN CONCLUSSION
Patients with Dravet syndrome caused by missense mutations in SCN1A are candidates for the clinical trials with ASOs and gene therapies to increase SCN1A expression, and will be candidate for this therapies after approval.