cystic fibrosis

Cystic Fibrosis: What do all these mutations do?

It’s May, which means it’s Cystic Fibrosis Awareness Month! I’m excited to share more about the science behind CF with you all. Let me know what you want to hear about this month and beyond!

Many of you probably know that cystic fibrosis is a genetic disease, but what does that mean? What’s a genetic mutation? What effect do all these mutations have? What do the mutations have to do with the fancy new drugs that are out now? Today, we’re going to go to biology class. It’ll be fun.

Biology 101

Let’s imagine that we have a cookie factory. See? Already fun! In this cookie factory, there is a control room that contains all of our recipes for the different cookies we’re going to make. The factory workers have to take each recipe down to the factory floor, but we don’t want to risk ruining the master copy of the recipe. Instead, the factory workers make a copy of the recipe and carry that copy to the floor. If the copy gets ruined, no big deal, we can make another one. The recipe then gets turned in to our different kinds of cookies.

To bring this back to biology, in this analogy our cookie factory is a cell of our body. A cell is a building block of our body, like bricks of a house. The control room is the nucleus, which is a compartment inside the cell. The nucleus holds DNA, which is like the recipe book or instruction book for everything that your body does. Your DNA recipe really does stay inside your nucleus to keep it safe, and it does get copied into something called RNA. The RNA, instead of getting turned into cookies, gets turned into proteins. Protein isn’t a good hunk of meat – rather, you can think of proteins as little tiny machines that do all kinds of jobs like making our muscles move, breaking down our food, carrying cargo around our cells, and deciding what comes in and out of our cells. One protein that helps transport material in and out of cells is called CFTR. This is the protein that is “broken” in CF. The way you can think of this transport process is that CFTR acts like a gate in a fence on a farm. Its job is to open and close for the cows on the farm. It should only open for the right cows at the right time. In CF, this goes wrong.

Mutation Classes

In CF, there is a misspelling somewhere in the DNA that codes for the CFTR gene, or recipe (which will ultimately make CFTR RNA, which will then make CFTR protein). That’s what it means to have a genetic mutation. We divide these misspellings or mutations into 6 general categories:

Classes of CFTR mutations – Distribution of CFTR mutations into ...

The little green blobs are our CFTR protein “gates.” The job of CFTR is to move chloride (Cl-) in and out of the cell, but just think of those little Cl- as cows. You can see on the far left that in normal people, you have plenty of CFTR gates and they’re really good at moving chloride cows – no problems here. That’s not the case for people with CF. Let’s go through each of the 6 mutation classes:

  1. A class 1 mutation is called a stop mutation. Somewhere in the recipe, there’s an error that says “stop reading. stop copying this.” So the RNA does get made, but the translator who is supposed to make the CFTR gate just quits. They might quit halfway through, they might quit 3/4 of the way through; it depends on where the “stop” instruction is. In a stop mutation no CFTR gate ends up getting made most of the time, and as you can see, that means that there isn’t any gate to let chloride cows move in or out of the cell.
  2. A class 2 mutation has a misspelling somewhere; some kind of typo. The result of this misspelling is usually that even though the CFTR gate gets made, the typo gets carried all the way through and there’s an error in the construction of the gate. It’s usually not a very good gate and isn’t put together correctly. A lot of the time, that means that the cell inspects the gate and says “oh wow. We did a very bad job making this gate. This doesn’t mean our quality control standards. Gotta throw this one out.” On the off chance that the cell quality control allows the gate through to try to perform as a cow gate, it’s just not a very good gate. It’s not very good at opening and it might not stay in the fence for very long before it falls apart.
  3. A class 3 mutation is a typo just like class 2, but the effect of the typo is a little different. In this case, the gate is put together ok, but it just doesn’t work. So the cell allows it to get through the quality control mechanism, but when the gate is installed in the fence, it just…doesn’t really do anything. Think of it as being locked shut.
  4. A class 4 mutation is, again, a typo. But in this case, the gate is made ok, and it actually does open and shut a little. It’s not completely useless – it just doesn’t open and shut as much as it should.
  5. Class 5 mutations can have multiple causes, so let’s talk about the effect first. The protein that is made from a class 5 mutation actually works ok usually – the gate is good and it opens and closes pretty well. However, there aren’t enough gates made, so enough cows still can’t get in and out. So why would that happen? One reason could be, again, a typo. The recipe typo could mean that somewhere along the line, the cell just doesn’t do a good job building the gate and we lose more than we should during the gate building process. But another way would be if the mutation is what we call a splicing mutation. Going back to our recipe book, all the mutations we’ve been talking about are inside the recipes themselves. But sometimes a mutation is actually in the space between the recipe chapters; in our DNA, there is sequence that to us looks random, but to our cells is definitely not random. So if we have a gene (remember: a DNA gene is translated to RNA, which is turned into protein), that gene is actually made of multiple chapters which we know how to read, and in between those chapters is “nonsense” sequence that we don’t know how to read. When the DNA gets copied to RNA, the chapters which we know how to read have to be bound together and the “nonsense” sequence gets left out. But the “nonsense” sequence is still important, and it turns out that it contains instructions about how to bind chapters together. So, if you have a mutation in the “nonsense” sequence, then your chapter binding might not be very good. That means that down the line, you’ll get less RNA and less protein, so you’ll get less gate in the fence and fewer cows going in and out. Even though you have a perfect gate, there just isn’t enough of it.
  6. Class 6 mutations are typos that result in unstable proteins. That might mean that you make a gate that kind of works, but when it gets put in the fence it just doesn’t stick around very long, so even though some cows pass through, there just aren’t enough that pass through.

Do mutations correlate with disease severity?

When I was born in 1994, we only knew about maybe 5-10 different CFTR mutations or recipe typos. Now, we know about more than 1500. In recent years as we have learned more about how these different mutations affect how the protein works. This is very important for scientists to understand as we are discovering drugs that actually are targeted to the CFTR protein, which I’ll discuss next. It has also, naturally, led to a discussion about whether the different mutations lead to more or less severe disease.

The short answer is: yes. The longer answer is: it’s complicated.

Before I go into more detail, I want to say this: to any new parent or anyone trying to learn about their mutations, I don’t want you to think that your individual mutation defines your disease. I have seen too many stories about “severe cystic fibrosis strains.” There are general trends with some of these mutations, but we have a lot of control with how well we do our treatments, how good our doctors are, how much we exercise, etc. I myself have two “severe” mutations but am 26 with over 90% lung function (and was in the 80s before even Orkambi). Having “severe” mutations has ended up being an advantage because a lot of the personalized medicine research has gone to more severe mutations and has resulted in our being eligible for the latest and greatest therapies. And finally, 90% of us have the same “severe” mutation but we do not all have the same outcome. Mutations do not define our outcomes!

Ok, so what are the trends?

You may have noticed that as I went from class 1 up to 6, it sounded like the mutations were less bad/severe and that’s exactly right. Having no protein at all is generally worse than having some working protein. This is a nice study that looked a people who had two copies of the same mutation (remember: for every gene, we get one copy from Mom and one from Dad. So for our CFTR gene, if we have CF we could have the same mutation for each copy of that gene or two different mutations. For instance, I have the same mutation on each of my copies.). The study wanted to know whether there was any correlation between the amount of function of the CFTR protein – that is, how well that gate let the cows through – and how healthy the CF patients were. They found that the more functional the protein was, the better the patients’ lung function, pancreas function, and sweat chloride (how salty our sweat is, which is how we diagnose CF) were. In other words, yes, mutation severity did correlate with disease outcome. This study also found that more severe mutations increased the risk of developing cystic fibrosis related diabetes.

So that is what the data tells us: when we look at lots of people, we do see that if you have a CFTR gate that works better, your experience with CF will be that you have milder disease.

I want to, again, push back against this idea just on the individual level. Roughly 90% of people with CF have 1 or 2 copies of a class 2, “severe” mutation called dF508. In other words, most people with CF have a severe mutation. And yet, there is a very wide spectrum of severity and experience with this disease and we really cannot predict exactly what any one person is going to experience based on mutation alone. There are other factors in play that we don’t fully understand. As the saying goes, “If you’ve met one person with CF, you’ve met one person with CF.” I’ll get off my soapbox now, but I really don’t want anyone to take away the idea that their mutation is going to dictate their disease path because we do have a lot of control.

How does my mutation dictate drug eligibility?

When I was growing up, everybody with CF took the same drugs. Genetic mutation didn’t come into the picture – it didn’t matter. But today, we have drugs that are designed to target a specific kind of broken protein, and so the way that your gate is broken matters. What are these drugs?

Kalydeco: This drug has been approved for quite some time now – since 2012 – for some class 5 mutations, those ones where the gate is in the fence but it’s kind of stuck shut. Think of Kalydeco like WD-40; it helps get that gate opening properly so that the cows can come in and out. Only about 4-6% of people with CF actually have the right mutations that lead to proteins that are broken in the right way for Kalydeco to work.

Orkambi: Orkambi is a combination of 2 drugs, Kalydeco and one called lumacaftor. This is for people with my mutation, dF508, so a class 2 mutation. You have to have 2 copies of dF508 to take Orkambi (about 50% of patients).. Lumacaftor is kind of like glue; it holds the gate together so that the cell quality control workers won’t throw it away. That way the gate gets put into the fence so that the Kalydeco WD-40 can make it open and shut. Orkambi was approved in 2015.

Symdeko: Symdeko, like Orkambi, is a combination of 2 drugs, Kalydeco and tezacaftor. Symdeko kind of replaced Orkambi because it has fewer side effects, but it works in the same way at the cell level. It also works a little bit better than Orkambi, so more gate gets to the fence. It is approved for people with 2 copies of dF508 like Orkambi, but there are some mutations other than dF508 that are eligible for Symdeko. Symdeko was approved in 2018.

Trikafta: You can read much more about Trikafta here and here, but Trikafta is Symdeko plus elexacaftor – three drugs. Elexacaftor is also like superglue, so it works together with tezacaftor to really hold the gate together. It was necessary to get both of those drugs in combination because tezacaftor alone just wasn’t working well enough to see a big enough effect. With all 3 of these drugs combined, we get quite a lot of CFTR gate into the fence and it makes a big difference in how well the drug works. Because this drug combination works so well, people with only one copy of dF508 are also eligible for taking Trikafta, not just people with 2 copies. We also hope and expect that people with other class 2 and maybe other classes of mutation will be eligible soon – maybe 2020, maybe 2021 – for taking Trikafta. Trikafta was approved in 2019 and will ultimately be available for ~90% of patients.

These are drugs that are currently approved, but there are also some drugs that are in development that I want to mention that get at the root cause of CF. There are also several other Trikafta-type drugs in development to give people more options in that space to 1) try to make a better Trikafta, 2) try to expand these types of drugs to other mutations, and 3) give people more options if Trikafta has intolerable side effects or just doesn’t work that well for them.

Eloxx Pharmaceuticals: Eloxx is developing a drug for class 1, or stop, mutations. Remember, these are the ones that tell the cell to just quit bothering to translate the RNA recipe into protein. Eloxx is making a drug to say no, keep going, ignore the stop message. They are in human trials. Eloxx has decided to very carefully study 1 mutation at a time, but it is my understanding that they believe their drug will work for multiple different stop mutations.

Translate Bio: this will not be a mutation-specific therapy. The approach that Translate is taking is a little different than everything else we’ve talked about today, and it is really exciting. Everything that I’ve talked about so far is to basically take something broken and try to make it less broken. We have been quite successful in this approach! But Translate is going one level up, to the RNA level – remember, the recipe copy. Translate is not trying to fix our recipe copies (though that is also something that a different company is doing). Instead, they just want to replace it. They have made an inhaled therapy where we will inhale a normal copy of CFTR RNA so that we’ll have a good copy of the gate recipe instead of trying to fix something broken. It’s exciting to have a therapy that could work for everyone instead of these therapies that stratify us by our different mutations. One disadvantage of this approach is that it will only work for the lungs and maybe the sinuses, but it still could be a great step forward and I’m excited to see the next set of results when they come out.

I hope you’ve learned something about how DNA, RNA, and protein fit together, what happens when CFTR is mutated, how the new CFTR-targeted drugs work, and what’s coming in the next few years in CF therapies. I’m always happy to answer questions and I hope that any new CF parents – and anyone with CF – can see that this is a very hopeful time in the CF community!

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