Different mutations and their effects

In my last post I looked at a common mutation that causes deafness: the c.35DelG mutation. This type of mutation, where one of the DNA letters just goes missing, is called a 'frameshift deletion' mutation. Another one, 235DelC, is quite common among Asians and has pretty much the same effect.

Let's pretend that, instead of being a majestic molecule that encodes the very essence of life itself, DNA is a drab children's book. It still is only read as 3 letter words (remember codons). And it has the following line:

Pat and Ann ate ham and ran off

A frameshift mutation might delete a letter and give the following:

Pat and Ann ate ama ndr ano ffa

The sentence is now meaningless, just like the protein that such a mutation creates. But instead of deleting a letter, you could swap it with a different one:

Pat and Ann ate Pam and ran off

You know have a sentence with very different, and sinister, meaning. What are we subjecting our poor kids to? It's function has changed, and this is what happens with DNA - these mutations create proteins that do something, just not what they are meant to do.

Swapping one letter of DNA for another is called a missense mutation. When this happens with Connexin 26, you can get other problems as well as deafness. This is called Syndromic hearing loss.

The picture below shows the Connexin 26 molecule. Each of the coloured circles with a letter represents an amino acid. Scientists have noticed mutations that change a lot of different parts of the molecule. The ones that change the blue circles just cause deafness. But at the yellow parts, the mutations cause other problems too - mostly skin disorders, because that's where Cx26 is most active. And these tend to be missense mutations.

The skin problems can be severe, and can sometimes lead to loss of blood flow to fingers and toes, causing them to drop off, or to blindness.

But if these Cx26 mutations have such a big effect on skin, why does not having Cx26 leave your skin perfectly fine?

Scientists aren't sure, but they suspect it is because of 'gain of function'. The missense mutations mean that the Connexin 26 does things it isn't supposed to do. In this case it is likely it is letting more chemicals pass between cells, which might cause to much skin to grow (hyperkeratosis).

If there are no working Cx26, the skin doesn't seem to have any problems. They reckon this is because there are other Connexin proteins (like Cx30 or Cx43) that do more or less the same thing - you have redundancy there that isn't in the ear for some reason. It is possible that the missense Cx26 molecules also interfere with these other guys and stop them working properly. In genetics this is called Trans-dominance, where a mutated protein prevents healthy proteins from doing their job.

I wrote before about how Connexin molecules bunch together in groups of 6 to form the channels that connect cells. These aren't always the same Connexin molecules - Cx26 might combine with Cx30 or Cx43. These would give different channels, that let different molecules pass through. It might be that a mutated Cx26 is too eager to join up with these other Cx molecules. All the Cx43 and Cx30 proteins join up with the broken Cx26, instead of making their own channels that the skin needs.

So in this case, having a slightly-changed version of Cx26 can be worse than having none at all.

Most of this comes from a paper by Jack Lee & Thomas White, you can read it here if you fancy.
And if you want to know more about different mutation types here is a good guide.

More on mutations

So I know both of my son's GJB2 genes have mutations. What does this mean on a molecular level? Do his cells not make Connexin 26 at all? Or do they all come out wonky?

It seems that this depends on the mutation. And surprisingly enough, having wonky Cx 26 proteins might cause more problems than having none at all.

Genetics is a field of science which still holds a lot of mysteries, despite the fact that all DNA is made of just 4 chemicals. These are called A, G, C, T (for Adenine, Guanine, Cytosine, Thymine), and the whole genetic code for a person can be stored as a (rather large) collection of books with those 4 letters repeated again and again. 

Three of these letters together (called a codon) are enough to send a message to your cells. In fact that seems to be how the DNA is read, three letters at a time. Just like how a computer reads bytes, which is a group of eight 1s or 0s. There are 64 different 3-letter combos (4 x 4 x 4). 61 of these create molecules (amino acids) and the other 3 mark the end of a protein.

You can also think of it in terms of lego. Each codon (three letters) causes the cell to make a different brick, these all stick together in a specific way until you finish with your toy. Except the bricks are called amino acids and the toys are proteins. 

The c.35DelG that I carry is the most common mutation associated with hearing loss. Its ugly name actually describes a lot about it. The 'c' at the start means its a mutation in coding DNA  - this is DNA that is used specifically for making proteins. 'Del' means something has been deleted. In this case it's a Guanine, hence the 'G'. The 35 tells us where the deletion is - 35 codons in.
This turns the 35th codon into something called a stop codon - a 3 letter combo that basically tells your cell to stop making this protein. So it ends up just making the first part of Cx26, then stops.
This picture probably shows what normal Cx26 looks like:

And this one probably shows what my mutated Cx26 looks like:

Fairly shite isn't it? Looks like it does feck all. It is in fact completely useless. Mutations like this, that leave the protein doing nothing, are called 'knock out' mutations. Knock-out mutations in Cx26 seem to always cause hearing loss, with no other effects.
However different mutations can change how Cx26 works, and this leads to other issues. I'll look at this...... next time.


Terminology

• Nucleotide A molecule with a particular structure. The four building blocks of DNA (Adenine, Guanine, Cytosine, Thymine) are nucleotides.
• Codon A group of 3 nucleotides in a row on a DNA strand
• Amino Acid A molecule with a particular structure. They can be built through the use of codons and joined together to form proteins
• Protein One of the molecules constituting a large portion of the mass of every life form and necessary in the diet of all animals, composed of 20 or more amino acids linked into one or more long chains. Proteins include such specialized forms as collagen for supportive tissue, hemoglobin for transport, antibodies for immune defense, and enzymes for metabolism

Cx-Men: Rise of the mutants

Connexin 26 mutations are quite common in Caucasians. About 2% of the population carry them. As well as deafness, they can cause severe problems with skin, and in some cases blindness.  So why are they so common? Especially considering most of them are believed to be caused by a single person getting a mutation in the past, and passing it on (the Founder Effect).

Geneticists believe that for these mutations to be so common there must be some advantage to them. And they think they know of at least one. It's to do with the gap junctions; those paths that allow things to pass between cells, and are made from Connexin proteins. Turns out that sometimes it's better to keep the gates closed.

Ever since humans have been around, viruses and bacteria have been looking for new ways to attack us. Every single aspect of our physiology gets probed for weaknesses, or for some way them to get an advantage over our immune system. At least one of them, a diarrhea-causing bacteria called Shigella flexneri, manipulates gap junctions in our digestive tract to spread itself. And these gap junctions are made from Cx26.

It has been shown that people carrying Cx26 mutations are far more resistant to Shigellosis, the disease this bacteria causes. Shigellosis causes 700,000 deaths a year these days - imagine how bad it must have been before modern hygiene practices came along. Perhaps villages would be struck with a plague of Shigellosis , and only the carriers of mutated Cx26 genes would be left standing? A similar resistance has been seen for certain E. Coli infections, which cause similar intestinal problems and are extremely common. 

From a personal perspective, I rarely get any gastrointestinal illnesses. I had always assumed this was due to my parents' proclivity for foraging in the 'reduced to clear' aisles in Tesco's. The regular consumption of near-rancid meat had led to my steely constitution, or so I believed. Perhaps the true reason was my c.35delG GJB2 mutation.

Scientists have also noticed that people carrying Cx26 mutations tend to have thicker skin. It's not sure whether this provides an advantage, but skin is a barrier to infection, so who knows?

The theory that having one copy of seemingly bad genetic mutations can actually work out for you is called 'Heterozygote advantage'. For example, carriers of the mutation that causes Cystic Fibrosis are resistant to the effects of cholera, and carriers of the mutation that causes Sickle-cell anemia are resistant to Malaria. There's an article on it here if you want to know more.

Cx-Men: Origins

Mutations.
If it wasn't for mutations, we'd all still be bacteria, and my ability to type this would be severely hampered by my lack of appendages.

The GJB2 gene is the part of our DNA that creates the Connexin 26 protein. That's more or less what DNA is used for - instruction code for creating proteins. So how did my son ended up with a mutated version? Where did this mutation originate?

There's different versions of all the genes we have, which is why we are all different - for example, there are genes for blue eyes, brown eyes, grey eyes, also blonde hair, red hair, black hair, etc. Pretty much all of our physical characteristics are determined by genes, though environmental impacts have a role too, such as malnutrition, lack of exercise etc. As such there's no such thing as 'normal' and 'abnormal' genes - who decides what a 'normal' eye colour is? (some, such as Adolf Hitler, have tried). Geneticists refer to the more common functioning genes as 'wild' type, and the less common, possibly non-functional genes as mutants.

We inherit two versions of all of our genes, one from each parent. I have one 'wild' type GJB2 gene, and one with a specific mutation called c.35delG, which probably came from my mother. So does my wife. The c.35delG mutation is 'recessive'. That means you need two copies of it for it to have a notable impact. The single 'wild' GJB2 gene I have can create enough Cx26 for my hearing to work - though I could probably do with a bit more. So I carry the deafness-causing mutation, but I'm not actually deaf.

So where did this c.35delG mutation originate? There are over 300 different variations of the GJB2 gene, and most of these are considered mutations. Some are more common among Asians, some among Caucasians, some among specific Jewish populations. The c.35delG is one of the most common causes of deafness among Caucasians (such as my family), but isn't seen much in other ethnic groups. Around 1 in 50 white people carry it.

There are two reasons the mutation could be so common. The first is the 'hot-spot' theory. This proposes that the structure of the GJB2 gene has a weakness that means it keeps breaking the same way, like the ways zips always break on cheap trousers. But this wouldn't explain why it's only common among white people. If it kept breaking like that, wouldn't it be common among Africans and Asians too?

A more likely cause is what's known as the 'founder effect'. It basically says that all people carrying the mutation have a common ancestor - a single great-great-great....-great grandparent who somehow got a mutated copy of GJB2, had loads of kids and passed it on. Some geneticists think they know who here he or she was - or rather where they lived. Ancient Greece of all places, around 10,000 years ago. I think that's about 400 generations ago.

So if you have a c.35delG mutation, we are most likely related! Just like me and my wife. Though I guess everyone is related really when you think about it.

I knew very little about genetics when I started digging into this stuff. It's really fascinating, I found this book to be really good and accessible - The Gene: An Intimate History by Siddhartha Mukherjee. It's very accessible, I recommend a read of it if you have any interest.


Terminology
I'm going to start building a glossary in these blogs. I had to look up a lot of words when reading this stuff so I might save some of you the bother.

• Heterozygous This means you have one copy of a particular gene. Both me and my wife are heterozygous for the c.35delG mutation. 
• Homozygous This means you have two copies of a particular gene. My son is homozygous for the c.35delG mutation
• Genotype  The particular type of gene you have. My sons' genotype would be 35delG/35delG for the GJB2 gene
• Phenotype Your characteristic that are caused by a particular genotype. One phenotype of the 35delG/35delG mutated GJB2 genes is typically deafness
• Allele A particular form of a gene. The 35delG mutation is an allele of the GJB2 gene.[I often write gene where I should have written allele, mainly because most people don't know what an allele is.]

The Inner Ear Battery and Cx26

So much for weekly updates! In my last blog entry (51 weeks ago) I wrote about how the Connexin 26 protein was used to make Gap Junctions, which in turn allow things to pass between cells. But I wasn't really sure of the role they had in hearing. I thought it might be to do with allowing electrical signals to pass between cells. Turns out I may have been wrong 😲.

I've done a bit more reading in the year since. turns out these so-called experts don't really know. There's a few theories out there though. Some researchers now think that the main role of Cx26 in hearing is to do with the Potassium cycle, and the Inner Ear Battery.

Part of the ear acts like a big battery. The energy from this battery is used to turn small hair vibrations into big electrical pulses that the brain converts to our perception of sound. The charge in the 'ear battery' is carried by Potassium ions. The theory is that without Cx26, the Potassium ions build up in the hair cells, and they die.

Potassium ions are usually referred to as K+. (K is the atomic symbol for Potassium, and the + means it has a positive charge because it is missing an electron). There is a membrane in the ear, one one side you have lots of K+, the other side has less. The K+ wants to get to the side with less. This happens when you hear something, and it causes the Voltage across that membrane to change. This change in voltage drives a signal along the nerve cells to the brain.

The process of how K+ gets across the membrane, and back again, is called the Potassium Cycle. K+ ions pass through the hair cells in the ear and back again. How exactly this happens is uncertain, but some think Gap junctions play a major role, specifically those built using Cx26, and possibly Cx30 as well.

I am not sure exactly why K+ build up causes the hair cells to die, maybe the charge form the ions interferes with other chemical reactions necessary for cell life. I have read that Cx mutations cause inner ear cells to die soon after the onset of hearing (while the fetus is still in the womb), so it doesn't take them long to die.

I'll finish on something cool - scientists have already tapped the 'ear battery' to get an electrical current, which was used to power electronics. Maybe one day they can use this to power hearing aids and cochlear implants. Read about it in the LA times

There you have it - more confused ramblings! If you want more authoritative info on the ear battery, check out this page from Baylor College of medicine. And if you want to know why I'm so confused check out this paper on Gap junctions and the Potassium Cycle