Kristine

SNPs, CNVs, and our mind-blowing genome

Before we get to SNPs and CNVs, let’s look at some wild facts about the human genome.

Here’s something that is hard to believe.

Ready? The DNA in any two humans is very, very similar – over 99.5% of it is exactly the same.

Wait, really?? YES! Really! (I’m not making this up; see Robbins, page 2).

(Also, our DNA is about 99% the same as chimpanzee DNA, which makes me uncomfortable for some reason.)

But back to the human DNA thing. This incredible genomic similarity between humans means that all our inherited human differences are encoded in less than 0.5% of our DNA. WOW.

So what kinds of variations exist in that tiny amount of DNA? The two most common DNA variations in the human genome are single-nucleotide polymorphisms and copy number variations.

Single-nucleotide polymorphisms (SNPs)

SNPs are DNA variations at one single nucleotide position. They are almost always biallelic, meaning that there are only two possible variant nucleotides in that place (say, A or T). Some SNPs are inherited along with a disease-associated gene (because they are close together on a chromosome) – so some SNPs might turn out to be disease markers.

Copy number variations (CNVs)

CNVs are variations in the number of big stretches of DNA (1000 base pairs to millions of base pairs). One person might have two copies of a particular stretch of DNA, and another person might have 10 copies. Many CNVs are located right in gene-coding regions – so they probably help generate some of the incredible phenotypic diversity that exists in humans.

Yikes. I’m still stuck on the chimp thing.

What’s the relationship between aneurysm, thrombosis, and stenosis?

I got this really great question from one of my students, and it got me thinking about how important it is to have really clear definitions of pathologic conditions. These three conditions – aneurysm, thrombosis, and stenosis – are totally different things. And yet they can sometimes co-occur, or one can cause another – so it can become confusing!

I thought I’d share the question and my answer here, because I’m sure there are other students who are having trouble understanding these disorders.

Here’s the question:

I was reviewing the Blood Vessel Pathology lecture notes from this past week and was having a bit of trouble differentiating between aneurysm, thrombosis and stenosis. I’ve written what I believe to be the differences, but would you mind giving me some feedback on if this is correct?

“An aneurysm is when a clot occurs, widening the blood vessel to unhealthy proportions due to high blood pressure and or atherosclerosis, and it may rupture with no warning signs, leading to internal bleeding. The difference between aneurysm and thrombosis is that aneurysm causes damage to the lining wall of the blood vessel. Thrombosis is clotting of a blood vessel without damage to the walls. Stenosis is narrowing of the artery to cause clotting, and it comes with the warning sign of severe chest pain.”

Great question!! You’re on the right track – but there are some things in your statement that aren’t quite right – so I’ll give you my definitions and then comment on what you wrote.

Aneurysm

An aneurysm is an abnormal widening (or dilation, or outpouching) of a blood vessel. It’s focal in nature, which means that it’s just in one place; you can point to where it is (it’s not like the entire vessel is just a little bit wider). Here’s an image of a normal vessel and a vessel with an aneurysm:

Aneurysms can be caused by lots of things (like trauma and atherosclerosis), or they can be congenital. Sometimes aneurysms just sit there and never cause any problems. But sometimes they get larger and larger, and the vessel wall weakens to the point where it eventually ruptures.

Thrombosis

A thrombosis (or thrombus) is an abnormal blood clot. It’s not just a normal little blood clot formed to repair a hole in a vessel – it’s a blood clot that’s been made when it isn’t needed. The most common place for a thrombus is in the deep veins of the legs – but you can form a thrombus anywhere in the body.

It’s not good to have a thrombus for a few reasons:

If it’s big enough, the thrombus can block blood flow through the vessel, and the tissues fed by that vessel can be damaged or even die as a result.
Thrombi can weaken and damage the vessel wall, leading to other problems (like aneurysms, or even rupture of the vessel if it gets weak enough).

Here’s a related term: embolus. An embolus is a blood clot that’s floating in the blood (maybe it broke off from a thrombus in the leg, or maybe it formed on its own somewhere). The point is that it is mobile, and it’s going to move with the blood until it gets to a vessel that’s too small for it to pass through, and it will lodge there. If the embolus is tiny, you may not notice anything clinically. But if the embolus is big enough to block off an important vessel (say, one of the vessels in the brain), that means that the tissue fed by that blood vessel won’t get blood, and it will die.

Stenosis

Stenosis just means “narrowing.” It can be used to describe abnormal narrowing of lots of different structures in the body (like heart valves and the spine). When a blood vessel is stenotic, that means its lumen is smaller than normal.

There are many possible causes of stenosis in vessels. Here are some common ones: atherosclerosis (formation of plaques that take up space and narrow the lumen), thrombosis (formation of an abnormal clot that takes up space within the vessel lumen), and vasculitis (inflammation of the vessel).

Like the other abnormalities we talked about above, stenosis can be asymptomatic if it is mild. But if a vessel is very stenotic (for example, if the vessel lumen is only 20% of its normal diameter), that can impair blood flow enough to cause serious problems to the tissue downstream. This is particularly a problem if the vessel feeds the heart or the brain; in these places, restriction of blood flow can cause severe symptoms (or even death).

Why these things are confusing

These three conditions are distinct and separate entities – but they can occur together, and they can also occur sequentially – and this can be confusing. For example, if you have a thrombus in a vessel, that can weaken the vessel wall enough to cause an aneurysm. Or you can have a thrombus that simply sits there and takes up space in the vessel lumen, causing stenosis of the vessel.

So the best way to approach this is to make sure you understand what each of these disorders is – and then once you have that down, you can go on to learn about what causes them and what they can lead to.

Back to the statement part of the question – my comments are in blue.

An aneurysm is when a clot occurs, widening the blood vessel to unhealthy proportions due to high blood pressure and or atherosclerosis, and it may rupture with no warning signs, leading to internal bleeding. You’re correct in saying that an aneurysm is a widening of a blood vessel that may be caused by high blood pressure or atherosclerosis, and that it may rupture. And it’s true that aneurysms can be caused by abnormal blood clots (thrombosis) – but just to clarify – not all aneurysms are caused by clots. The main point is that an aneurysm is an abnormal widening of a blood vessel – and there are many potential causes. The difference between aneurysm and thrombosis is that aneurysm causes damage to the lining wall of the blood vessel. Thrombosis is clotting of a blood vessel without damage to the walls. No; the difference between aneurysm and thrombosis is that an aneurysm is an abnormal dilation/widening of a blood vessel, whereas a thrombosis is a blood clot that forms within a blood vessel. Both aneurysms and thromboses can damage the vessel wall. Stenosis is narrowing of the artery Yes! to cause clotting Not exactly. Stenosis is just the narrowing of a vessel lumen; it doesn’t necessarily cause the formation of a blood clot. However, thrombosis (abnormal clotting) can lead to stenosis (narrowing of the vessel lumen)! This is where you have to be really strict about your definitions, otherwise it gets confusing! and it comes with the warning sign of severe chest pain Sometimes! If the stenotic vessel is one that supplies the heart, and if the stenosis is moderately severe (meaning that the lumen is narrowed enough to decrease the amount of blood that can flow through the vessel), then the patient will experience chest pain (because there’s less blood flow to the heart than usual). This is a warning sign – it tells you that the tissue isn’t getting quite enough blood flow, and you better go see a cardiologist and get those vessels looked at. However, if the stenosis is really severe (like if the lumen is only 10% of its normal diameter), then almost no blood is getting through, and that may be enough to actually cause tissue death (myocardial infarction, or heart attack). In this case, the chest pain the patient experiences isn’t just a warning sign – it’s a sign that the tissue is actually dying right now.

Does pyknosis occur in necrosis or apoptosis?

Q. Would a pyknotic cell be a form of necrosis or apoptosis? Or am I totally off base here?

A. No you’re totally not off base – that’s a really good question!!

We typically use the word “pyknosis” to mean one of the three nuclear patterns seen in necrotic cells…but pyknosis can also occur in apoptosis! I’ll explain a bit more.

When cells undergo necrosis, they show a lot of different morphologic abnormalities. Overall, necrotic cells appear enlarged and more eosinophilic, and their nuclei look abnormal due to breakdown of DNA. There are three specific patterns of nuclear change in necrosis, which are:

Pyknosis (the nucleus shrinks and becomes dark blue/black)
Karyorrhexis (the nucleus breaks apart, or fragments, like a cookie crumbling into bits)
Karyolysis (the nucleus just fades away)

Here’s a nice diagram I found (I modified it a bit from the original) showing these changes:
When cells undergo apoptosis, they also show a lot of different morphologic features. Overall, apoptotic cells appear shrunken, with really dense, dark, eosinophilic cytoplasm, and the chromatin in the nucleus aggregates into a dense mass which can fragment. Here’s a photo from Robbins showing an apoptotic cell:

The word “pyknosis” isn’t typically used when describing an apoptotic cell – but Robbins does say that pyknosis can be a feature of apoptotic cells, so there you go.

So…the bottom line is that pyknosis is a nuclear change in which the nucleus shrinks and becomes dark blue/black. Typically, we associate the word “pyknosis” with necrotic cells – but apoptotic cells can show pyknosis too.

How to study diseases

If you want to be precise, the word pathology means “the study (logos) of pain (pathos).” And it’s true, in a way, because a lot of the things we discuss in pathology involve some sort of pain. Not to mention the pain of studying pathology itself, but we won’t get into that, since this is a pain-free space.

What we really study in pathology isn’t pain, exactly, but disease. So if you’re starting out in a pathology course – or even if you’re halfway through – it’s not a bad idea to come up with a little plan of attack for studying diseases.

Why use a plan when learning new diseases?

Because it reduces your cognitive load. You have to hold and process information in your working memory before you can put it in your long-term memory. And your working memory has limited space! So if you approach every disease a different way, and just try to memorize everything, you won’t actually get that information into your long-term memory – and obviously, that’s important for passing exams.

But if you have a little mental template that you use for each disease, that organizes the information into smaller, meaningful chunks that WILL stay in your working memory. Also, if you do that for every disease, it lets your brain relax a bit, because your brain likes categories and consistency.

Here’s a good plan.

Here is a disease plan that works well for pathology because it’s simple, straightforward, and widely applicable. It breaks information down into four categories:

Etiology (cause)
Pathogenesis (mechanism)
Morphology (gross and microscopic appearance)
Clinical manifestations (signs and symptoms)

Can I see an example?

But of course! Let’s take a look at how this would work for a particular disease: squamous cell carcinoma of the lung.

Etiology: smoking
Pathogenesis: The epithelium of the lung passes through several stages – including dysplasia and carcinoma in situ – before developing into invasive carcinoma. Each stage is characterized by different and new genetic abnormalities within the epithelial cells.
Morphology: squamous cell carcinoma cells are large, with abundant cytoplasm and intercellular bridges.
Clinical manifestations: persistent cough and weight loss.

There you go! Obviously you’d want to flesh out these categories a bit more – but this would be a good start.

One last piece of advice

One more nice thing about this plan is that it helps you avoid the “can’t see the forest for the trees” problem so common when you’re first learning about a disease. This plagued me during medical school. I’d learn so much about tiny details that I couldn’t zoom out and give you a big picture. It’s better to start with the big picture and then add in details later.

Your brain will say “Thank you for reducing my cognitive load! I’m so happy!”

Is Factor V Leiden a Mendelian Disorder?

Here is a great question I got from a student about the genetics of Factor V Leiden.

Q. Factor V Leiden is autosomal dominant – but it doesn’t seem to follow Mendel’s laws. Would you say it shows incomplete dominance?

A. This is such a good question! Factor V Leiden is an autosomal dominant disease – and you’re right: it does NOT follow Mendelian laws. However, the non-Mendelian pattern it follows is not incomplete dominance, but incomplete penetrance.

First, here’s why Factor V Leiden is a non-Mendelian disorder.

Factor V Leiden is an autosomal dominant disease. If it followed Mendel’s laws, everyone who inherited ether one or two copies of the Factor V Leiden gene (which is the dominant gene) would display the same phenotype (in this case, they’d all have the same exact amount of abnormal clot formation). But that’s not how it works in this disease.

Patients with factor V Leiden have an increased risk of developing abnormal clots. But not everyone with an FVL gene (or even with two FVL genes) develops a clot! Some do, and some don’t. So the phenotype is not the same in everyone with the FVL gene.

So how would you describe this non-Mendelian weirdness?

This weird phenomenon is called incomplete penetrance.

In Mendel’s experiments, his dominant alleles showed complete penetrance. In other words, every plant with a genotype containing a dominant allele (or two!) always displayed the same phenotype.

But in real life, that’s not always the case – sometimes penetrance is not complete, and factor V Leiden is a good example. As we mentioned above, the factor V Leiden gene confers an increased risk of abnormal clotting – but that’s all it is, just a risk, not a certainty. So some patients with the FVL gene display the disease phenotype, and some do not.

Incomplete dominance is also a non-Mendelian pattern of gene expression – but it’s different than incomplete penetrance.

In Mendelian dominance, there are two alleles and two phenotypes. In the left image below, the two phenotypes are purple and white flower colors – and as long as you have at least one dominant allele (in this case, P), you’ll get a purple flower.

In incomplete dominance, there are two alleles and three phenotypes. In the right image below, the phenotypes are red, white, and pink flower colors. If you are homozygous for either the R or the W allele, you’ll get a red or a white flower. But if you have both the R and the W allele, you’ll get a “blend” of the two other phenotypes – a pink flower!