Evolutionary aspects of sickle cell anaemia.
BIO00074H: Advanced Topics in Evolution and Genetics in Ecology.
Updated 1/11/2021.
In this workshop we will learn about some of the molecular biology of SCD, and then think about the effects of this allele on evolution.
Learning Outcomes:
By the end of this session you will:
understand how changes at the DNA level change a protein, which has an emergent property as a phenotype
understand how one allele can be affected by the environment, and by other alleles
understand how some disadvantageous alleles can be maintained in a population due to pleiotropic effects and heterozygote advantage
be able to evaluate which factors determine the equilibrium allele frequencies in a complex system
appreciate that parasites evolve in response to host traits and be able to discuss eco-evolutionary dynamics in host-parasite systems
Articles to read
Introduction
Sickle cell disease (SCD) is a genetic disease, caused by various mutations in the gene that encodes β globin. Along with α globin, it is the most common form of haemoglobin in adult humans. Haemoglobin is the protein that carries oxygen in red blood cells. About 96% of red blood cells dry weight is haemoglobin.
Structure of human haemoglobin. α and β subunits are in red and blue. The iron-containing heme groups are in green.
The most common form of SCD is caused by the HbS allele, but there are many others (see: Rees et al.). The HbS mutation is nonsynonymous polymorphism (GAG to GTG) that changes the sixth amino acid in the β-globin chain from glutamic acid to valine, like so:
DNA mutation: GAG -> GTG
β globin protein change: Glu -> ValThis amino acids change in the protein usally does not affect it. But lack of oxygen causes the mutant (valine-containing) protein to polymerise the HbS molecules into hemoglobin fibers that deform the red blood cell membrane, as below.
Normal blood cells next to a sickle blood cell, colored scanning electron microscope image.
About 80% of SCD cases occur in Sub-Saharan Africa. The frequency of the HBS allele, and the overlap between the distribution of malaria caused by Plasmodium falciparum (which can be fatal), led to the hypothesis that this allele helps to protect against malaria.
This it is now fairly well established that heterozygotes with one HbS allele and one normal allele (called HbA) are protected against malaria.
(A) Distribution of the HbS allele. (B) Distribution of malaria (red) before interventions to control it.
In a homozygous state (HbS/HbS), the allele leads to sickle cell disease itself, which includes episides of sever pain, anaemia (lack of oxygen that cause tiredness and shortness of breath), and an increased risk of serious infections. Prior to modern treatments, sickle cell disease would frequently be fatal.
Workshop
Molecular aspects
Complexity of the SCD
The OMIM (Online Mendelian Inheritance in Man) database is an Online Catalog of Human Genes and Genetic Disorders.
Visit the OMIM entry.
Look at the Gene-Phenotype Relationships. Note the Inheritance pattern of Sickle cell anemia.
Now, check that you know:
- What is the name of the gene that causes SCD?
- What does the protein do and where in the body is it found?
Remember that proteins in cells do not act alone. They are part of a cellular network of proteins, DNA, RNA, other molecules (eg: oxygen), and pathogens. A mutation in one protein can have multiple effects on a complex organism. This is called pleiotropy.
OMIM allows you to explore pleiotropy. Use the PheneGene Graphics tool in OMIM to browse the relationships beween the SCD-causing gene, other symptoms (traits) and other genes. You will notice that the HBB gene is related to other medical conditions (such as beta-thalassemia), and in turn to other genes. Simple genetic changes can have multiple phenotypic consequences.
Phenotypic heterogeneity and genetic interactions
Read (or re-read) the section on Phenotypic heterogeneity in the Rees et al. article here. You will notice that genotypes at other locations in the genome affect the severity of SCD. These are known as genetic interactions.
While OMIM shows you some apects of genetic interactions the BioGRID database shows this in more detail. Visit BioGRID and search for the SCD gene (this is listed under Gene/Locus in OMIM). Be sure to select Homo sapiens when you search.
Once you have found the list of interactors, click on the network button in the maroon Switch View bar. You will see diagram of the interacting genes. Youll see that this is a complex network of possible protein or genetic interactions.
To make this simpler, limit the interactions you see by using the drop down menu to see only interactions with Minimum evidence of 3 (this is the number of experimental analysis that implicate an interaction). Or you can hide high throughput interactions (available in the FILTERS menu).
You should then see a window that looks like the image below (results may vary as interactions are added when new data comes in).
At this point, discuss these questions with your classmates or a tutor.
Based on OMIM and BioGRID, is SCD a simple (Mendelian) trait, or a complex trait?
Given the numerous negative aspects of SCD, why has this HBB allele not been removed by purifying selection?
Population Genetics
As you have seen above, the sickle cell trait is common in areas where malaria is common and we have already discussed that the sickle cell allele protects from malaria infection. In this section we will evaluate the selection pressure that leads to an equilibrium frequency of the two alleles and discuss how this frequency is likely to change in the future.
Table 1 shows the frequency of affected births. Assuming that the populations are in Hardy-Weinberg equilibrium, calculate the allele frequency of the HbS allele in each region. You will neeed to recall the equilibrium the genotype frequencies under Hardy-Weinberg. The frequency of affected births is the frequency of HbSS homozygote individuals.
| Region | Frequency of births with SCD |
|---|---|
| France | 0.00042 |
| Central Africa | 0.007 |
| Gabon | 0.029 |
Table 1. The proportion of births in different regions that have sickle cell disease (SCD), i.e. that are homozygous for the HbS allele.
Using population genetic theory to understand sickle cell anaemia
As you have seen above and in the Rees paper, people who have SCD in Central Africa usually die in childhood because the disease is not diagnosed and they do not receive the available medical treatments. People who are heterozygous have a mixture of the two Hb forms, and thus a much milder form of the disease that often goes unnoticed.
Heterozygous individuals do, however, often have other medical problems, so carrying just one HbS allele is not cost free. It has long been suggested that heterozygote people are to some extent protected from malaria infection and thus have an advantage over individuals that are homozygote for the normal HbA allele.
We will now use population genetic theory to explore the disadvantage that HbA homozygotes have in areas with malaria. As you may recall from Stage 1 and Stage 2 we can express the relative fitness of a genotype using selection coefficients, where the selection coefficient is the reduction of relative fitness compared to the fittest genotype. SCD is an example of heterozygote advantage, where both homozygotes have lower fitness than the heterozygote.
| Genotype | Type | Relative Fitness |
|---|---|---|
| HbAA | homozygous for the normal allele (HbA/HbA) | 1-s |
| HbAS | heterozygous (HbA/HbS) | 1 |
| HbSS | homozygous for 'sickle' allele (HbS/HbS) | 1-t |
Table 2. Selection coefficients (s and t) when there is heterozygote advantage.
The equilibrium allele frequency \(q\) (of the HbS allele in this case) when there is heterozygote advantage is:
In this case, \(t = 1\)
Make sure you understand why this is. Hint: what was a common outcome for people that were homozygous for 'sickle' allele, prior to modern treatments?
and we can thus calculate \(s\) as:
Exercises
Calculate \(s\) for a range of equilibrium frequencies of the allele that span the observed frequencies from France to Central Africa.
You will have observed that \(s\) varies with the equilibrium allele frequency. Explain why you see these differences.
A recent study screened apparently healthy adults for whether they carried Plasmodium falciparum that causes malaria and for their Hb genotype. They found no individuals with the HbSS, confirming that this genotype is effectively lethal. They also found that the incidence of malaria infection increased by 10% with every 4.3% of HbAS heterozygotes across populations.
Compare this increase in malaria infection with the increase in the selection coefficient that you calculated in (b). How are the two related? Discuss whether you would expect this relationship.
Consider the population in France, why is the HbS allele present at all given that malaria is absent?
The researchers also found that for every 10 year increase in age of the participants, the percentage of HbAS individulas increased by 5.5%. Explain why you might see this relationship.
Discuss with a classmate what is likely to happen if better treatments for or vaccines against malaria became more widely available. Predict the changes in the frequency of the HbS allele. For a more quantitative exploration of this question, use this model simulation and the parameters that you calculated above.
Screenshot of the Selection Model input.
To use this model
Under the Population Data (top left of the blue panel), select an infinite population size.
Enter initial frequencies of the A1 allele (here: HbA allele) and the fitnesses of the three genotypes (note that these should be \(w = 1-s\) or \(w = 1-t\)).
Start with using observed fitnesses and frequencies.
Then change the fitnesses to what you might expect if medical treatments were more readily available.
Observe the changes to allele frequencies and how long these take.
Finally, try this again with smaller finite population sizes. Observe how the change in allele frequency with time is different with smaller populations.
The data for this part of the workshop are taken from a paper by Elguero et al., which you may wish to have a look at. Note that this study examined only asymptomatic infections (samples from healthly people).
Host-Parasites Dynamics
So far, we have only considered the human host. However, the parasite and its vector may both play a role in the evolution of SCD. We will concentrate only on the parasite here.
In a group, discuss how different frequencies of the HbS are likely to affect Plasmodium falciparum. Consider how the parasite might 'respond', in ecological and evolutionary terms. Develop a flow chart or other diagram that illustrates these dynamics.
Now discuss any change in humans that might occur due to changes in the parasite and so on; incorporate this in your diagram.
And finally, discuss in more general terms how hosts and parasites might affect each other’s population in both ecological and evolutionary terms.
Summary
To sum up, we suggest you consider these questions:
Is the HBB mutation (Glu -> Val) pleiotropic?
What is the evidence that the effects of this mutation are modified by other alleles?
How does population genetic theory explain the maintenance of the deleterious HbS allele in malaria endemic regions?