ArsTechnica.com
What's a SNP?
SNP stands for single nucleotide polymophism. A nucleotide is a single base—A, C, T, or G—and polymorphism means "many forms" (single, we hope, is self explanatory). So, an SNP is just a single base at a defined position within the genome that will exist in many forms within a population. So, I might have an A there on one of my chromosomes, but a C on the other one; another person might have a C/G combination. Because these are located at specific places in the genome, the SNP will be inherited in the same way that everything else is.
Because of the vagaries of our genetic past, such as founder effects, migrations, and genetic bottlenecks, SNPs can be used to provide some hint of a person's family background, indicating what area of the globe a person's ancestors came from. New mutations, including those that cause diseases, will often arise near a known SNP. They can be used to track inheritance of the disease. Since malaria resistance is the result of a new mutation, it can be tracked using SNPs in the same way.
Over the last few decades, malarial parasites have evolved resistance to most of the drugs that we've thrown at them. This development leaves us with just one effective treatment: artemisinin. Artemisinin is currently delivered as part of a combination therapy (ACT) with other drugs that are intended to take out any resistant parasites. But recent developments in Southeast Asia have suggested that time may be running out for ACTs, as they're taking much longer to clear parasites.
Understanding artemisinin resistance is complicated by the fact that we're not entirely sure how the drug works. We also lack any understanding of the biochemical basis for resistance. All of that makes devising a test for resistant malaria a big challenge. Now, researchers have taken the first step toward nailing things down by identifying a chunk of the parasite's genome that accounts for a significant percentage of the resistance.
How do you identify the genes for drug resistance when you're not even sure how the drug works? The researchers took advantage of a set of samples from different countries in Southeast Asia. Since parasites rarely respect national boundaries, these populations should have started out with genomes that were very similar: largely identical, but with a common set of variations. But there has been little evidence of resistance in Laos, while it's very common in Cambodia. Any genetic differences between the two populations may be associated with the evolution of drug resistance. (Samples from Thailand, where resistance is erratic, were also included.)
The authors went looking for evidence of what's termed a "selective sweep." When a highly favorable mutation occurs (like one conferring drug resistance), it often rapidly sweeps through a population. Because this happens so rapidly, the DNA around the mutation doesn't have a chance to mix in with the general background of genetic differences typically present in a population. In short, the region around the mutation will look identical in every individual in the population.
To detect evidence for a selective sweep, the authors looked at single nucleotide polymorphisms, or SNPs, searching for areas of the genome where all the SNPs were identical. They identified 33 regions, covering about 2.4 percent of the malaria parasite's genome. Not all of these would help the organism adapt to tolerate atermisinin, however. At least 10 were already known because they help Plasmodium tolerate other drugs. Others showed evidence of selection in the samples from Laos, indicating they were beneficial for some trait unrelated to drug use.
With a limited number of regions to look at, the team turned to a unique and precious set of samples: thousands of blood spots taken from Thai patients. The spots were taken over the course of a decade in which resistance to artemisinin went from nonexistent to fairly common. This helped rule out two genes that had previously been suggested as mediating resistance to artemisinin. And it allowed them to focus on a very small area of the genome: about 35,000 bases out of 23 million. As a conservative estimate, this section of the genome accounts for over a third of the drug resistance.
Unfortunately, that was as far as they could get. There are seven genes in this area, and the authors have now sequenced six of them. There are some mutations present, but all of them predate the use of artemisinin in Southeast Asia, so they are unlikely to be linked with resistance. Two of the genes were expressed at a higher level in resistant lines, which makes them good candidates for further study. Unfortunately, this doesn't tell us anything definitive.
That said, these further studies are undoubtedly under way, since this is such a hugely important issue. As the authors themselves note, "The spread of ART-resistant parasites would be catastrophic for malaria control." Knowing the mutation(s) responsible for that resistance would allow us to develop tests that would help us track and hopefully contain the spread of resistance.
In the longer term, understanding resistance could be helpful for the design of future therapies. Some of the ones in the works have chemical features that are similar to artemisnin, and it would be good to know whether they're likely to face a population that's already primed to resist them.
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