Plasmodium falciparum Proteome Library Created

Researchers at Chan Zuckerberg Biohub–San Francisco and UC San Francisco have created a high-resolution map of the human immune response to Plasmodium falciparum, offering insight into what makes this parasite such a persistent pathogen. 

In the study, published in eLife, the researchers employed a sophisticated method to break down the proteins that make up P. falciparum into the pieces recognized by our immune system, and then exposed them to blood from 198 Ugandan adults and children. The results showed that antibodies bind to many P. falciparum regions that do not generate a long-lived antibody response, an apparent “diversion tactic” that forces the immune system into generating shorter-lived responses.

“Malaria is a professional when it comes to immune evasion,” said  Joe DeRisi, co–senior author of the study. “But rather than using stealth, our new findings suggest that the malaria parasite is basically throwing up a fireworks show that distracts the immune system, keeping it chasing targets that ultimately aren’t helpful for developing long-term protection.”

As for why a durable malaria vaccine has been so hard to come by, experts point to the complexity of the parasite’s life cycle. P. falciparum changes profoundly as it moves through the human body, first gliding through the bloodstream like a single-celled worm and then multiplying in cells of the liver before exploding into the circulatory system to repeatedly devour the contents of red blood cells as fuel to multiply. The parasite is also genetically complex, featuring hundreds of proteins thought to be dedicated to immune evasion. The proteins of the parasite also feature large numbers of simple repeated sequences that have baffled scientists for decades.  

To better understand why it’s so hard to develop malaria immunity, the team used PhIP-Seq, which allowed them to analyze in the laboratory how the immune systems of people exposed to P. falciparum have reacted to it. The approach involved taking all of the roughly 5,400 proteins that make up the P. falciparum parasite—the parasite’s proteome —and chopping them into hundreds of thousands of chunks, approximating the scale our immune system works on when hunting for pieces of pathogens to target. The researchers then engineered viruses to display each of these tiny chunks and mixed them in laboratory dishes with the blood of study participants.

“What we’ve done is to create a library of all the components of all the proteins malaria could show to our immune system,” said DeRisi. “We can see exactly what our immune system sees and try to figure out how it’s responding.” 

Now the researchers could analyze which pieces of the parasite triggered antibodies in human blood to fight off the disease. If the immune system has encountered a chunk before and produced antibodies, then the antibodies should show reactivity to those chunks in the PhIP-seq platform. As expected, samples collected from a control group of U.S. adults, who, for the most part, had probably never been exposed to malaria, showed very little reactivity to protein chunks from the parasite. But when the team looked at blood donated by Ugandans, they observed interesting patterns. 

The blood of Ugandans contained antibodies to many components of the malaria parasite but most commonly to protein chunks dubbed “repeat elements.” Repeat elements are areas of a protein where the amino acid sequences that make it up repeat over and over again and are thought to serve little purpose in the protein’s function. Curiously, the response to repeat elements depended heavily on exposure. Ugandan children living with extremely high malaria exposure—an average of 49 times a year through bites from infected mosquitoes—showed about twice as much reactivity to many of these repeat elements than children who lived in areas of moderate exposure—five infected bites per year. But reactivity to some of these repeat elements waned with time more than reactivity to non-repeated regions. The stark difference suggests that while antibodies to these repeat elements dominate the immune response to malaria, this response is fleeting and can disappear more quickly than responses to non-repeated regions. 

“Those repeats don’t tend to be very good targets when it comes to creating a long-term defense,” said Madhura Raghavan, lead author of the new study. “Immune resources are limited, and in the case of malaria our bodies seem to be making a major miscalculation in what they’re targeting to create natural immunity.”