Malaria Cell Atlas: mapping a murderous parasite’s life cycle

Malaria – and the parasite that causes it – is complicated. Not only does the single-celled parasite move between humans and mosquitoes, but it exists in different forms, each with different shapes and functions. Researchers have now mapped out its life cycle in more detail than ever before.

Written by Ali Cranage, Science Writer at the Wellcome Sanger Institute
Illustrations by Petra Korlevic, Postdoctoral Fellow at EMBL-EBI.

Malaria Cell Atlas research. Image credit: Petra Korlevic

Malaria is caused by microscopic Plasmodium parasites, just a single cell large. The parasites infect 220 million people a year, and kill around half a million, most of them children under five.[1] To eradicate malaria, scientists face a complicated picture. Plasmodium species, like other parasites, have a complex life cycle. They change size and shape, morphing from donuts to croissants, eyelashes and spheres. At one stage they have tail-like flagella. The parasites invade our liver and then our blood. They multiply and some become male or female before traveling to their next host via mosquitos, mating and multiplying along the way.

Malariologists frame everything through the life cycle, whether they are developing new antimalarial drugs, a vaccine, or trying to understand the complex biology of Plasmodium and how it interacts with humans and with mosquitos. Understanding the life cycle underpins the work to tackle this deadly disease.

So how do scientists delve into the life of Plasmodium? How much do we know? And how can that knowledge be used in the fight against malaria?

The history of Plasmodium

Malaria, as an illness, was possibly first documented as early as 2700 BC in China. Reports also  appear in clay tablets from 2000 BC Mesopotamia and in Egyptian papyri from 1570 BC. For thousands of years it was thought that malaria was caused by miasmas rising from swamps.

It was not until 1880, following on from the discovery that bacteria can cause disease, that parasites were discovered in the blood of malaria patients. Over the next 100 years, scientists uncovered the various stages of the Plasmodium life cycle in mammals and mosquitos, filling in pieces of the puzzle.

The situation as understood in 1900 is summarised by Grassi in his monograph, Studi di uno Zoologo Sulla Malaria. The work remains relevant today.

Human hosts

Plasmodium species exploit their hosts, including humans, to survive. When a parasite first enters a person, it invades a liver cell. Most species then rapidly replicate, leave the liver cell and invade red blood cells.

In red blood cells, parasites absorb nutrients and multiply, tucked out of sight of the immune system. This is where some of the shape-shifting occurs, with cells growing first to a donut shape, then becoming larger and then dividing. They burst out of the cells, killing them in the process. This behaviour repeats and parasites rapidly grow in number, infecting more and more red blood cells. It’s at this stage that people experience some of the symptoms of the disease; vomiting, high fever and shaking.

A single person can harbour billions of parasites in their body at any one time – as many parasites in one person as stars in our whole galaxy. Without treatment, infection causes anaemia, multiple organ failure and sometimes death.

Let’s talk about sex

A small percentage of parasites don’t continue this frantic stage of division; instead they change into male or female forms. These remain in the blood. If a mosquito bites an infected person, it drinks blood containing the male and female malaria parasites. 

The parasites then mature and mate in the mosquito’s gut. The offspring develop the ability to move, and embed themselves in the exterior wall of the gut where they begin to divide. This time, large numbers of small eyelash shaped parasites emerge. These migrate to the salivary glands and the next time the mosquito bites, they are injected into a new human host and the cycle begins again.

Plasmodium parasite’s life cycle

It’s all in the DNA

The malaria parasite’s life cycle is critical for its ability to infect and spread. But where are the weak links? Which stage should researchers target when developing new drugs? Is there a critical stage that, if blocked, means all the parasites could be eliminated?

From the perspective of Sanger Institute researchers, the answers lie in the parasites’ genomes: in their DNA. The genome contains genes and regulatory information on how the genes should be used; every instruction that’s needed for them to live their lives. Sanger scientists have led the sequencing of most Plasmodium species’ genomes, decoding the instructions that they use to build themselves.

The parasite’s ability to morph into different forms – each uniquely designed to invade, replicate, or mate – is orchestrated by tight regulation of its genome. And better understanding of gene use and gene function throughout the parasite’s life cycle is needed. It can help researchers  develop much-needed new drugs, vaccines, and transmission blocking strategies.

The function of 40 per cent of the genes in Plasmodium species remains unknown.

A Malaria Cell Atlas

Now, Wellcome Sanger Institute researchers have created the most comprehensive picture of the plasmodium life cycle – the Malaria Cell Atlas. The team have analysed the transcriptomes (the parts of the genome that are active at any given time) in thousands of individual parasite cells from across the life cycle.

They have pioneered the techniques for doing this. [2][3] They have pushed the boundaries of technology to give the most detailed insight into the parasite’s lifecycle to date.

The team’s approach uses single-cell RNA sequencing, or scRNA-seq. They use it to sequence the transcriptome of an individual cell, uncovering the true diversity of thousands of parasites. Sequencing can be performed using just a tiny amount of RNA. Previously, it was only possible to sequence many parasites mixed up together, as the amount of RNA needed was larger. It was not possible to ensure that all the cells pooled for sequencing were at exactly the same stage of their life cycle. This meant that important variation in the transcriptome was hidden.

In 2017 the same team used the technology to sequence the transcriptomes of 500 parasite cells. They uncovered previously unknown aspects of the parasite’s progression through its life cycle. They showed how the activity of different groups of genes waxes and wanes, controlling how the parasites grow and develop. Genes previously only associated with immune evasion were shown to also be involved in sexual development.

Now, the team have sequenced the transcriptome of thousands of cells across 10 life stages.

The result is a ‘reference atlas’ with gene activity data from tiny, individual parasites, from all the stages of the Plasmodium life cycle.

It is possible to see the continuum of the life cycle, as gene activity ramps up or dims down. The data can be visualised as a beautiful 3D plot.

Animated 3-D plot of gene activity in malaria parasite cells at different stages of its life cycle
Animated 3-D plot of gene activity in malaria parasite cells at different stages of its life cycle

X marks the spot

The data shows which genes behave similarly – enabling researchers to infer their function based on the point at which they are active. It’s likely that the functions of some of the 40 per cent of genes which aren’t currently characterised will be uncovered. The data will also help scientists understand the transitions between different developmental stages. All of this could uncover potential leads for developing new treatments.

Perhaps most importantly, the data provides a reference set that can be used to understand how parasites develop in their natural environments. The parasite species that formed the bulk of the Malaria Cell Atlas infects mice. It is harder to study some parts of the lifecycle in species that infect people, but the team wanted to be sure that the atlas represents those parasites too.

They undertook high-throughput scRNA-seq of the blood stages in two species which infect humans, collecting transcriptomes from thousands of cells. They also undertook field work in Kenya, where they collected blood samples from infected individuals. They developed a method to preserve the parasites, so that scRNA-seq could be undertaken back at the Sanger Institute. The data from those parasites cleanly mapped onto the Malaria Cell Atlas. The researchers could see which stages were present in an individual, even if that person was infected with multiple species of Plasmodium. This important validation means the atlas can be used to understand multiple Plasmodium species, including those deadly to people.


Each point on these plots represents an individual parasite cell. Those coloured orange or pink are stages in the mammal. Those in blue and green are in the mosquito.

Dr Virginia Howick, who co-led the development of the Malaria Cell Atlas, said: “This resource can be used by researchers world-wide. It will help studies aimed at understanding and defeating malaria. It will help research studying the parasites response to antimalarial drugs, including how resistance emerges.

“It’s a tool that we hope will transform malaria research.”

All the data from the Malaria Cell Atlas are freely accessible through the project’s website.

It is a vital part of the fight against malaria.


References

  1. http://www.who.int/malaria/publications/world-malaria-report-2018/en/
  2. https://www.biorxiv.org/content/10.1101/105015v1
  3. https://elifesciences.org/articles/33105

Find out more