How is genomics being used to tackle neglected tropical diseases?

The World Health Organization (WHO) characterises neglected tropical diseases as a diverse group of diseases that thrive among the poorest of the world’s populations. Currently there are 17 neglected tropical diseases on the WHO’s priority list. They are split into four main groups:

• Protozoa: single-celled eukaryotic (cells that have a nucleus) microorganisms
  • Chagas disease (American trypanosomiasis)
  • Sleeping sickness (African trypanosomiasis)
  • Leishmaniasis
• Bacteria: single-celled prokaryotic (cells that don’t have a nucleus) microorganisms
  • Buruli ulcer
  • Leprosy
  • Trachoma
  • Yaws
• Helminths: parasitic worms
  • Tapeworm
  • Guinea worm
  • Echinococcosis
  • Foodborne trematodiases
  • Lymphatic filariasis
  • Onchocerciasis
  • Schistosomiasis
  • Nematodes
• Viruses: microscopic infectious agents with a very simple structure
  • Dengue
  • Rabies

Neglected tropical diseases affect over 1.4 billion people in 149 countries.

Collectively, neglected tropical diseases affect over 1.4 billion people in 149 countries costing developing economies billions of dollars each year. They are diseases that trap people in a cycle of poverty. People in poverty are more likely to get these diseases because of a lack of access to clean water leaving them unable to work when they are ill, trapping them in poverty. As a result there is rising political pressure to increase funding to prevent and treat these diseases.

In terms of genomics, knowledge of neglected tropical diseases is a relatively small, niche area. For smaller groups of researchers it is more of a struggle to get research into high profile publications making it harder for their findings to reach the wider scientific community. However, huge efforts are now being made to raise the profile of neglected tropical diseases in the research community.

The genomes of many of the organisms that cause neglected tropical diseases have either been fully sequenced or are currently being sequenced. This means scientists are now able to find out much more about how they develop and cause disease.

Schistosomiasis is a neglected tropical disease that is currently a major focus for the World Health Organization (WHO).

What is schistosomiasis?

Schistosomiasis is a tropical disease caused by a group of parasitic worms called schistosomes or Schistosoma. Schistosomes are transmitted by snails that live in fresh water, such as rivers and lakes, in sub-tropical and tropical regions of the world. People become infected if they come into contact with the larval form of the parasite, often when washing or playing in contaminated water in lakes and rivers.

Schistosomiasis affects around 240 million people worldwide and kills more than 200,000.

Schistosomiasis is particularly common in poor communities that do not have proper sanitation. The symptoms of schistosomiasis can range from acute, such as a high temperature and muscle aches, to chronic ill health. Chronic symptoms are caused by schistosome eggs becoming trapped in the tissues and organs of the host causing inflammation and scarring. Schistosomiasis affects around 240 million people worldwide, and takes more than 200,000 lives each year.

Tiny worm, big genome

A valuable step in understanding how to tackle neglected tropical diseases is to understand the genomes of the parasites that cause the disease.

Sequencing the genomes of parasites such as Schistosoma is a first step to understanding how they live and grow. This can eventually lead to the development of new and targeted medicines to help eradicate the parasites and the diseases they cause.

Currently you can explore the human, mouse or malaria genome sequences and have confidence that the gene you’re looking for is where it is supposed to be. A reference genome like this is an essential resource that can be shared with scientists across the world.

Despite being a tiny parasitic worm, schistosomes have a surprisingly big genome – about 3.6 million letters long. That is a 10th of the size of the human genome! But while the human genome was worked on by research groups across the world at a cost of 3 billion dollars, the schistosome genome is being worked on by a much smaller team” of scientists. It is therefore a slow and painstaking process. The first draft of a Schistosoma genome (S. mansoni, one of the major schistosome species that cause the disease) was published in 2009, with higher quality genomes of two other schistosome species (S. japnonicum and S. haematobium) published in 2019. These high quality genome sequences will help scientists better understand the parasites and work towards vaccine development.

The schistosome life cycle

As well as constructing a high-quality genome sequence a lot of work is focusing on investigating the various stages of the schistosome life cycle. Finding a way to interfere with the life cycle of the parasite in the host could help us stop the parasite from causing disease altogether. It is an approach that has been explored with other parasitic diseases such as malaria.

A few laboratories around the world are now able to replicate the full life cycle of Schistosoma mansoni in house. This is incredibly useful because it ensures that there is a constant supply of schistosomes for scientists to work on. Schistosoma mansoni is one of the three species of schistosome that most commonly affects humans so is an important one to understand. The species Schistosoma haematobium is the most deadly to humans but it is not yet possible to construct its full life cycle in the lab.

To maintain S. mansoni in the laboratory, scientists keep the parasite’s intermediate vector, a snail, in tropical conditions of around 28˚C. The snails are then ‘shedded’, which involves placing them under UV light so that the schistosome larvae are encouraged to burrow out of the snail into the surrounding water. The larvae can then infect a model organism, usually a mouse. Inside the mouse the schistosome larvae continue their life cycle and can be studied by scientists at each stage.

It is unusual to be able to take a human-infecting parasite and put it in another animal, so it is a huge advantage for studying schistosomiasis that S. mansoni infects mice. The only limitation is that in humans, schistosome parasites can stay in the body for 10 years or more. Mice don’t live this long so it is not possible to study the long term effects of the parasite.

Schistosome metamorphosis

When the schistosome larvae burrow through the skin they undergo a dramatic transformation

When the schistosome larvae burrow through the skin of their new host they undergo a dramatic transformation in order to get ready for their new life inside the host. Scientists are studying the genes which are expressed at this point in the life cycle to pin down which ones are essential for this transformation.

Later on in the life cycle the parasite starts wandering through bloodstream, from wherever it entered the body to the liver. Along the way the parasite changes again, into a long, thin worm. Scientists studying this portion of the life cycle want to find out if there are any particular signals that help the parasite find its way to the liver. Is there something it is sensing in the host that helps it get to where it needs to go to complete its life cycle? Are any of the developmental stages in the worm triggered by knowing it’s in the liver, or knowing it’s in the gut?

Many changes happen at specific points in the life cycle as if by clockwork. It is hoped that scientists will discover proteins that are expressed on the surface of the parasite that help it interact with its host, perhaps acting like a GPS to help the parasite get to its desired location.

Boy meets girl

A key feature of the parasite that the scientists are particular interested in is how the male and female schistosome worms differ and communicate with each other. For most of their adult lives male and female schistosomes stay bound together to breed. The female then releases eggs. Without the male present the female regresses to a less mature form but nobody knows how this process works.

If scientists can work out how to interfere with the breeding adult worms they could potentially halt the life cycle altogether. To do this however, they will have to study and sequence the sex chromosomes of the worms. If they can find key differences or similarities between the male and female chromosomes it may reveal the mechanism that allows them to find each other and breed.

By identifying the genes that are crucial to the growth and development of the schistosome parasite scientists hope to be able to target them with drugs or vaccines.

Large-scale knock-down

Some research institutes are participating in large-scale gene knock-down programmes. This means that out of perhaps 11,000 genes in a genome, scientists will pick 3,000 genes that they believe have an important role in the parasite’s ability to cause disease. Then, one by one, they will silence or remove these genes to identify the function of each of them and examine the resulting effect on the parasite.

Doing this highlights which genes are essential to the parasite and provides scientists with a whole list of genes to focus on when developing drugs or vaccines.

Leishmaniasis

Another neglected tropical disease that is receiving interest from the genomics research community is leishmaniasis. This is a tropical and sub-tropical disease caused by protozoan parasites which are transmitted to humans by the bite of infected sandflies.

The first entire genome sequence of the Leishmania major parasite was completed in 2005.

The first entire genome sequence of the Leishmania major parasite was completed in 2005 and since then several other Leishmania species have also been sequenced, including L. infantum, L. braziliensis, L. mexicana and L. donovani. Having these genome sequences available has enabled scientists to advance their understanding of the parasites’ complex biology and the interactions between the parasites, host and vector, the sandfly.

There are three main forms of leishmaniasis, each associated with different species of the Leishmania parasite:

1. Visceral – the most serious and potentially fatal form of the disease
2. Cutaneous – the most common form which causes skin lesions such as ulcers
3. Mucocutaneous – the form which can lead to partial or total destruction of the mucous membranes of the nose, mouth and throat.

Although only a small fraction of people infected with Leishmania parasites will actually develop leishmaniasis it nevertheless causes around 30,000 deaths each year. Leishmania donovani is therefore the most important species to study as it causes visceral leishmaniasis which is often fatal.

Although scientists have been working on Leishmania for a while it is only relatively recently that they have been able to study its genetic diversity across the globe. Over 20 species of Leishmania, that affect humans, have been reported in the literature. However, the definition of a species is very fuzzy and scientists are keen to provide a genetic rationale to that. This will then help them to define exactly how the parasite varies in different regions of the world.

Asexual vs sexual reproduction

Leishmania parasite species seem to differ quite a lot

Scientists have found that Leishmania parasite species seem to differ depending on which part of the world they are found. This is because the parasite is able to vary the way it reproduces.

In some areas scientists have discovered that Leishmania parasites reproduce in a similar way to bacteria – by way of clonal expansion. This means that all the new generations or ‘daughter’ cells arise originally from a single cell. As a result these populations of Leishmania grow and grow from a fairly limited genetic pool; they are almost exact copies of each other.

In contrast, in other parts of the globe the parasites are reproducing sexually. Leishmania parasites with a lot of genetic variation are coming together and exchanging chunks of their DNA to generate even more diversity and gradually drifting apart into more and more distinct organisms. The concern with this scenario is that different parasites could eventually be transmitted by vectors other than the sandfly. If Leishmania species are starting to mix it could result in the emergence of a more deadly parasite transmitted by an unexpected or, as yet unidentified, vector.

Dogs vs humans

The control of leishmaniasis generally relies on early diagnosis, control of the sandfly vector and management of other animal hosts. Dogs are the main animal hosts of Leishmania and transmission of some Leishmania species relies on circulation of the parasite in canine populations.

Some gaps still exist in our understanding of the similarities and differences between human leishmaniasis and the disease that occurs in dogs. Knowing more about these similarities and differences could reveal if Leishmania has an ‘Achilles’ heel’ that scientists can target to help break the transmission cycle.

The main push with research into all neglected tropical diseases is, primarily, to find ways to prevent them, rather than just focusing on treatments. With genomics, scientists may be able to pinpoint the changes that are occurring during reproduction and transmission of these parasites. This may then enable them to develop effective treatments and control strategies against this devastating group of diseases.