The San Antonio-based Texas Biomedical Research Institute reports that its researchers and their colleagues have developed a new method for isolating and genome sequencing an individual malaria parasite cell. Texas Biomed says this advance will allow scientists to improve their ability to identify which of the multiple types of malaria parasites is infecting patients, and lead to ways to best design drugs and vaccines to tackle what remains the world’s deadliest parasitic disease, that killed 655,000 people — more than one per minute — in 2010.
Texas Biomed notes that the malaria parasite infects more than half a billion people each year, leading to approximately one million deaths across sub-Saharan Africa, South East Asia and South America, and observes that mutations in the parasite genome are central to the sustained disease burden associated with malaria. Drug resistance mutations have occurred rapidly, limiting the use of the cheapest and most readily available treatments.
Parasitic diseases still plague many of the world’s developing countries, reducing childhood survival rates and stunting economic growth. However, malaria deaths have declined by 30 percent over the past decade, largely because of treatment with combination therapies containing artemisinin, a plant-derived antimalarial drug developed in China, and genome sequence data for the pathogens involved and funding from organizations such as the Bill and Melinda Gates Foundation have generated new hope of controlling or even eliminating these diseases.
There is some urgency. The spread of drug resistant malaria parasites from Southeast Asia to Sub-Saharan Africa occurred during the 1970s, when the drugs chloroquine and fansidar lost potency. This resulted in a resurgence of disease and the collapse of political will to combat malaria. Should history repeat itself for artemisinin resistance, this would be a public health disaster resulting in millions of deaths. Thus, there is enormous urgency to generate the tools needed to combat the spread of drug resistance.
Malaria parasite infections are complex, often containing multiple different parasite genotypes and even different parasite species. The multiple highly polymorphic gene families in the parasite genome slow the host’s acquisition of natural immunity against infection and limit the efficacy of tested vaccines. Consequently, when researchers take a blood sample from a malaria infected patient, and look at the parasite DNA within they are confronted with a complex mixture that is difficult to interpret.
“This has really limited our understanding of malaria parasite biology” says Ian Cheeseman, Ph.D. , who led the Texas Biomed research project in a release. “It’s like trying to understand human genetics by making DNA from everyone in a village at once. The data is all jumbled up – what we really want is information from individuals.”
Dr. Cheeseman joined the Foundation in May 2010 to work with Tim Anderson, Ph.D., of Texas Biomed’s Infectious Disease Research Laboratory, in researching the genetics of human malaria parasites. Dr. Anderson’s lab focuses on two of the most important malarial human parasites, the protozoan Plasmodium falciparum, and Schistosomiasis, caused by the blood fluke in the genus Schistosoma. These parasites, which utilize a snail as an intermediate host, infect more than 200 million people in South America, Asia and Africa. One of Dr. Anderson’s work focuses is on understanding the genetic basis of resistance to the drug oxamniquine.
The Anderson lab is using several different strategies to identify genes that underlie resistance and better understand resistance evolution. First, genome-wide association methods are employed to systematically search for the genes involved. As the malaria genome is relatively small, the scientists can use whole genome sequence information from populations of parasites to achieve this goal. Second, they are examining the role of copy number variation, and Dr. Anderson notes that already this approach has characterized an important gene involved in drug resistance. Finally, the researchers are selecting resistant parasites in the laboratory and using next generation sequencing methods to identify the genetic changes that have occurred. The lab’s work involves collaborators in South America, Africa, and Southeast Asia.
In his research, Dr. Cheeseman combines microarray technology, ‘next generation’ sequencing, and in vitro parasite culture to measure the mutation rate in the parasite genome. He says that a better understanding of the mutational process in the malaria parasite is key to tackling public health aspects of malaria infection, notably the emergence of drug resistance and the development of efficacious vaccines.
To achieve a better understanding of malaria parasites — single celled organisms that infect red blood cells — Dr. Cheeseman and his colleague Shalini Nair developed a novel method for isolating an individual parasite cell and sequencing its genome. These “single cell genomics” approaches have been adopted in cancer research to identify how tumors evolve during the progression of a disease but it has been difficult to adapt them to other organisms.
“One of the real challenges was learning how to cope with the tiny amounts of DNA involved. In a single cell we have a thousand million millionth of a gram of DNA. It took a lot of effort before we developed a method where we simply didn’t lose this,” says Nair, the first author on the work.
Their method is set to change how researchers think about infections. “One of the major surprises we found when we started looking at individual parasites instead of whole infections was the level of variation in drug resistance genes,” Nair notes. “The patterns we saw suggested that different parasites within a single malaria infection would react very differently to drug treatment.”
“We’re now able to look at malaria infections with incredible detail. This will help us understand how to best design drugs and vaccines to tackle this major global killer,” Dr. Cheeseman observes.
A paper describing this work, funded by the Texas Biomedical Forum, National Institutes of Health, a Cowles Postdoctoral Training Fellowship and the Wellcome Trust, is to be published online May 8 in the journal Genome Research. The work was led by Texas Biomed’s Ian Cheeseman with collaborators at the University of Texas Health Science Center San Antonio, Case Western Reserve University, the Cleveland Clinic Lerner Research Institute, the Shoklo Malaria Research Unit, Thailand, and the Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Malawi. The other Texas Biomed author on is Tim Anderson, Ph.D.
Texas Biomed’s Dr. Tim Anderson was also named “health care hero for biomedical research” by San Antonio Business Journal in 2013.
“We are extremely proud of Tim for his groundbreaking work on resistance to malaria treatments in Southeast Asia. It is changing the global approach to fighting this disease,” said Kenneth P. Trevett, Texas Biomed’s president and CEO, of the award.
Sarah Williams-Blangero, Ph.D., Chair of the Texas Biomed Department of Genetics, commented that: “Tim’s novel research program is highly productive and is yielding new insights into why malaria, one of the world’s major public health problems, is so difficult to control. He brings the power of a strong research team here in San Antonio and an outstanding network of collaborators from countries in which malaria has a devastating impact to the battle to understand the changing efficacy of malarial drug treatments.”
Dr. Anderson and his collaborators recently documented the emergence of resistance to artemisinin in western Thailand which represents a critical problem in global efforts to control the disease. They also found a major region of the malaria parasite genome associated with resistance, raising the hope that there will soon be effective molecular markers for monitoring the spread of resistance.
In a study published in the British medical journal The Lancet, Dr. Anderson’s team and their collaborators in Thailand studied 3,202 patients in clinics in Northwestern Thailand. From 2001 until 2010, they observed a dramatic decline in the potency of artemisinin. By measuring drug potency in patients infected with genetically identical malaria parasites, they were able to show that the decline in potency results from the spread of resistance genes.
In a second study published in the journal Science, the Anderson team examined the genetic changes that occur in these drug resistant parasites. This study narrows the search to a region of the parasite genome containing around 10 genes. Identification of a molecular marker for resistance will be critical for monitoring the spread of resistance, determining how resistance occurs, and understanding artemisinin’s mechanism of action. This is an important advance in the race to avert a global public health crisis.
Dr. Anderson’s group compared genomes of parasites from Laos, which are sensitive to the drug, with parasites from Cambodia, which show high levels of resistance, and those from Thailand, where both resistant and sensitive parasites occur. They found that 33 genome regions were very different in the parasites collected from these three countries. When they examined these regions in more detail in a large collection of parasites from Thailand, they found that one small section of the malaria parasite’s chromosome 13 is strongly associated with parasite resistance.
For its achievements during over a decade of work on the evolution and spread of resistance to antimalarial drugs, Anderson’s laboratory was recognized in 2012 by a MERIT award from the National Institutes of Health. This extends his laboratory’s currently active five-year, $3 million grant for this work by an additional three to five years (until 2019-2021) without peer review. The prestigious MERIT award program extends funding for experienced researchers who have made a significant and sustained impact in a high priority research area and is a symbol of scientific achievement in the research community.
Texas Biomed, formerly the Southwest Foundation for Biomedical Research, is one of the world’s leading independent biomedical research institutions dedicated to advancing health worldwide through innovative biomedical research. Located on a 200-acre campus on the northwest side of San Antonio, Texas, the Institute partners with hundreds of researchers and institutions around the world, targeting advances in the fight against cardiovascular disease, diabetes, obesity, cancer, psychiatric disorders, problems of pregnancy, AIDS, hepatitis, malaria, parasitic infections and a host of other diseases. For more information on Texas Biomed, go to:
Texas Biomedical Research Institute
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