The Modern Age of Malaria Research: Finding New Ways to Combat an Old Disease
October, 2003
Swat! A dozen mosquito bites have turned yesterday's fun-filled summer picnic into today's irritating nuisance. Mosquito bites, however, can become much more than a nuisance. 300 million people become infected annually by Plasmodium, a class of parasites that infect red blood cells and cause malaria. 2.7 million die from this disease every year, making malaria one of the deadliest infectious diseases in circulation.
To better study malaria, Dr. Elizabeth Winzeler directs laboratories at both the Scripps Research Institute and the Genomics Institute at the Novartis Research Foundation. "It is very difficult to work with the intracellular parasite and as a result there is very little known about gene function," states Winzeler. "There are not very good genetic systems developed and thus far, slow and laborious biochemical methods have been the only way to examine gene function." Understanding the function of individual genes is critical, such that scientists can then find ways to disrupt those functions—effectively stopping the parasite in its tracks.
Using the Affymetrix CustomExpress™ Array program, Dr. Winzeler and her team created a customized GeneChip microarray, representing the complete genome of Plasmodium falciparum, the most lethal species of the malaria parasite. The Affymetrix CustomExpress program enables researchers to use any available sequence information to create a GeneChip microarray focused on their specific research needs. As reported in the September 12 issue of Science Magazine, Winzeler's research group used their CustomExpress array to better understand global gene activity during the different stages of the P. falciparum life cycle that transfers from mosquito to man and back to mosquito.
Disrupting certain points of the Plasmodium life cycle may effectively prevent disease progress. For this reason, scientists have searched for genes involved in particular aspects of that cycle. However, with only 35 percent of P. falciparum genes having a known function "it has been difficult to find genes involved in any particular process," says Winzeler, senior author of the new Science publication. Still, she believes "interesting drug targets may be found in genes expressed during the erythrocytic stage," the major stage under study in this investigation.
Prior to GeneChip analysis, scientists would painstakingly evaluate each individual gene. Having developed a custom P. falciparum GeneChip microarray, however, the research team was able to examine the simultaneous activity of 95 percent of the 5300 genes present within the parasite. The true power of their study was that they used a statistically complex method to rationally predict gene function from gene activity data. The first step was arranging genes based on their expression at different stages of the P. falciparum life cycle. They then identified groups of genes that were expressed at the same times and categorized them into fifteen distinct 'clusters'.
Strikingly, the researchers found that genes known to function in the same cellular processes had been grouped together. "I was surprised how well these genes clustered," says Winzeler. "Many genes described as having a role in cell invasion, ended up next to each other on the expression map. Genes of hypothetical function that reside within that cluster may be involved in invasion as well."
Using similar grouping techniques, the researchers were able to predict functions for other genes—uncovering many potential targets for novel drug or vaccine design. They are now using other scientific approaches to confirm these potential targets as items of genuine interest that may one day generate a viable vaccine.
Additionally, the research team found a wide class of consistently expressed P. falciparum genes. "From the point of drug development, one would likely be most interested in these genes," says Winzeler. Such genes likely encode proteins essential for broad cellular functions. Developing a drug to disrupt these functions would probably have a lethal effect on the parasite—the ultimate goal for an effective therapeutic.
"It all starts with identifying as many drug targets as possible," explains Winzeler. "Having many drug targets leads to many new drugs in the pipeline. This results in a multitude of potential drugs that can then be screened for the best pharmacological properties."
The need for novel anti-malarial drugs has never been greater. The lack of an established vaccine and the emergence of drug-resistant parasites have allowed this disease to continue as a major world wide health hazard.
Despite the tremendous wealth of data that Winzeler's team has unearthed, the scientists see this work as a humble starting point. By examining gene regulation under other conditions and stresses, they hope to develop more precise sets of functionally related genes. And these scientists see their recent findings, serving as a check list for currently accepted concepts in P. falciparum infection. Already, their predicted gene functions have forced reevaluations of accepted gene functions. Thus far, the accuracy of their predictions have borne out.
Combining classical biology, modern genomics, and intense statistical algorithms, this international research team has created the most complete overview of P. falciparum infection to date. "If left to classical methods, it might have taken twenty years of research to generate the quality of data generated in this study," says Winzeler. With further research efforts—including additional GeneChip studies—scientists ultimately hope to understand enough of the biology to better treat and more effectively prevent malaria.
To this end, Affymetrix will soon be commercializing a new microarray tool for malaria research. It will be the the first widely available GeneChip array to include sequence information from two organisms, the Plasmodium parasite and the Anopheles mosquito. The GeneChip Plasmodium/Anopheles Array will feature comprehensive coverage of both genomes(1,2), including probe sets to over 5,000 Plasmodium falciparum transcripts and over 15,000 Anopheles gambiae transcripts.
The content for this array is based on completed genome assemblies and recent annotation updates for both organisms. Designed in collaboration with researchers at The Johns Hopkins Malaria Research Institute, this array will be sold to the public through the Affymetrix Made-to-Order program later this year.
Using the newly developed Plasmodium/Anopheles GeneChip array in conjunction with the recently released Human Genome Plus 2.0 GeneChip array, scientists will for the first time, be able to simultaneously study every aspect of malaria, complete gene expression from parasite, insect, and human. This level of information marks a hallmark for the study of complex infectious diseases such as malaria—1 disease, 2 arrays, 3 organisms.
(1) Gardner, M.J., et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419(6906):498-511 (2002).
(2) Holt, R.A., et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science. 298:129-149 (2002).
The author, Thomas Broudy, interviewed Elizabeth Winzeler in September, 2003. He received his Ph.D. in Microbiology at The Rockefeller University. Dr. Broudy continued his research in this field, first as a postdoctoral associate at The Rockefeller University and later as a postdoctoral scholar at Stanford University.
