"The control of malaria," observed microbiologist Elizabeth Winzeler, "is one of the greatest challenges to global public health today." An assistant professor at the Scripps Research Institute in La Jolla, Calif., her field covers genetics and genomics. She serves in a joint appointment as group leader at the Novartis Research Foundation's Drug Discovery Institute in San Diego.

"Malaria is a nasty and often fatal disease," Winzeler continued. "It can lead to seizures, kidney failure, permanent neurological damage, coma and death. About 1,200 cases of malaria are diagnosed in the U.S. each year, most of them imported by travelers from malaria-infested regions. Malaria is rightly termed the world's most important parasitic disease.'

"The World Health Organization (WHO) estimates that 300 million acute cases of malaria occur annually," Winzeler went on, "and more than 1 million people die of the disease each year. Most of these victims are children under the age of 5. Many of them suffer six episodes of malaria every year. To make matters worse," Winzeler pointed out, "drug-resistant strains of the parasite that causes malaria have evolved over the last few decades, making malaria more deadly and expensive to treat. There is a profound need for new drugs and effective vaccines to prevent it."

The deadliest malarial parasite is a microorganism called Plasmodium falciparum. It's airborne and off-loaded onto human skin by a single-purpose mosquito, Anopheles gambiae. A blow against this detestable duo was struck last year when an international consortium solved the 23-megabase nuclear genome of the Plasmodium parasite. It numbers 14 chromosomes encoding 5,268 genes.

In a sense, Elizabeth Winzeler took it from there. She is senior author of a paper in today's Science, dated July 31, 2003. Its title: "Discovery of gene function by expression profiling of the malaria parasite lifecycle."

"What we did as soon as the genome sequence was completed," Winzeler told BioWorld Today, "was construct an oligonucleotide array - a gene chip - that contained 250,000 different oligonucleotides, each consisting of Plasmodium falciparum genome sequence extending to virtually every region of the parasite's genome. The probes on our chip covered about every 75 to 100 bases. So we've been in essence synthesizing a 20 percent fraction of the parasite's genome on the chip. Then we collected RNA from different stages of Plasmodium and dissected sporozoites from an infected, mosquito-carrying, blood-invading stage and put them on the chip. We also collected a number of samples that the parasite forms around the human red blood cells [RBCs] it invades. We also collected some of the sexual phases of the parasite, gametocytes, which we hybridized to the arrays."

At Novartis, Winzeler and her co-authors created a malaria-specific gene chip with probes for the entire genome of the malaria pathogen.

At Parasite's Core: Red Blood Cell Invasion

"I think the most striking discovery we made was the genes that were involved in similar processes - for example, the invasion of the RBCs. When a merozoite bursts out of the red blood cell it had penetrated, it is free living for only seconds before finding itself a new red cell. It's very vulnerable to attack when it's free living within the circulatory system. So it needs to invade a new red cell instantly.

"Many of the current blood-stage malaria vaccine targets are in a single cluster - one of Plasmodium's 15 clusters. Perhaps the uncharacterized genes in that same cluster may prove to be potential vaccine targets as well," Winzeler commented, adding, "We have about 2,300 genes that appear to be changing through the Plasmodium lifecycle, which we grouped into 15 clusters based on similarity."

Reverting to the Science paper, Winzeler noted that the researchers' "overall finding is this idea that one can predict what a gene is likely to be doing in the parasite simply by determining when it is transcribed, on a global scale. It's been relatively difficult to find out what genes in the Plasmodium falciparum parasite are doing. Current methods for knocking out genes tend to be fairly laborious and time-consuming, with a low efficiency. A lot of these conventional approaches traditionally rely on biochemical purification. There had been no forward genetics in this parasite. As a consequence, the function of the genes in the parasite genome are not well understood. It's a much higher proportion than with many other organisms that have been studied in the lab.

"And therefore, having now a structured list of potential functions for a large proportion of the genes in the genome, we should really accelerate the research and development effort on new vaccines and new drugs. In some ways, it's analogous to obtaining a genome sequence. For example, when you obtain a genome sequence, there might be interesting observations that ultimately provide a sort of road map to identify genes that might be potential drug targets, based on sequence homology. Likewise," Winzeler concluded, "we can identify genes that might be involved in a particular process based on their expression profile."

Conventional Protein Analysis Found Lacking

When the genome sequence of Plasmodium falciparum was published last year, Winzeler recalled, "scientists saw the functions of an incredible 65 percent of the parasite's genes were completely unknown. Our research data connect the majority of these mystery genes with the minority that have been characterized.

"Vaccine and drug development," Winzeler summed up, "relies on identifying molecules that may be vulnerable to attack by the immune system or by man-made drugs. Our research helps to establish which of Plasmodium falciparum's unknown genes may be potential targets.

"I think at the end of the day, this work represents how quickly one can go from genome sequence to gene expression data to putative function. This should be potentially a model for target discovery and validation in any number of microorganisms in emerging infectious diseases. A new parasite, for example. Or a new bacterium associated with what was deemed to be a public health threat."