My laboratory focuses on the evolution of drug resistant malaria parasites. The malaria parasite, Plasmodium falciparum, continues to kill people at an alarming rate while eluding massive global efforts to combat it with drugs. In fact, malaria is resurging in many parts of the world where previous control strategies are no longer effective due to widespread evolution of drug resistance. Classical gene-wise, biochemical, and molecular approaches to understanding drug resistance have fallen short in the quest to conquer this organism. New opportunities to dissect the molecular bases of previously inaccessible complex phenotypes are significantly enhanced by the recent infusion of sequence data and exciting whole-genome methods. The new tools of genomics available for malaria research include the complete sequence and the accompanying power of bioinformatics, a dense microsatellite linkage map (Su et al., 1999), a database of single nucleotide polymorphism (SNPs) (Mu et al., 2002; 2003), and genome-wide transcriptional profiling. Consequently, discovery of multi-gene pathways and biological processes (i.e. the genomic “context”) underlying drug resistance is feasible. I believe solving malaria will require this whole-genome perspective.

Dr. Ferdig's departmental homepage

The malaria parasite, Plasmodium falciparum, continues to kill people at an alarming rate while eluding massive global efforts to combat it with drugs. In fact, malaria is resurging in many parts of the world where previous control strategies are no longer effective due to widespread evolution of drug resistance. Classical gene-wise, biochemical, and molecular approaches to understanding drug resistance have fallen short in the quest to conquer this organism. New opportunities to dissect the molecular bases of previously inaccessible complex phenotypes are significantly enhanced by the recent infusion of sequence data and exciting whole-genome methods. The new tools of genomics available for malaria research include the complete sequence and the accompanying power of bioinformatics, a dense microsatellite linkage map (Su et al., 1999), a database of single nucleotide polymorphism (SNPs) (Mu et al., 2002; 2003), and genome-wide transcriptional profiling. Consequently, discovery of multi-gene pathways and biological processes (i.e. the genomic “context”) underlying drug resistance is feasible. Solving malaria will require this whole-genome perspective.

Due to the recent, well-documented history of sweeping antimalarial drug use, malaria parasite in the field provide a unique ‘natural experiment’ for investigating the effects of selection on genome evolution. To date, studies of drug resistance generally have consisted of searches for “resistance” genes and development of diagnostic markers of resistant parasite populations. Clearly, this approach is ‘after-the-fact’ and does little to illuminate the evolutionary processes that shape the genome. Given the new tools and perspectives of genomics, this classical question can be rephrased so that, instead of hunting for “R” genes, we can begin to dissect the cellular processes (and their component genes) which, upon intense drug selection, can yield alleles that allow the parasite to survive while maintaining basic biological function of the cell. Significantly, the constraints on P. falciparum are extraordinary because of its obligatory multi-host lifecycle, including massive asexual reproduction in the human host during which the haploid parasite is simultaneously exposed to drugs and host defenses.

Recent studies in malaria parasite populations have demonstrated profound roles for drugs in shaping the parasite genome by selective sweeps (Wootton et al., 2002). The next step will be to decipher the genetic context in which major resistances have evolved, e.g. identifying the multigenic/fitness features co-selected with R genes. This knowledge will facilitate the ability to begin to anticipate genomic responses to drugs yet unseen by the parasite and, ultimately, the application of this knowledge in tailoring drug choices specific to geographic regions with distinct drug selection histories.

In my laboratory we are focusing on natural physiological processes that can ‘contribute’ resistance genes. This is done by QTL mapping of quantitative dose responses to antimalarial drugs in a segregating population constructed from a cross between a multiple drug resistant line, Dd2, and a sensitive line, HB3. We have outlined the genetic architecture of numerous drug responses and have identified several loci that control variation in these responses (see website). The defined loci carry positional candidate genes that may be involved in the membrane transport processes that underlie the complex physiology of drug responsiveness. The next step will be to investigate these genes in natural parasite populations for evidence of selection of resistance and/or compensatory mutations and possible epistatic roles for these genes in comprising a genetic background of drug resistance.

Our approach requires the identification and genotyping of single nucleotide polymorphisms (SNPs) in these candidate genes in hundreds of parasites from around the world (Mu et al., 2003). These SNPs represent candidate quantitative trait nucleotides (QTN). Additionally, because key genetic variation might represent regulatory rather than coding mutations, we are using microarrays to explore the transcriptional profile of the genes in these loci. Only through such a parallel and integrated approach can we extend our in vitro findings in the genetic cross to events in natural populations. Therefore, in addition to QTL mapping and physiology studies, it is essential to incorporate 1) a bioinformatic exploration of these loci to develop lists of candidates and their biological process along with their coding variants in parasite populations 2) comprehensive analysis of the transcriptional expression variants genes in the QTL loci, and 3) genome scanning using microsatellite and SNP markers in outbred natural populations to uncover linkage disequilbreum and selected genome segments.

It is an exciting time in malaria research. Genomic tools have opened new avenues for study and this once intractable organism is beginning to reveal its secrets. It is now possible to explore the fundamental molecular nature of its complexity and begin to use this information to understand the role of specific alleles that balance parasite fitness with an ability to withstand drug treatment. It may be possible to apply this knowledge in forming rational drug policies to slow or stall the seemingly inexorable march to multiple drug resistance.

Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol Microbiol. 2003 Aug;49(4):977-89. Mu J, Ferdig MT, Feng X, Joy DA, Duan J, Furuya T, Subramanian G, Aravind L, Cooper RA, Wootton JC, Xiong M, Su XZ.

Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum.
Nature. 2002 Jul 18;418(6895):320-3. Wootton JC, Feng X, Ferdig MT, Cooper RA, Mu J, Baruch DI, Magill AJ, Su XZ.

Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum.
Nature. 2002 Jul 18;418(6895):323-6. Erratum in: Nature 2002 Oct 3;419(6906):487. Mu J, Duan J, Makova KD, Joy DA, Huynh CQ, Branch OH, Li WH, Su XZ.

A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum. Science. 1999 Nov 12;286(5443):1351-3.Su X, Ferdig MT, Huang Y, Huynh CQ, Liu A, You J, Wootton JC, Wellems TE.