Plasmodium falciparum: chloroquine selection of a cloned line and DNA rearrangements

How can we identify parasite genes that underlie antimalarial drug resistance?

This article outlines genome-scale approaches that can be used to identify mutations in malaria (Plasmodium) parasites that underlie drug resistance and contribute to treatment failure. These approaches include genetic mapping by linkage or genome-wide association studies, drug selection and characterization of resistant mutants, and the identification of genome regions under strong recent selection. While these genomic approaches can identify candidate resistance loci, genetic manipulation is needed to demonstrate causality. We therefore also describe the growing arsenal of available transfection approaches for direct incrimination of mutations suspected to play a role in resistance. Our intention is both to review past progress and highlight promising approaches for future investigations.

Chloroquine susceptibility and reversibility in a Plasmodium falciparum genetic cross

Mutations in the Plasmodium falciparum chloroquine (CQ) resistance transporter (PfCRT) are major determinants of verapamil (VP)-reversible CQ resistance (CQR). In the presence of mutant PfCRT, additional genes contribute to the wide range of CQ susceptibilities observed. It is not known if these genes influence mechanisms of chemosensitization by CQR reversal agents. Using quantitative trait locus (QTL) mapping of progeny clones from the HB3 × Dd2 cross, we show that the P. falciparum multidrug resistance gene 1 (pfmdr1) interacts with the South-East Asia-derived mutant pfcrt haplotype to modulate CQR levels. A novel chromosome 7 locus is predicted to contribute with the pfcrt and pfmdr1 loci to influence CQR levels. Chemoreversal via a wide range of chemical structures operates through a direct pfcrt-based mechanism. Direct inhibition of parasite growth by these reversal agents is influenced by pfcrt mutations and additional loci. Direct labelling of purified recombinant PfMDR1 protein with a highly specific photoaffinity CQ analogue, and lack of competition for photolabelling by VP, supports our QTL predictions. We find no evidence that pfmdr1 copy number affects CQ response in the progeny; however, inheritance patterns indicate that an allele-specific interaction between pfmdr1 and pfcrt is part of the complex genetic background of CQR.

In vitro selection of Plasmodium falciparum drug-resistant parasite lines

The in vitro selection of antimicrobial resistance in important pathogens can provide critical information on the genetic basis of drug resistance, and such information can be used to predict, anticipate and even contain the spread of resistance in clinical practice. For instance, the discovery of the role of pfmdr1 in mefloquine resistance in malaria parasites resulted from in vitro studies. However, the in vitro selection of resistance is difficult, challenging and time consuming. In this review, we discuss the key parameters that impact on the efficiency of the in vitro selection of resistance, and propose strategies to improve and streamline this process.

Identification and bioinformatic characterization of a multidrug resistance associated protein (ABCC) gene in Plasmodium berghei

Background

The ATP-binding cassette (ABC) superfamily is one of the largest evolutionarily conserved families of proteins. ABC proteins play key roles in cellular detoxification of endobiotics and xenobiotics. Overexpression of certain ABC proteins, among them the multidrug resistance associated protein (MRP), contributes to drug resistance in organisms ranging from human neoplastic cells to parasitic protozoa. In the present study, the Plasmodium berghei mrp gene (pbmrp) was partially characterized and the predicted protein was classified using bioinformatics in order to explore its putative involvement in drug resistance.

Methods

The pbmrp gene from the P. berghei drug sensitive, N clone, was sequenced using a PCR strategy. Classification and domain organization of pbMRP were determined with bioinformatics. The Plasmodium spp. MRPs were aligned and analysed to study their conserved motifs and organization. Gene copy number and organization were determined via Southern blot analysis in both N clone and the chloroquine selected line, RC. Chromosomal Southern blots and RNase protection assays were employed to determine the chromosomal location and expression levels of pbmrp in blood stages.

Results

The pbmrp gene is a single copy, intronless gene with a predicted open reading frame spanning 5820 nucleotides. Bioinformatic analyses show that this protein has distinctive features characteristic of the ABCC sub-family. Multiple sequence alignments reveal a high degree of conservation in the nucleotide binding and transmembrane domains within the MRPs from the Plasmodium spp. analysed. Expression of pbmrp was detected in asexual blood stages. Gene organization, copy number and mRNA expression was similar in both lines studied. A chromosomal translocation was observed in the chloroquine selected RC line, from chromosome 13/14 to chromosome 8, when compared to the drug sensitive N clone.

Conclusion

In this study, the pbmrp gene was sequenced and classified as a member of the ABCC sub-family. Multiple sequence alignments reveal that this gene is homologous to the Plasmodium y. yoelii and Plasmodium knowlesi mrp, and the Plasmodium vivax and Plasmodium falciparum mrp2 genes. There were no differences in gene organization, copy number, or mRNA expression between N clone and the RC line, but a chromosomal translocation of pbmrp from chromosome 13/14 to chromosome 8 was detected in RC.

pfcrt is more than the Plasmodium falciparum chloroquine resistance gene: a functional and evolutionary perspective

Genetic, physiological and pharmacological studies are gradually revealing the molecular basis of chloroquine resistance (CQR) in the malaria parasite, Plasmodium falciparum. Recent highlights include the discovery of a key gene associated with resistance, pfcrt (Plasmodium falciparum chloroquine resistance transporter; PfCRT), encoding a novel transporter, and the characterization of global selective sweeps of haplotypes containing a K76T amino acid change within this protein. Little is known about the cellular mechanism by which resistant parasites escape the effects of chloroquine (CQ), one of the most promising drugs ever deployed, due in part to an unresolved mechanism of action. The worldwide spread of CQR argues that investigations into these mechanisms are of little value. We propose, to the contrary, that the reconstruction of the evolutionary and molecular events underlying CQR is important at many levels, including: (i) its potential to assist in the development of rational approaches to thwart future drug resistances; (ii) the stimulation of the use of CQ-like compounds in drug combinations for new therapeutic approaches; and (iii) the consideration of how the CQ-selected genome will function as the context in which current and future drugs will act, particularly in light of the many reports of multidrug resistance. The purpose of this review is to highlight, discuss and in some cases challenge the interpretations of recent findings on CQR. We consider the natural function of the PfCRT protein, the role of multiple genes and "genetic background" in the CQR mechanism, and the evolution of CQR in parasite populations. Genetic transformation techniques are improving in P. falciparum and continue to provide important insight into CQR. Here, we also discuss more subtle, yet important pharmacological approaches that may have been overlooked in a traditional "gene for drug resistance" way of thinking.

Alternative mutations at position 76 of the vacuolar transmembrane protein PfCRT are associated with chloroquine resistance and unique stereospecific quinine and quinidine responses in Plasmodium falciparum

Chloroquine resistance (CQR) in Plasmodium falciparum is associated with multiple mutations in the digestive vacuole membrane protein PfCRT. The chloroquine-sensitive (CQS) 106/1 line of P. falciparum has six of seven PfCRT mutations consistently found in CQR parasites from Asia and Africa. The missing mutation at position 76 (K76T in reported population surveys) may therefore be critical to CQR. To test this hypothesis, we exposed 106/1 populations (10(9)-10(10) parasites) to a chloroquine (CQ) concentration lethal to CQS parasites. In multiple independent experiments, surviving CQR parasites were detected in the cultures after 28 to 42 days. These parasites showed novel K76N or K76I PfCRT mutations and corresponding CQ IC(50) values that were approximately 8- and 12-fold higher than that of the original 106/1 IC(50). A distinctive feature of the K76I line relative to 106/1 parasites was their greatly increased sensitivity to quinine (QN) but reduced sensitivity to its enantiomer quinidine (QD), indicative of a unique stereospecific response not observed in other CQR lines. Furthermore, verapamil had the remarkable effect of antagonizing the QN response while potentiating the QD response of K76I parasites. In our single-step drug selection protocol, the probability of the simultaneous selection of two specific mutations required for CQR is extremely small. We conclude that the K76N or K76I change added to the other pre-existing mutations in the 106/1 PfCRT protein was responsible for CQR. The various mutations that have now been documented at PfCRT position 76 (K76T, K76N, K76I) suggest that the loss of lysine is central to the CQR mechanism.

Of mice and malaria mutants: unravelling the genetics of drug resistance using rodent malaria models

It is well recognized that drug resistance is the most significant obstacle to gaining effective malaria control. Despite the enormous advances in the knowledge of the biochemistry and molecular biology of malaria parasites, only a few genes determining resistance to the commonly used drugs have been identified. The idea that rodent malaria parasites should be exploited more widely for such work, in view of the practical problems of studying this subject experimentally in human malaria, is presented.

Pleiotropic resistance to diverse antimalarials in actinomycin D-resistant Plasmodium falciparum

The development and spread of multidrug-resistant Plasmodium falciparum are major health concerns. The molecular mechanisms of multidrug resistance, including resistance to many quinoline-based antimalarials, are largely unknown. In this study, we report on the isolation and partial characterization of actinomycin D (actD)-resistant P. falciparum (3D7(R)/actD2.3) from a chloroquine-susceptible strain, 3D7. The stepwise selection of an actD-resistant clone (3D7(R)/actD2.3) led to the isolation and cloning of P. falciparum that grew in the presence of 2 ng/mL of actD. The parental isolate (3D7) did not grow in the presence of a 10-fold lower drug concentration (0.2 ng/mL). The latter estimate of parasite growth was determined by direct counting of parasites in infected red blood cells. Estimates of drug resistance levels to actD, using a [(3)H]hypoxanthine uptake and incorporation method, showed a 3-fold difference in the IC(50) between 3D7 and 3D7(R)/actD2.3. Interestingly, 3D7(R)/actD2.3 P. falciparum parasites were less sensitive to several antimalarials (chloroquine, mefloquine, quinidine, and artemisinin) and to the mitochondrial specific dye Rhodamine 123. Drug transport studies using [(3)H]actD showed that 3D7(R)/actD2.3 accumulated less drug than 3D7. Moreover, the accumulation of [(3)H]actD was energy dependent. To determine if Pfmdr1 expression, previously implicated in drug resistance to certain antimalarials, mediated the resistance phenotype of 3D7(R)/actD2.3, Pfmdr1 levels in 3D7 and 3D7(R)/actD2.3 were compared by Southern and northern blot analyses. Our results revealed no differences in Pfmdr1 copy number or mRNA levels between 3D7 and 3D7(R)/actD2.3. Furthermore, comparison of Pfmdr1 sequences between 3D7 and 3D7(R)/actD2.3 showed no differences. In addition, verapamil, which reverses P-glycoprotein-mediated drug resistance in mammalian cells, did not reverse the resistance of 3D7(R)/actD2.3 to actD or chloroquine. Taken together, the findings of this study demonstrated that in vitro selection of P. falciparum for resistance to actD leads to decreased sensitivity to diverse drugs and that this pleiotropic drug resistance is associated with reduced drug accumulation not mediated by Pfmdr1.

Correlation of in vivo-resistance to chloroquine and allelic polymorphisms in Plasmodium falciparum isolates from Uganda

The efficacy of chloroquine in the treatment of uncomplicated falciparum malaria in Africa is heavily compromised by high levels of drug resistance. The occurrence of active site mutations in the Plasmodium falciparum multi drug resistance-gene 1 (pfmdr1) has been associated with development of resistance to chloroquine. This study investigates the occurrence of several mutations at codons 86, 1042 and 1246 of the pfmdr1-gene in infected blood samples taken from Ugandan children before treatment with chloroquine and their relationship to clinical and parasitological resistance. Even though a clear association of CQR to one certain pfmdr1 single point mutation could not be substantiated, the frequency of resistance was consistently higher for samples revealing any of the mutations than among wild type samples, and 90% of the clinically resistant samples did present a mutation. Thus detection of these allelic pfmdr1 polymorphisms is not a decisive factor for prediction of clinical chloroquine resistance, but an interplay of the different mutations with unknown cofactors is to be assumed and the possible role of other genetic alterations remains to be investigated.

Direct binding of chloroquine to the multidrug resistance protein (MRP): possible role for MRP in chloroquine drug transport and resistance in tumor cells

Multidrug resistance protein (MRP) transports a range of compounds that include glutathione S-conjugates, amphiphilic anionic drugs, and natural-product toxins. However, the mechanism of MRP drug binding and transport is presently unclear. We recently demonstrated the direct binding of a quinoline-based photoactive drug, N-[4-[1-hydroxy-2-(dibutylamino)ethyl]quinolin-8-yl]-4-az idosalicylamide (IAAQ), to MRP at a biologically relevant site [Vezmar et al., Biochem Biophys Res Commun 241: 104-111, 1997]. In the present report, we demonstrated that the lysosomotropic or antimalarial drug chloroquine is a substrate for MRP. Specifically, our results showed that chloroquine, similar to leukotriene C4 (LTC4) and 3-(3-(2-(7-chloro-2-quinolinyl)ethenyl-phenyl)((3-(dimethyl amino-3-oxo propyl)thio)methyl)thio) propanoic acid (MK 571), inhibits the photoaffinity labeling of MRP by IAAQ. Furthermore, cell growth assays showed MRP-expressing multidrug-resistant cells (H69/AR and HL60/AR) to be more resistant to chloroquine than their parental cells (i.e., IC50 of 121 microM versus 28 microM chloroquine for H69/AR and H69, respectively). Moreover, MK 571, an LTD4 receptor antagonist, reversed the resistance of H69/AR cells to chloroquine. Drug transport studies using [14C]chloroquine demonstrated that MRP-expressing cells accumulate less drug than the parental drug-sensitive cells. The reduced accumulation of [14C]chloroquine in resistant cells was ATP dependent and was due to enhanced drug efflux. Taken together, the results of this study show that MRP modulates the transport of chloroquine by direct binding.

A comparison of the phenomenology and genetics of multidrug resistance in cancer cells and quinoline resistance in Plasmodium falciparum

Plasmodium falciparum is the causative agent of the most deadly form of human malaria. Chemotherapy traditionally has been the main line of defense against this parasite, and chloroquine, the drug of choice, has been one of the most successful drugs ever developed. Unfortunately, the evolution and spread of resistance to chloroquine and other quinoline-containing drugs means that these compounds are now virtually useless in many endemic areas. Future prospects for the use of quinoline compounds improved considerably when it was demonstrated that chloroquine resistance could be circumvented in vitro by a number of structurally and functionally unrelated compounds such as verapamil and desipramine. The phenomenon of resistance reversal by compounds such as verapamil is also a key feature of drug resistance in mammalian cells, and this has raised the possibility that the underlying mechanisms of drug resistance of the two cell types could be similar. This hypothesis has prompted a large number of studies into the genetics and biochemistry of resistance to quinoline-containing drugs in P. falciparum. Both the genetic and the biochemical studies have raised issues of controversy and stimulated much debate. These issues are discussed in this review, in the context of a comparison with the genetics and biochemistry of multidrug resistance in mammalian cells.

Assessment of pfmdr 1 gene copy number by tandem competitive polymerase chain reaction

The pfmdr 1 gene encodes a Plasmodium falciparum homologue of the human P-glycoprotein expressed on the surface of the parasite food vacuole. Variation in copy number and specific codon mutations of pfmdr 1 have been implicated in the development of parasite resistance to antimalarial drugs. We describe here the technique of Tandem-Competitive Polymerase Chain Reaction (TC-PCR), which allows accurate measurement of pfmdr 1 copy number in parasite DNA obtained directly from small quantities (100 microliters) of red blood cells. We reliably quantified pfmdr1 in previously well characterised strains of Plasmodium falciparum with differing pfmdr1 gene copy numbers using starting amounts of between 3,000 and 40,000 gene copies. We then used TC-PCR to determine pfmdr1 gene copy number in field specimens of venous blood taken from 10 patients with malaria contracted along the Thai-Burmese border. In this region of high grade parasite resistance to mefloquine greater than 70% of samples had a copy number greater than 1 of pfmdr1 determined with a repeatability coefficient of 0.58.