Exploring metabolomic approaches to analyse phospholipid biosynthetic pathways in Plasmodium

Recent metabolomic developments for antimalarial drug discovery

Malaria is a parasitic disease that remains a global health issue, responsible for a significant death and morbidity toll. Various factors have impacted the use and delayed the development of antimalarial therapies, such as the associated financial cost and parasitic resistance. In order to discover new drugs and validate parasitic targets, a powerful omics tool, metabolomics, emerged as a reliable approach. However, as a fairly recent method in malaria, new findings are timely and original practices emerge frequently. This review aims to discuss recent research towards the development of new metabolomic methods in the context of uncovering antiplasmodial mechanisms of action in vitro and to point out innovative metabolic pathways that can revitalize the antimalarial pipeline.

Adapt or Die: Targeting Unique Transmission-Stage Biology for Malaria Elimination

Plasmodium parasites have a complex life cycle that includes development in the human host as well as the Anopheles vector. Successful transmission of the parasite between its host and vector therefore requires the parasite to balance its investments in asexual replication and sexual reproduction, varying the frequency of sexual commitment to persist within the human host and generate future opportunities for transmission. The transmission window is extended further by the ability of stage V gametocytes to circulate in peripheral blood for weeks, whereas immature stage I to IV gametocytes sequester in the bone marrow and spleen until final maturation. Due to the low gametocyte numbers in blood circulation and with the ease of targeting such life cycle bottlenecks, transmission represents an efficient target for therapeutic intervention. The biological process of Plasmodium transmission is a multistage, multifaceted process and the past decade has seen a much deeper understanding of the molecular mechanisms and regulators involved. Clearly, specific and divergent processes are used during transmission compared to asexual proliferation, which both poses challenges but also opportunities for discovery of transmission-blocking antimalarials. This review therefore presents an update of our molecular understanding of gametocyte and gamete biology as well as the status of transmission-blocking activities of current antimalarials and lead development compounds. By defining the biological components associated with transmission, considerations for the development of new transmission-blocking drugs to target such untapped but unique biology is suggested as an important, main driver for transmission-blocking drug discovery.

Multi-omics approaches to improve malaria therapy

Malaria contributes to the most widespread infectious diseases worldwide. Even though current drugs are commercially available, the ever-increasing drug resistance problem by malaria parasites poses new challenges in malaria therapy. Hence, searching for efficient therapeutic strategies is of high priority in malaria control. In recent years, multi-omics technologies have been extensively applied to provide a more holistic view of functional principles and dynamics of biological mechanisms. We briefly review multi-omics technologies and focus on recent malaria progress conducted with the help of various omics methods. Then, we present up-to-date advances for multi-omics approaches in malaria. Next, we describe resistance phenomena to established antimalarial drugs and underlying mechanisms. Finally, we provide insight into novel multi-omics approaches, new drugs and vaccine developments and analyze current gaps in multi-omics research. Although multi-omics approaches have been successfully used in malaria studies, they are still limited. Many gaps need to be filled to bridge the gap between basic research and treatment of malaria patients. Multi-omics approaches will foster a better understanding of the molecular mechanisms of Plasmodium that are essential for the development of novel drugs and vaccines to fight this disastrous disease.

Perturbations of Metabolomic Profiling of Spleen From Rats Infected With Clonorchis sinensis Determined by LC-MS/MS Method

Clonorchiasis is an important zoonotic parasitic disease worldwide. In view of the fact that parasite infection affects host metabolism, and there is an intricate relationship between metabolism and immunity. Metabolic analysis of the spleen could be helpful for understanding the pathophysiological mechanisms in clonorchiasis. A non-targeted ultra high performance liquid tandem chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF MS) approach was employed to investigate the metabolic profiles of spleen in rats at 4 and 8 weeks post infection with Clonorchis sinensis (C. sinensis). Then a targeted ultra-high performance liquid chromatography multiple reaction monitoring mass spectrometry (UHPLC-MRM-MS/MS) approach was used to further quantify amino acid metabolism. Multivariate data analysis methods, such as principal components analysis and orthogonal partial least squares discriminant analysis, were used to identify differential metabolites. Finally, a total of 396 and 242 significant differential metabolites were identified in ESI+ and ESI− modes, respectively. These metabolites included amino acids, nucleotides, carboxylic acids, lipids and carbohydrates. There were 38 significantly different metabolites shared in the two infected groups compared with the control group through the Venn diagram. The metabolic pathways analysis revealed that pyrimidine metabolism, aminoacyl-tRNA biosynthesis, purine metabolism and phenylalanine, tyrosine and tryptophan biosynthesis were significantly enriched in differential metabolites, which was speculated to be related to the disease progression of clonorchiasis. Furthermore, 15 amino acids screened using untargeted profiling can be accurately quantified and identifed by targeted metabolomics during clonrochiasis. These results preliminarily revealed the perturbations of spleen metabolism in clonorchiasis. Meanwhile, this present study supplied new insights into the molecular mechanisms of host-parasite interactions.

Early prediction of cerebral malaria by (1)H NMR based metabolomics

BACKGROUND

Cerebral malaria (CM) is a life-threatening disease, caused mainly by Plasmodium falciparum in humans. In adults only 1-2% of P. falciparum-infected hosts transit to the cerebral form of the disease while most exhibit non-cerebral malaria (NCM). The perturbed metabolic pathways of CM and NCM have been reported. Early marker(s) of CM is(are) not known and by the time a patient exhibits the pathological symptoms of CM, the disease has progressed. Murine CM, like the human disease, is difficult to assign to specific animals at early stage and hence the challenge to treat CM at pre-clinical stage of the disease. This is the first report of prediction of CM in mice using a novel strategy based on (1)H nuclear magnetic resonance (NMR)-based metabolomics.

METHODS

Mice were infected with malarial parasites, and serum was collected from all the animals (CM/NCM) before CM symptoms were apparent. The assignment of mice as NCM/CM at an early time point is based on their symptoms at days 8-9 post-infection (pi). The serum samples were subjected to (1)H NMR-based metabolomics. (1)H NMR spectra of the serum samples, collected at various time points (pi) in multiple sets of experiments, were subjected to multivariate analyses.

RESULTS

The results from orthogonal partial least square discriminant analyses (OPLS-DA) suggest that the animals with CM start to diverge out in metabolic profile and were distinct on day 4 pi, although by physical observation they were indistinguishable from the NCM. The metabolites that appeared to contribute to this distinction were serum lipids and lipoproteins, and 14-19% enhancement was observed in mice afflicted with CM. A cut-off of 14% change of total lipoproteins in serum predicts 54-71% CM in different experiments at day 4 pi.

CONCLUSION

This study clearly demonstrates the possibility of differentiating and identifying animals with CM at an early, pre-clinical stage. The strategy, based on metabolite profile of serum, tested with different batches of animals in both the sex and across different times of the year, is found to be robust. This is the first such study of pre-clinical prognosis of CM.

Changes in lipid composition during sexual development of the malaria parasite Plasmodium falciparum

Background

The development of differentiated sexual stages (gametocytes) within human red blood cells is essential for the propagation of the malaria parasite, since only mature gametocytes will survive in the mosquito’s midgut. Hence gametocytogenesis is a pre-requisite for transmission of the disease. Physiological changes involved in sexual differentiation are still enigmatic. In particular the lipid metabolism—despite being central to cellular regulation and development—is not well explored.

Methods

Here the lipid profiles of red blood cells infected with the five different sexual stages of Plasmodium falciparum were analysed by mass spectrometry and compared to those from uninfected and asexual trophozoite infected erythrocytes.

Results

Fundamental differences between erythrocytes infected with the different parasite stages were revealed. In mature gametocytes many lipids that decrease in the trophozoite and early gametocyte infected red blood cells are regained. In particular, regulators of membrane fluidity, cholesterol and sphingomyelin, increased significantly during gametocyte maturation. Neutral lipids (serving mainly as caloriometric reserves) increased from 3 % of total lipids in uninfected to 27 % in stage V gametocyte infected red blood cells. The major membrane lipid class (phospholipids) decreased during gametocyte development.

Conclusions

The lipid profiles of infected erythrocytes are characteristic for the particular parasite life cycle and maturity stages of gametocytes. The obtained lipid profiles are crucial in revealing the lipid metabolism of malaria parasites and identifying targets to interfere with this deadly disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-016-1130-z) contains supplementary material, which is available to authorized users.

Inward cholesterol gradient of the membrane system in P. falciparum-infected erythrocytes involves a dilution effect from parasite-produced lipids

Plasmodium falciparum (Pf) infection remodels the human erythrocyte with new membrane systems, including a modified host erythrocyte membrane (EM), a parasitophorous vacuole membrane (PVM), a tubulovesicular network (TVN), and Maurer's clefts (MC). Here we report on the relative cholesterol contents of these membranes in parasitized normal (HbAA) and hemoglobin S-containing (HbAS, HbAS) erythrocytes. Results from fluorescence lifetime imaging microscopy (FLIM) experiments with a cholesterol-sensitive fluorophore show that membrane cholesterol levels in parasitized erythrocytes (pRBC) decrease inwardly from the EM, to the MC/TVN, to the PVM, and finally to the parasite membrane (PM). Cholesterol depletion of pRBC by methyl-β-cyclodextrin treatment caused a collapse of this gradient. Lipid and cholesterol exchange data suggest that the cholesterol gradient involves a dilution effect from non-sterol lipids produced by the parasite. FLIM signals from the PVM or PM showed little or no difference between parasitized HbAA vs HbS-containing erythrocytes that differed in lipid content, suggesting that malaria parasites may regulate the cholesterol contents of the PVM and PM independently of levels in the host cell membrane. Cholesterol levels may affect raft structures and the membrane trafficking and sorting functions that support Pf survival in HbAA, HbAS and HbSS erythrocytes.

Plasmodium falciparum is dependent on de novo myo-inositol biosynthesis for assembly of GPI glycolipids and infectivity

Intra-erythrocytic stages of the malaria parasite, Plasmodium falciparum, are thought to be dependent on de novo synthesis of phosphatidylinositol, as red blood cells (RBC) lack the capacity to synthesize this phospholipid. The myo-inositol headgroup of PI can either be synthesized de novo or scavenged from the RBC. An untargeted metabolite profiling of P. falciparum infected RBC showed that trophozoite and schizont stages accumulate high levels of myo-inositol-3-phosphate, indicating increased de novo biosynthesis of myo-inositol from glucose 6-phosphate. Metabolic labelling studies with (13) C-U-glucose in the presence and absence of exogenous inositol confirmed that de novo myo-inositol synthesis occurs in parallel with myo-inositol salvage pathways. Unexpectedly, while both endogenous and scavenged myo-inositol was used to synthesize bulk PI, only de novo-synthesized myo-inositol was incorporated into GPI glycolipids. Moreover, gene disruption studies suggested that the INO1 gene, encoding myo-inositol 3-phosphate synthase, is essential in asexual parasite stages. Together these findings suggest that P. falciparum asexual stages are critically dependent on de novo myo-inositol biosynthesis for assembly of a sub-pool of PI species and GPI biosynthesis. These findings highlight unexpected complexity in phospholipid biosynthesis in P. falciparum and a lack of redundancy in some nutrient salvage versus endogenous biosynthesis pathways.

A quantitative liquid chromatography tandem mass spectrometry method for metabolomic analysis of Plasmodium falciparum lipid related metabolites

Plasmodium falciparum is the causative agent of malaria, a deadly infectious disease for which treatments are scarce and drug-resistant parasites are now increasingly found. A comprehensive method of identifying and quantifying metabolites of this intracellular parasite could expand the arsenal of tools to understand its biology, and be used to develop new treatments against the disease. Here, we present two methods based on liquid chromatography tandem mass spectrometry for reliable measurement of water-soluble metabolites involved in phospholipid biosynthesis, as well as several other metabolites that reflect the metabolic status of the parasite including amino acids, carboxylic acids, energy-related carbohydrates, and nucleotides. A total of 35 compounds was quantified. In the first method, polar compounds were retained by hydrophilic interaction chromatography (amino column) and detected in negative mode using succinic acid-(13)C(4) and fluorovaline as internal standards. In the second method, separations were carried out using reverse phase (C18) ion-pair liquid chromatography, with heptafluorobutyric acid as a volatile ion pairing reagent in positive detection mode, using d(9)-choline and 4-aminobutanol as internal standards. Standard curves were performed in P. falciparum-infected and uninfected red blood cells using standard addition method (r(2)>0.99). The intra- and inter-day accuracy and precision as well as the extraction recovery of each compound were determined. The lower limit of quantitation varied from 50pmol to 100fmol/3×10(7)cells. These methods were validated and successfully applied to determine intracellular concentrations of metabolites from uninfected host RBCs and isolated Plasmodium parasites.

Metabolomic analysis of patient plasma yields evidence of plant-like α-linolenic acid metabolism in Plasmodium falciparum

Metabolomics offers a powerful means to investigate human malaria parasite biology and host-parasite interactions at the biochemical level, and to discover novel therapeutic targets and biomarkers of infection. Here, we used an approach based on liquid chromatography and mass spectrometry to perform an untargeted metabolomic analysis of metabolite extracts from Plasmodium falciparum-infected and uninfected patient plasma samples, and from an enriched population of in vitro cultured P. falciparum-infected and uninfected erythrocytes. Statistical modeling robustly segregated infected and uninfected samples based on metabolite species with significantly different abundances. Metabolites of the α-linolenic acid (ALA) pathway, known to exist in plants but not known to exist in P. falciparum until now, were enriched in infected plasma and erythrocyte samples. In vitro labeling with (13)C-ALA showed evidence of plant-like ALA pathway intermediates in P. falciparum. Ortholog searches using ALA pathway enzyme sequences from 8 available plant genomes identified several genes in the P. falciparum genome that were predicted to potentially encode the corresponding enzymes in the hitherto unannotated P. falciparum pathway. These data suggest that our approach can be used to discover novel facets of host/malaria parasite biology in a high-throughput manner.

Harnessing genomics and genome biology to understand malaria biology

Malaria is an important human disease and is the target of a global eradication campaign. New technological and informatics advancements in population genomics are being leveraged to identify genetic loci under selection in the malaria parasite and to find variants that are associated with key clinical phenotypes, such as drug resistance. This article provides a timely Review of how population-genetics-based strategies are being applied to Plasmodium falciparum both to identify genetic loci as key targets of interventions and to develop monitoring and surveillance tools that are crucial for the successful elimination and eradication of malaria.

Application of genomics to field investigations of malaria by the international centers of excellence for malaria research

Success of the global research agenda toward eradication of malaria will depend on development of new tools, including drugs, vaccines, insecticides and diagnostics. Genomic information, now available for the malaria parasites, their mosquito vectors, and human host, can be leveraged to both develop these tools and monitor their effectiveness. Although knowledge of genomic sequences for the malaria parasites, Plasmodium falciparum and Plasmodium vivax, have helped advance our understanding of malaria biology, simply knowing this sequence information has not yielded a plethora of new interventions to reduce the burden of malaria. Here we review and provide specific examples of how genomic information has increased our knowledge of parasite biology, focusing on P. falciparum malaria. We then discuss how population genetics can be applied toward the epidemiological and transmission-related goals outlined by the International Centers of Excellence for Malaria Research groups recently established by the National Institutes of Health. Finally, we propose genomics is a research area that can promote coordination and collaboration between various ICEMR groups, and that working together as a community can significantly advance the value of this information toward reduction of the global malaria burden.

Extraction of hydrophilic metabolites from Plasmodium falciparum-infected erythrocytes for metabolomic analysis

Metabolomics is an increasingly common analytical approach for investigating metabolic networks of pathogenic organisms. This may be of particular use in the study of parasitic infections due to the intrinsic metabolic connection between the parasite and its host. In vitro cultures of the malaria parasite Plasmodium falciparum present a valuable platform to elucidate the structure and dynamics of the parasite's metabolic network and to determine the mechanisms of action of antimalarial drugs and drug resistance mutations. Accurately measuring metabolite levels requires a reproducible method for quantifying intracellular metabolites. Here we present a simple protocol for extracting hydrophilic metabolites from P. falciparum-infected erythrocyte cultures.

Target identification and validation of novel antimalarials

It has been recognized that new antimalarials with a novel mode of action are critical to combat the continued emergence and dissemination of drug-resistant parasites that threaten the efficacy of current malaria treatments. Thus, recent high-throughput screening campaigns have been initiated using asexual intraerythrocytic stage cell-based assays of Plasmodium falciparum. These have led to the unprecedented identification of over 10,000 new antimalarial compounds. Inherently, novel compounds identified by cell-based assays will have poorly defined modes of action. While some of these compounds may have recognizable targets, the majority of cell-based hits are comprised of unique chemical scaffolds usually lacking cross-resistance with known drugs. It is likely that these novel antimalarial scaffolds will reveal new targets. A challenge for the community will be to assign these small molecules to their targets. In this article, we review methodologies to assist in the determination of a compound's mode of action.

A research agenda for malaria eradication: basic science and enabling technologies

Today's malaria control efforts are limited by our incomplete understanding of the biology of Plasmodium and of the complex relationships between human populations and the multiple species of mosquito and parasite. Research priorities include the development of in vitro culture systems for the complete life cycle of P. falciparum and P. vivax and the development of an appropriate liver culture system to study hepatic stages. In addition, genetic technologies for the manipulation of Plasmodium need to be improved, the entire parasite metabolome needs to be characterized to identify new druggable targets, and improved information systems for monitoring the changes in epidemiology, pathology, and host-parasite-vector interactions as a result of intensified control need to be established to bridge the gap between bench, preclinical, clinical, and population-based sciences.

Metabolomics and malaria biology

Metabolomics has ushered in a novel and multi-disciplinary realm in biological research. It has provided researchers with a platform to combine powerful biochemical, statistical, computational, and bioinformatics techniques to delve into the mysteries of biology and disease. The application of metabolomics to study malaria parasites represents a major advance in our approach towards gaining a more comprehensive perspective on parasite biology and disease etiology. This review attempts to highlight some of the important aspects of the field of metabolomics, and its ongoing and potential future applications to malaria research.

Central carbon metabolism of Plasmodium parasites

The central role of metabolic perturbation to the pathology of malaria, the promise of antimetabolites as antimalarial drugs and a basic scientific interest in understanding this fascinating example of highly divergent microbial metabolism has spurred a major and concerted research effort towards elucidating the metabolic network of the Plasmodium parasites. Central carbon metabolism, broadly comprising the flow of carbon from nutrients into biomass, has been a particular focus due to clear and early indications that it plays an essential role in this network. Decades of painstaking efforts have significantly clarified our understanding of these pathways of carbon flux, and this foundational knowledge, coupled with the advent of advanced analytical technologies, have set the stage for the development of a holistic, network-level model of plasmodial carbon metabolism. In this review we summarize the current state of knowledge regarding central carbon metabolism and suggest future avenues of research. We focus primarily on the blood stages of Plasmodium falciparum, the most lethal of the human malaria parasites, but also integrate results from simian, avian and rodent models of malaria that were a major focus of early investigations into plasmodial metabolism.

Eating at the table of another: metabolomics of host-parasite interactions

The application of metabolomics, the global analysis of metabolite levels, to the study of protozoan parasites has become an important tool for understanding the host-parasite relationship and holds promise for the development of direly needed therapeutics and improved diagnostics. Research advances over the past decade have opened the door for a systems biology approach to protozoan parasites with metabolomics, providing a crucial readout of metabolic activity. In this review, we highlight recent metabolomic approaches to protozoan parasites, including metabolite profiling, integration with genomics, transcription, and proteomic analysis, and the use of metabolic fingerprints for the diagnosis of parasitic infections.