The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen-encoding var genes.

Within the human host, the malaria parasite Plasmodium falciparum is exposed to multiple selection pressures. The host environment changes dramatically in severe malaria, but the extent to which the parasite responds to-or is selected by-this environment remains unclear. From previous studies, the parasites that cause severe malaria appear to increase expression of a restricted but poorly defined subset of the PfEMP1 variant, surface antigens. PfEMP1s are major targets of protective immunity. Here, we used RNA sequencing (RNAseq) to analyse gene expression in 44 parasite isolates that caused severe and uncomplicated malaria in Papuan patients. The transcriptomes of 19 parasite isolates associated with severe malaria indicated that these parasites had decreased glycolysis without activation of compensatory pathways; altered chromatin structure and probably transcriptional regulation through decreased histone methylation; reduced surface expression of PfEMP1; and down-regulated expression of multiple chaperone proteins. Our RNAseq also identified novel associations between disease severity and PfEMP1 transcripts, domains, and smaller sequence segments and also confirmed all previously reported associations between expressed PfEMP1 sequences and severe disease. These findings will inform efforts to identify vaccine targets for severe malaria and also indicate how parasites adapt to-or are selected by-the host environment in severe malaria.

Activation and clustering of a Plasmodium falciparum var gene are affected by subtelomeric sequences.

The Plasmodium falciparum var multigene family encodes the cytoadhesive, variant antigen PfEMP1. P. falciparum antigenic variation and cytoadhesion specificity are controlled by epigenetic switching between the single, or few, simultaneously expressed var genes. Most var genes are maintained in perinuclear clusters of heterochromatic telomeres. The active var gene(s) occupy a single, perinuclear var expression site. It is unresolved whether the var expression site forms in situ at a telomeric cluster or whether it is an extant compartment to which single chromosomes travel, thus controlling var switching. Here we show that transcription of a var gene did not require decreased colocalisation with clusters of telomeres, supporting var expression site formation in situ. However following recombination within adjacent subtelomeric sequences, the same var gene was persistently activated and did colocalise less with telomeric clusters. Thus, participation in stable, heterochromatic, telomere clusters and var switching are independent but are both affected by subtelomeric sequences. The var expression site colocalised with the euchromatic mark H3K27ac to a greater extent than it did with heterochromatic H3K9me3. H3K27ac was enriched within the active var gene promoter even when the var gene was transiently repressed in mature parasites and thus H3K27ac may contribute to var gene epigenetic memory.

Functional Antibodies and Protection against Blood-stage Malaria.

Numerous efforts to understand the functional roles of antibodies demonstrated that they can protect against malaria. However, it is unclear which antibody responses are the best correlates of immunity, and which antibody functions are most important in protection from disease. Understanding the role of antibodies in protection against malaria is crucial for antimalarial vaccine design. In this review, the specific functional properties of naturally acquired and vaccine-induced antibodies that correlate to protection from the blood stages of Plasmodium falciparum malaria are re-examined and the gaps in knowledge related to antibody function in malarial immunity are highlighted.

Differences in PfEMP1s recognized by antibodies from patients with uncomplicated or severe malaria.

BACKGROUND: Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) variants are encoded by var genes and mediate pathogenic cytoadhesion and antigenic variation in malaria. PfEMP1s can be broadly divided into three principal groups (A, B and C) and they contain conserved arrangements of functional domains called domain cassettes. Despite their tremendous diversity there is compelling evidence that a restricted subset of PfEMP1s is expressed in severe disease. In this study antibodies from patients with severe and uncomplicated malaria were compared for differences in reactivity with a range of PfEMP1s to determine whether antibodies to particular PfEMP1 domains were associated with severe or uncomplicated malaria. METHODS: Parts of expressed var genes in a severe malaria patient were identified by RNAseq and several of these partial PfEMP1 domains were expressed together with others from laboratory isolates. Antibodies from Papuan patients to these parts of multiple PfEMP1 proteins were measured. RESULTS: Patients with uncomplicated malaria were more likely to have antibodies that recognized PfEMP1 of Group C type and recognized a broader repertoire of group A and B PfEMP1s than patients with severe malaria. CONCLUSION: These data suggest that exposure to a broad range of group A and B PfEMP1s is associated with protection from severe disease in Papua, Indonesia.

A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression.

During red-blood-cell-stage infection of Plasmodium falciparum, the parasite undergoes repeated rounds of replication, egress, and invasion. Erythrocyte invasion involves specific interactions between host cell receptors and parasite ligands and coordinated expression of genes specific to this step of the life cycle. We show that a parasite-specific bromodomain protein, PfBDP1, binds to chromatin at transcriptional start sites of invasion-related genes and directly controls their expression. Conditional PfBDP1 knockdown causes a dramatic defect in parasite invasion and growth and results in transcriptional downregulation of multiple invasion-related genes at a time point critical for invasion. Conversely, PfBDP1 overexpression enhances expression of these same invasion-related genes. PfBDP1 binds to acetylated histone H3 and a second bromodomain protein, PfBDP2, suggesting a potential mechanism for gene recognition and control. Collectively, these findings show that PfBDP1 critically coordinates expression of invasion genes and indicate that targeting PfBDP1 could be an invaluable tool in malaria eradication.

Malaria preventive therapy in pregnancy and its potential impact on immunity to malaria in an area of declining transmission.

BACKGROUND: Regular anti-malarial therapy in pregnancy, a pillar of malaria control, may affect malaria immunity, with therapeutic implications in regions of reducing transmission. METHODS: Plasma antibodies to leading vaccine candidate merozoite antigens and opsonizing antibodies to endothelial-binding and placental-binding infected erythrocytes were quantified in pregnant Melanesian women receiving sulfadoxine-pyrimethamine (SP) with chloroquine taken once, or three courses of SP with azithromycin. RESULTS: Malaria prevalence was low. Between enrolment and delivery, antibodies to recombinant antigens declined in both groups (p<0.0001). In contrast, median levels of opsonizing antibodies did not change, although levels for some individuals changed significantly. In multivariate analysis, the malaria prevention regimen did not influence antibody levels. CONCLUSION: Different preventive anti-malarial chemotherapy regimens used during pregnancy had limited impact on malarial-immunity in a low-transmission region of Papua New Guinea. TRIAL REGISTRATIONS: NCT01136850.

High numbers of circulating pigmented polymorphonuclear neutrophils as a prognostic marker for decreased birth weight during malaria in pregnancy.

During gestational malaria, Plasmodium falciparum-infected erythrocytes can sequester within the placenta, contributing to poor pregnancy outcomes, especially low birth weight. In children and non-pregnant adults, pigmented leukocytes may serve as markers of sequestered parasite burden and predict clinical outcomes. Here, we investigated circulating pigmented leukocyte numbers as predictors of clinical outcomes in pregnant women presenting with malaria at enrolment. The number of circulating pigmented neutrophils at enrolment negatively correlated with birth weight (Rho=-25, P=.04), suggesting these cells may have a pathogenic role in, and could serve as prognostic markers for, malaria-associated low birth weight.

Decreasing malaria prevalence and its potential consequences for immunity in pregnant women.

BACKGROUND: As malaria control is intensified, pregnant women may be less exposed to malaria, thus affecting the acquisition of protective antibody. METHODS: Plasma samples were collected from Malawian and Papua New Guinean (PNG) pregnant women enrolled over 7-year periods, during which malaria prevalence fell by over two thirds. Immunoglobulin G (IgG) levels to schizont extract, merozoite antigens, and VAR2CSA-DBL5ε were measured by enzyme-linked immunosorbent assay (ELISA). Levels of IgG to variant surface antigens of infected erythrocytes (IEs) and merozoites and levels of opsonizing IgG to IEs were measured by flow cytometry. RESULTS: In both settings, levels of antibodies in pregnant women to recombinant antigens and to intact IEs but not of opsonizing antibodies decreased over time. After adjustment for coverage with insecticide-treated bed nets (ITNs), these differences disappeared in the Malawian cohort, whereas in the PNG cohort, time was independently associated with a decrease in several antibody responses measured by ELISA. CONCLUSIONS: The impact of falling parasite prevalence on anti-Plasmodium falciparum serological indicators in pregnant women varies by setting. Increased ITN coverage may affect development of antibodies to recombinant antigens, but levels of opsonizing IgG remained stable over time. Opsonizing IgG against placental-binding IEs may persist, thus offering longer-lasting protection against malaria during pregnancy.

Malaria vaccine research and development: the role of the WHO MALVAC committee.

The WHO Malaria Vaccine Advisory Committee (MALVAC) provides advice to WHO on strategic priorities, activities and technical issues related to global efforts to develop vaccines against malaria. MALVAC convened a series of meetings to obtain expert, impartial consensus views on the priorities and best practice for vaccine-related research and development strategies. The technical areas covered during these consultations included: guidance on clinical trial design for candidate sporozoite and asexual blood stage vaccines; measures of efficacy of malaria vaccines in Phase IIb and Phase III trials; standardization of immunoassays; the challenges of developing assays and designing trials for interventions against malaria transmission; modelling impact of anti-malarial interventions; whole organism malaria vaccines, and Plasmodium vivax vaccine-related research and evaluation. These informed discussions and opinions are summarized here to provide guidance on harmonization of strategies to help ensure high standards of practice and comparability between centres and the outcome of vaccine trials.

Soluble CD163, a product of monocyte/macrophage activation, is inversely associated with haemoglobin levels in placental malaria.

In Plasmodium falciparum malaria, activation of monocytes and macrophages (monocytes/macrophages) can result in the production of various inflammatory mediators that contribute to immunopathology. Soluble CD163 (sCD163) is a specific marker of monocyte/macrophage activation typically found at increased levels during various inflammatory conditions and can be associated with poor clinical outcomes. To better understand the relationships between levels of sCD163 and clinical parameters in women with placental malaria, we measured plasma sCD163 levels in maternal peripheral and placental blood compartments at delivery and determined their correlations with birth weight and maternal haemoglobin concentrations. sCD163 levels were negatively correlated with birth weight only in the placental compartment (r = -0.145, p = 0.03) and were inversely correlated with maternal haemoglobin concentrations, both in peripheral blood (r = -0.238, p = 0.0004) and in placental blood (r = -0.259, p = 0.0001). These inverse relationships suggest a potential role for monocyte/macrophage activation in the pathogenesis of malaria in pregnancy, particularly in relation to malaria-associated anaemia.

H2A.Z and H2B.Z double-variant nucleosomes define intergenic regions and dynamically occupy var gene promoters in the malaria parasite Plasmodium falciparum.

Histone variants are important components of eukaryotic chromatin and can alter chromatin structure to confer specialized functions. H2B variant histones are rare in nature but have evolved independently in the phyla Apicomplexa and Trypanasomatida. Here, we investigate the apicomplexan-specific Plasmodium falciparum histone variant Pf H2B.Z and show that within nucleosomes Pf H2B.Z dimerizes with the H2A variant Pf H2A.Z and that Pf H2B.Z and Pf H2A.Z occupancy correlates in the subset of genes examined. These double-variant nucleosomes also carry common markers of euchromatin like H3K4me3 and histone acetylation. Pf H2B.Z levels are elevated in intergenic regions across the genome, except in the var multigene family, where Pf H2A.Z/Pf H2B.Z double-variant nucleosomes are only enriched in the promoter of the single active var copy and this enrichment is developmentally regulated. Importantly, this pattern seems to be specific for var genes and does not apply to other heterochromatic gene families involved in red blood cell invasion which are also subject to clonal expression. Thus, Pf H2A.Z/Pf H2B.Z double-variant nucleosomes appear to have a highly specific function in the regulation of P. falciparum virulence.

MALVAC 2012 scientific forum: accelerating development of second-generation malaria vaccines.

The World Health Organization (WHO) convened a malaria vaccines committee (MALVAC) scientific forum from 20 to 21 February 2012 in Geneva, Switzerland, to review the global malaria vaccine portfolio, to gain consensus on approaches to accelerate second-generation malaria vaccine development, and to discuss the need to update the vision and strategic goal of the Malaria Vaccine Technology Roadmap. This article summarizes the forum, which included reviews of leading Plasmodium falciparum vaccine candidates for pre-erythrocytic vaccines, blood-stage vaccines, and transmission-blocking vaccines. Other major topics included vaccine candidates against Plasmodium vivax, clinical trial site capacity development in Africa, trial design considerations for a second-generation malaria vaccine, adjuvant selection, and regulatory oversight functions including vaccine licensure.

A review of malaria vaccine clinical projects based on the WHO rainbow table.

Development and Phase 3 testing of the most advanced malaria vaccine, RTS,S/AS01, indicates that malaria vaccine R&D is moving into a new phase. Field trials of several research malaria vaccines have also confirmed that it is possible to impact the host-parasite relationship through vaccine-induced immune responses to multiple antigenic targets using different platforms. Other approaches have been appropriately tested but turned out to be disappointing after clinical evaluation. As the malaria community considers the potential role of a first-generation malaria vaccine in malaria control efforts, it is an apposite time to carefully document terminated and ongoing malaria vaccine research projects so that lessons learned can be applied to increase the chances of success for second-generation malaria vaccines over the next 10 years. The most comprehensive resource of malaria vaccine projects is a spreadsheet compiled by WHO thanks to the input from funding agencies, sponsors and investigators worldwide. This spreadsheet, available from WHO's website, is known as "the rainbow table". By summarizing the published and some unpublished information available for each project on the rainbow table, the most comprehensive review of malaria vaccine projects to be published in the last several years is provided below.

Development of vaccines to prevent malaria in pregnant women: WHO MALVAC meeting report.

The major public health consequences of malaria in pregnancy have long been acknowledged. However, further information is still required for development and implementation of a malaria vaccine specifically directed to prevent malaria in pregnant women and improve maternal, fetal and infant outcomes. The WHO Malaria Vaccine Advisory Committee (MALVAC) provides guidance to the WHO on strategic priorities and research needs for development of vaccines to prevent malaria. Here we summarize the discussions and conclusions of a MALVAC scientific forum meeting on considerations in the development of vaccines to prevent malaria in pregnant women. This report includes brief summaries of what is known, and major knowledge gaps in disease burden estimation, pathogenesis and immunity, and the challenges with current preventive strategies for malaria in pregnancy. We conclude with the formulation of a conceptual framework for research and development for vaccines to prevent malaria in pregnant women.

Expression of P. falciparum var genes involves exchange of the histone variant H2A.Z at the promoter.

Plasmodium falciparum employs antigenic variation to evade the human immune response by switching the expression of different variant surface antigens encoded by the var gene family. Epigenetic mechanisms including histone modifications and sub-nuclear compartmentalization contribute to transcriptional regulation in the malaria parasite, in particular to control antigenic variation. Another mechanism of epigenetic control is the exchange of canonical histones with alternative variants to generate functionally specialized chromatin domains. Here we demonstrate that the alternative histone PfH2A.Z is associated with the epigenetic regulation of var genes. In many eukaryotic organisms the histone variant H2A.Z mediates an open chromatin structure at promoters and facilitates diverse levels of regulation, including transcriptional activation. Throughout the asexual, intraerythrocytic lifecycle of P. falciparum we found that the P. falciparum ortholog of H2A.Z (PfH2A.Z) colocalizes with histone modifications that are characteristic of transcriptionally-permissive euchromatin, but not with markers of heterochromatin. Consistent with this finding, antibodies to PfH2A.Z co-precipitate the permissive modification H3K4me3. By chromatin-immunoprecipitation we show that PfH2A.Z is enriched in nucleosomes around the transcription start site (TSS) in both transcriptionally active and silent stage-specific genes. In var genes, however, PfH2A.Z is enriched at the TSS only during active transcription in ring stage parasites. Thus, in contrast to other genes, temporal var gene regulation involves histone variant exchange at promoter nucleosomes. Sir2 histone deacetylases are important for var gene silencing and their yeast ortholog antagonises H2A.Z function in subtelomeric yeast genes. In immature P. falciparum parasites lacking Sir2A or Sir2B high var transcription levels correlate with enrichment of PfH2A.Z at the TSS. As Sir2A knock out parasites mature the var genes are silenced, but PfH2A.Z remains enriched at the TSS of var genes; in contrast, PfH2A.Z is lost from the TSS of de-repressed var genes in mature Sir2B knock out parasites. This result indicates that PfH2A.Z occupancy at the active var promoter is antagonized by PfSir2A during the intraerythrocytic life cycle. We conclude that PfH2A.Z contributes to the nucleosome architecture at promoters and is regulated dynamically in active var genes.

Priorities in research and development of vaccines against Plasmodium vivax malaria.

The WHO Initiative for Vaccine Research (IVR) Malaria Vaccine Advisory Committee (MALVAC) provides advice to WHO on priorities in malaria vaccine research and development (R&D). This document summarizes a MALVAC scientific consultation of leading vaccine scientists on priorities in Plasmodium vivax vaccine R&D. The meeting discussed recent advances and key challenges in addressing identified gaps in knowledge. Major areas of discussion included disease burden estimates, clinical disease spectrum definitions, potential target product profiles and immunological and clinical research needed to better inform antigen selection and vaccine design. The need for further development of the human challenge model for P. vivax vaccines and specific considerations for conduct of field trials with P. vivax vaccines was outlined. This report summarizes the discussion and conclusions of the consultation, with recommendations for priority targeted research.

Guidance on the evaluation of Plasmodium vivax vaccines in populations exposed to natural infection.

In this paper we give guidance for the design and conduct of vaccine trials against Plasmodium vivax malaria. The paper supplements earlier guidelines on the planning of vaccine trials against Plasmodium falciparum malaria [WHO. Guidelines for the evaluation of Plasmodium falciparum vaccines in populations exposed to natural infections. Geneva: World Health Organization; 1997, http://www.who.int/vaccine_research/feuill_1_4-2.pdf], with further considerations in two later documents [Moorthy VS, Reed Z, Smith PG. Measurement of malaria vaccine efficacy in phase III trials: report of a WHO consultation. Vaccine 2007 July 9;25(28):5115-23; Moorthy V, Reed Z, Smith P. MALVAC 2008: measures of efficacy of malaria vaccines in phase 2b and phase 3 trials - scientific, regulatory and public health perspectives. Vaccine 2009 January 29;27(5):624-8]. We deal specifically with study design and methodological issues for the assessment of pre-erythrocytic and blood-stage vaccines against P. vivax. The role of vaccines in blocking transmission of P. vivax is not considered as the methodological issues are similar to those for P. falciparum, though longer follow-up would be required because of the potential for relapse discussed below. In this paper we discuss the rationale and background to trials of P. vivax vaccines, requirements for Phase IIb and Phase III field trials, implementation of clinical trials, methods of measurement and analysis, and ethical aspects.

Building quality in health--the need for clinical researchers.

Integration of research and education into health care delivery leads to improved outcomes and facilitates rapid translation of results into policy and practice. Australia is at great risk of losing the important contribution of clinical research conducted in our public hospital system. This risk is increasing as research and educational training are targeted for expenditure reduction in the current business models of health service delivery, which focus only on short-term outcomes. The Centres of Clinical Research Excellence Scheme--initiated by the National Health and Medical Research Council (NHMRC)--is an excellent step towards redressing this problem, but it cannot succeed in isolation. We must improve and optimise care through promotion of attractive sustainable career pathways to provide strong clinical and translational research capabilities in hospital settings that address current health priorities and new disciplines. Targeted investment in talented people is the greatest long-term contribution that governments can make to guarantee quality in national systems of health.

Ectopic recombination of a malaria var gene during mitosis associated with an altered var switch rate.

The Plasmodium falciparum var multigene family encodes P. falciparum erythrocyte membrane protein 1, which is responsible for the pathogenic traits of antigenic variation and adhesion of infected erythrocytes to host receptors during malaria infection. Clonal antigenic variation of P. falciparum erythrocyte membrane protein 1 is controlled by the switching between exclusively transcribed var genes. The tremendous diversity of the var gene repertoire both within and between parasite strains is critical for the parasite's strategy of immune evasion. We show that ectopic recombination between var genes occurs during mitosis, providing P. falciparum with opportunities to diversify its var repertoire, even during the course of a single infection. We show that the regulation of the recombined var gene has been disrupted, resulting in its persistent activation although the regulation of most other var genes is unaffected. The var promoter and intron of the recombined var gene are not responsible for its atypically persistent activity, and we conclude that altered subtelomeric cis sequence is the most likely cause of the persistent activity of the recombined var gene.