Medical Biology - Theses
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ItemThe Transcription Factor T-bet in the Control of Germinal Centre Dynamics in Malaria( 2019)With reductions in the global malaria burden stalled, this preventable and curable infectious disease caused by the Plasmodium parasites, remains a public health challenge that affects the world’s most vulnerable populations. Naturally acquired immunity plays an important role in protection from disease; however, there is long-standing evidence that it requires years of repeated infections to develop. The reasons for this are largely elusive, but immuno-epidemiological studies support that protective antibodies and memory B cells are short-lived and inefficiently generated to infection. Moreover, recurrent infections are associated with an expansion of atypical memory B cells that may have impaired function. Histological analyses revealed significant disorganisation of the spleen in severe malaria patients, which led to the concept that acute infection may undermine the acquisition of B cell memory. T helper 1 pro-inflammatory responses induced by blood-stage infection were subsequently shown to compromise the induction of humoral immunity by inhibiting effective T follicular helper (Tfh) cell differentiation and germinal centre (GC) reactions. The relative contribution of the T helper 1 lineage-defining transcription factor, T-bet, in CD4+ T cells and B cells to GC development in malaria, was investigated using the P. berghei ANKA blood-stage infection model. T-bet expression in CD4+ T cells limited the differentiation of Tfh cells that supported GC development in the spleen. This led to an impaired generation of antibody-secreting cells and memory B cells following infection. In addition to its impact on CD4+ T cells, T-bet was highly up-regulated in GC B cells elicited by infection, and limited the magnitude of the GC response in a B cell-intrinsic manner. Strikingly, T-bet expression in the B cell compartment modulated the transcriptional landscape of GC B cells to promote the GC dark zone program but constrained light zone development. In particular, T-bet suppressed expression of the regulator of G-protein signaling 13, which down-regulates the responsiveness of B cells to migrate towards the chemokine CXCL12, for effective dark and light zone transition within the GC. T-bet-driven dark zone skewing of the GC reaction following malaria infection associated with enhanced somatic hypermutation of GC B cells, and improved the avidity of antibodies against the parasite. Therefore, this thesis supports a model in which malaria-elicited inflammation mediated by T-bet, exquisitely modulates the dynamics of the GC reaction, promoting GC B cell dark zone polarization that promotes the generation of B cells with increased affinity for antigen, consequently enhancing affinity maturation. This provides novel insight into the cellular mechanisms that underlie the development of humoral immune responses in malaria, and has implications for other chronic infections and autoimmune disease that are characterised by a similarly potent inflammatory milieu.
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ItemBiochemical and biophysical investigations into key malaria parasite proteins( 2017)Plasmodium falciparum, the most pestilential of the malaria parasite species, is responsible for ~450,000 direct deaths annually. Clinical disease is a consequence of the blood stage of the parasite’s lifecycle involving a plethora of host-parasite interactions. Key to these interactions are the P. falciparum reticulocyte binding-like homologue (PfRh) proteins responsible for binding erythrocyte receptors and gaining entry to host cells. For example, PfRh4 binds to human complement receptor-1 (CR1) on erythrocytes for sialic-acid-independent invasion. Another protein important for invasion is the PfRh5-interacting protein (PfRipr), an essential member of the PfRh5-associated invasion complex (PAIN-complex) along with CyRPA, the cysteine-rich protective antigen. Loss of function of PfRipr in P. falciparum parasites prevents erythrocyte entry and ablates Ca2+-influx into the erythrocyte; essential events during invasion. This study aimed to biochemically and structurally investigate truncated recombinant versions of PfRh4 and PfRipr. Homology modelling suggested that PfRh4 is rich in alpha-helical secondary structure. The sequence of PfRipr suggested the presence of ten epidermal growth factor-like (EGF) modules, two towards the N-terminus and eight in the C-terminal domain. In this project, monoclonal antibodies made against recombinant PfRh4 were shown, via indirect immunofluorescent assays, to localize to the apical tip of merozoites. Monoclonal antibody 5H12, raised against PfRh4, reduces parasite invasion of erythrocytes by ~75% in growth-inhibition assays with neuraminidase pre-treated erythrocytes. Attempts to produce a stable truncated recombinant PfRh4 protein for structural studies were unsuccessful. An ELISA-based assay using ten alanine-scan mutants suggested the CR1-binding site lies outside of amino acids 283 – 341 of PfRh4. PfRipr truncations, defined by the boundaries of EGF-like repeats predicted based on sequence homology, were produced recombinantly in Escherichia coli and Pichia pastoris. These proteins had a circular dichroism signature suggestive of β-strand-containing proteins with disordered regions. EGF-containing PfRipr truncations did not bind recombinant PfRh5 according to ELISA and size-exclusion chromatography assays. EGFs 1-2, 5-7 and 7-10 of PfRipr did not bind CyRPA via size-exclusion chromatography or NMR. Crystallisation trials performed on EGF modules failed to yield crystals suitable for data collection. A 15N isotopically-labelled sample of EGF5-7 gave good quality HSQC NMR spectra. A 15N isotopically-labelled sample of EGF5-7 gave good quality HSQC NMR spectra. A suite of three-dimensional NMR spectra collected on a 13C,15N-EGF5-7 sample, at three different temperatures, allowed for >86% of backbone assignments. T1/T2 relaxation analysis and heteronuclear NOE data were suggestive of an elongated, rigid protein undergoing intermolecular self-association. Further evidence for EGF5-7 being an elongated protein was provided via SAXS analysis. Chemical shifts facilitated prediction of secondary structure in EGF 5-7 consistent with an EGF-like fold. Melting studies performed on EGF5-7 showed no evidence of denaturation over the temperature range 20˚C - 95˚C indicating a thermally-stable protein. The addition of Ca2+ to the 15N-EGF5-7 sample caused chemical shift perturbations consistent with high-affinity binding. The discovery of inhibitory monoclonal antibodies recognising a conformational epitope on EGF7 provided evidence of the functional importance of this region within PfRipr. The work described in this thesis provides methods for the industrially-scalable production and biophysical investigations of P. pastoris or E. coli-produced disulfide-rich P. falciparum antigens of interest to vaccinologists.
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ItemPopulation and molecular level studies of malaria transmission( 2017)Charlie Jennison investigated the population genetics of two human malaria species in Papua New Guinea, revealing greater structure in Plasmodium falciparum than in P. vivax populations. He also discovered a role for the parasite protein Thrombospondin Related Sporozoite Protein in the motility and infectivity of P. falciparum sporozoites.
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ItemDissection of early events that govern protein export in malaria-infected erythrocytes( 2017)Following infection of human erythrocytes by Plasmodium spp. parasites, the host cell undergoes dramatic changes in its biophysical and mechanical properties. The parasite mediates these changes by the active export of more than 450 proteins into the erythrocyte cytoplasm and membrane. The majority of exported proteins contain an N-terminal pentameric amino acid motif known as the Plasmodium Export Element (PEXEL). The endoplasmic reticulum (ER)-localised aspartyl protease Plasmepsin V (PMV) cleaves the PEXEL motif and licenses protein export. PMV has been identified as a key checkpoint in protein export as inhibitors designed to block action of the protease leads to parasite death. In addition, PMV appears to be essential not only for PEXEL cleavage, but also to guide PEXEL-cleaved proteins into a defined export pathway originating at the ER. However, critical information about the function of PMV is still to be understood, including questioning of its essentiality for parasite survival and also the mode of recognition of PEXEL proteins and subsequent establishment of an export pathway for cleaved substrates. Research carried out during this PhD attempted to address these key issues by a combination of conditional gene knockdown and knockout technologies, as well as quantitative proteomics. PMV is confirmed as an extremely efficient protease that is critical for parasite survival. In order to cleave PEXEL proteins as soon as they enter the ER, PMV is linked to a unique translocon that is dedicated for the post-translational import of PEXEL proteins, by a previously uncharacterized interacting protein PfSPC25. Another PMV specific interacting partner, PfSR1, displays properties of a PEXEL cargo receptor and likely assists in establishment of an export pathway for mature PEXEL proteins. Collectively, these results have revealed key insights into the biology of a critical parasite protease and the overall process of protein export by the malaria parasite.
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ItemComplement evasion mechanisms of the deadly human pathogen Plasmodium falciparum( 2016)The human complement system is a front-line defence system against invading pathogens. It has over 50 different protein components that are involved either in pathogen clearance or in the regulation of complement. The two main mechanisms of clearance are direct membrane lysis or opsonisation leading to enhanced phagocytosis. Despite the presence of this potent system, many pathogens thrive in human serum due to the evolution of complement evasion strategies. One common evasion strategy involves pathogens recruiting host regulators of complement activation to down- regulate complement attack on their surfaces. Merozoites, the invasive stage of malaria parasites are exposed to serum after egress from the host red blood cell. In this thesis, we examined whether merozoites recruit human regulators of complement activation to their surface to evade complement-mediated destruction. We found that merozoites recruit the human regulators Factor H, Factor H-like 1 and C1 esterase inhibitor to their surface. Factor H and Factor H-like 1 are recruited by an interaction between the merozoite surface protein Pf92, a member of the six cysteine family of merozoite surface proteins, and the complement control protein modules 5-6 of the Factor H and Factor H-like 1 proteins. When bound to the merozoite surface, Factor H and Factor H- like 1 retain cofactor activity, a key function that allows them to down-regulate the alternative pathway of complement activation. Deletion of the Pf92 gene resulted in a loss of Factor H and Factor H-like 1 recruitment and an increased susceptibility of merozoites to immune destruction. We also showed that C1 esterase inhibitor is recruited to the merozoite surface by an interaction between PfMSP3.1, a member of the MSP3 family of merozoite surface proteins, and the C1 esterase inhibitor serpin domain. Bound C1 esterase inhibitor retained the ability to complex with complement activating proteases C1s, MASP1 and MASP2, allowing it to down-regulate both the classical and lectin pathways of complement on the merozoite surface. Deletion of the PfMSP3.1 gene led to a loss of C1 esterase inhibitor recruitment and an increase in complement deposition on merozoites. However, this resulted in enhanced merozoite invasion in the presence of active complement rather than merozoite destruction. Overall, the ability of merozoites to sequester host complement regulators has important implications for the immune evasion strategy of malaria parasites amid a growing body of evidence for an important role of complement in protection.
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ItemInvestigation of the export pathway in Plasmodium parasites utilising small molecule inhibitors of plasmepsin V( 2016)The human malaria parasite Plasmodium falciparum exports several hundred proteins into the host cell erythrocyte that are involved in cellular remodelling and severe virulence. The majority of proteins exported to the erythrocyte possess a conserved N-terminal export motif termed the Plasmodium export element (PEXEL). In order for proteins to be exported, the PEXEL motif (RxLxE/Q/D) must be processed by an ER-resident aspartic protease called plasmepsin V. Plasmepsin V is conserved across all Plasmodium species, including the most virulent human parasites P. falciparum and P. vivax, and is essential for blood-stage parasite survival. Therefore, plasmepsin V is considered a prime target for the development of new antimalarial therapies. Transition-state peptidomimetics of the natural PEXEL substrate are the most potent documented inhibitors of plasmepsin V to date. One such inhibitor, WEHI-916, showed that plasmepsin V plays a crucial role in protein export and that this process is essential for parasite survival, confirming that plasmepsin V is an important antimalarial target in the asexual blood stages. WEHI-916 has high affinity for plasmepsin V (IC50 20 nM), but only has moderate potency in blocking P. falciparum growth (EC50 2.5 μM). The large disconnect between biochemical and parasite growth inhibition can be attributed to the mimetic’s peptide-like character, which are known to possess poor membrane permeability and are susceptible to proteolytic degradation. Here, two strategies are described to overcome the liabilities associated with peptide-like molecules. These strategies were applied to transition-state mimetics that are potent inhibitors of plasmepsin V, with the aim of improving their membrane permeability and proteolytic stability, in order to enhance their activity against Plasmodium parasites. The first strategy utilised to improve these properties involved N-methylation of the backbone amide bonds. The second approach that was undertaken explored the structure-activity relationship within the S3 pocket of plasmepsin V to find a suitable isostere to replace the highly polar PEXEL P3 arginine, with the aim to improve membrane permeability. To further explore the biological role of plasmepsin V across multiple stages of the Plasmodium lifecycle, preliminary studies were also preformed towards the generation of a novel fluorescent probe that would fluoresce only once irreversibly bound to plasmepsin V. The synthesis of these analogues and the outcome of these strategies are discussed.
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ItemPre-clinical evaluation of glycosylphosphatidylinositol as a potential multi-stage malaria vaccine( 2016)As part of the global effort to eliminate and eradicate Plasmodium malaria parasites, vaccine development has proven to be difficult. This is due in part to the high complexity of the Plasmodium parasite that consists of up to thirteen differentiated forms in the life cycle, and five different Plasmodium parasite species that can infect humans. Furthermore, proteins expressed by the parasite are capable of antigenic variation and exhibit high allelic diversity. For these reasons, vaccine candidates that only target single antigens are likely to be inadequately protective, making an effective subunit malaria vaccine difficult to achieve. In order to overcome the problem presented by variable and allelic diverse proteins presented by the malaria parasite, a novel carbohydrate target known as glycosylphosphatidylinositol (GPI) was selected as an attractive target for our vaccine development program. This is because parasite GPI is structurally conserved and it is found on most malaria parasite life forms, thus making it a potential multi-stage and pan-species target. Furthermore, GPI is also known as a parasite toxin that contributes to the pathogenesis of malaria clinical symptoms during infection. Hence, Plasmodium GPI seemed to be a compelling target for vaccine development. If successful, the vaccine targeting a conserved structure might be able to prevent both parasite infection and malarial disease. To test the above hypothesis, our lab had previously developed a synthetic GPI vaccine based on the structure of Plasmodium falciparum GPI and found that it prevented malarial disease in the Plasmodium berghei rodent malaria model. This finding suggested the need for further investigation on the potential of this vaccine in preventing malaria infection. In order to align our vaccine development goals with the target product profile (TPP) of a malaria vaccine required for the malaria eradication agenda, the studies undertaken for this PhD thesis aimed to test proof-of-concept of the efficacy of the synthetic GPI vaccine against Plasmodium sporozoites infection and parasite transmission in a rodent malaria model. The data provided in this dissertation have proven the possibility of targeting Plasmodium GPI as a multi-stage and pan-species antigen and have provided evidence to support future vaccine development towards the malaria eradication agenda.
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ItemThe molecular epidemiology of malaria in Solomon Islands( 2016)Historically, Solomon Islands in the Southwest Pacific has endured considerable P. falciparum and P. vivax burden. In the last 20 years, it has achieved 90% reduction in malaria cases through sustained, intensified malaria interventions (long lasting insecticide nets, indoor residual sprays and artemisinin-combination therapy) and is aiming for elimination by 2030. In 2012 and 2013, we conducted two cross-sectional surveys (study 1, all age, n=3501; study 2, age 0.5-12 years, n=1078) in Ngella, an area of low to moderate transmission. We aimed to investigate the natural reservoir and local epidemiology of P. vivax and P. falciparum. The contrast was striking. In the 2012 survey, only five clonal P. falciparum infections were identified from a single village and had the same msp2 genotpye. P. vivax prevalence was found to be moderately high (PCR, 13.4%), with predominantly afebrile, submicroscopic infections. The P. vivax infections displayed high genetic complexity (by genotyping with msp1F3 and MS16) and considerable spatial heterogeneity among and within different Ngella regions, and even at sub-village level with some households disproportionately harboring more infected co-inhabitants than others. In the 2013 study, a further seven P. falciparum infections were found in multiple locations, indicating that transmission of this species is continuing but at very low levels and infections are predominantly asymptomatic. To investigate the transmission scenario of the two species in more detail, we undertook population genetics analyses. We typed the five 2012 P. falciparum infections at 10 polymorphic microsatellite loci and 323 P. vivax infections at nine microsatellite loci. The five P. falciparum infections also clonal by this panel of 10 markers. Subsequent analyses of diversity (FST, GST, Jost’s D) and structure (Bayesian clustering) for P. vivax, revealed a genetically diverse population, but spatially fragmented, even among villages 6-15km apart. This indicates that whilst P. vivax may be more difficult to eliminate than P. falciparum, local parasite populations of both species have been affected by control interventions. A noteworthy epidemiological result from the 2012 survey was that living in a household with at least one other P. vivax carrier increased the risk of P. vivax infection, suggesting possible intra-household transmission. Subsequent analysis of genetic relatedness of P. vivax infections within households vs. among households indicated supported this hypothesis. Isolates from the same household were more genetically related than isolates from different households, and a high level of genetic kinship was retained among households located up to 100 meters of each other. Associations of P. vivax infection with human genetic factors known to confer protection against infection (α-thalassemia and Southeast Asian ovalocytosis, SAO) have been investigated in a second cross-sectional study conducted in 2013 in children aged 6 months to 12 years of age. SAO was not found in Ngella, whereas approximately a third of 1078 subjects were found to harbor the α-thalassemia alleles. The findings presented in this thesis will be discussed in the context of factors which may impact on follow-up elimination strategies in Solomon Islands, the Southwest Pacific and elsewhere in the endemic world where both P. falciparum and P. vivax are co-endemic.
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ItemMerozoite surface protein 1: insights into complex formation and function in erythrocyte invasion( 2016)The invasion of Plasmodium falciparum into host erythrocytes during the parasites’ asexual blood stage is a critical step in the perpetuation of symptomatic infection of malaria in the human host. Merozoites, the invasive form of the parasite, express a glycosylphosphatidylinositol-anchored 190 kDa Merozoite Surface Protein 1 (MSP1) on the surface. This abundant, essential protein exists in a large complex that includes other peripheral Merozoite Surface Proteins (MSPs). Together, these large macromolecular complexes are thought to mediate the initial stages of invasion. MSPs are of great interest to the field as they are exposed to the host immune system and also contribute directly to the invasion process. Therefore, there is a strong consideration for considering them as therapeutic targets. The majority of the work assessing these molecules as potential vaccine candidates has been performed with single MSP antigens and vaccine trials on these MSPs have shown variable results. A main concern arising from these trials is the fact that these antigens are often found in complex with other antigens and therefore have regions that are masked when found on the parasite surface. In order to address this, the work presented in this thesis utilises parasite-derived complexes to understand how peripheral MSPs: MSP3, MSP6, MSPDBL1, MSPDBL2 and MSP7 utilise MSP1 as a platform to be presented on the merozoite surface to form an array of complexes with different functional roles. In addition, multiple forms of erythrocyte binding complexes were found to have overlapping functions in invasion. Complexes that are involved in erythrocyte binding were characterised, where two components, MSPDBL1 and MSPDBL2 were shown to mediate erythrocyte binding directly. Overall, this study has identified and validated the presence of multiple Merozoite Surface Protein 1 complexes that are involved in mediating the interaction of the merozoite to receptors on the red blood cell surface, which is a vital process for successful invasion of parasites into host erythrocytes. Together, these findings have provided valuable insights into the complexity of MSP1 complexes and have contributed to the most complete model for the molecular arrangements that occur on the parasite surface to date.
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ItemCell-cell interactions during malaria parasite invasion of the human erythrocyte( 2015)Red blood cells are remarkably resilient, flexible and dynamic structures. These properties are required for their passage through small capillaries and are imparted by the cytoskeleton, a network of proteins that underlies and links to the cell membrane. To successfully invade the blood stage malaria parasite, called a merozoite, must induce rapid and drastic changes to the structure of the target erythrocyte, including the formation of a tight junction and a new cellular compartment, the parasitophorous vacuole. These key modifications involve the infolding of the red blood cell membrane, membrane fusion and fission events and the secretion of parasite proteins into the host. Although detailed cellular descriptions of merozoite invasion have been achieved over the past few decades, comparatively little is known about the molecular basis of how the host cell responds to parasite entry. In fact, in contrast to what is known about the invasion strategies of most other intracellular pathogens, the prevailing model of Apocomplexan invasion imagines a largely binary system within which an active parasite, driven by its acto-‐ myosin motor, invades a passive host cell. There is a growing body of evidence, however, that suggests that Apicomplexan host cells may not be as inactive as initially thought. Nonetheless, to date, there is no direct evidence for the notion that erythrocytes contribute actively to merozoite invasion. This PhD took at its starting point the hypothesise that to invade, merozoites interface with endogenous erythrocyte pathways that regulate membrane and cytoskeletal remodelling, and that the tight junction is a key structure that coordinates the this host-‐pathogen interaction during the brief moment of entry. To address this proposition, this PhD studied P. falciparum merozoite invasion using a combination of in silico bioinformatic screening, high-‐definition imaging, quantitative and high-‐throughput invasion inhibition assays and quantitative phospho-‐proteomics. Work presented in this thesis further elaborates the molecular architecture of the P. falciparum merozoite tight junction, outlines a model for the secretion of virulence factors by the parasite during entry, establishes that an active erythrocyte is a prerequisite for successful merozoite invasion and demonstrates, for the first time, that the red blood cell responds to early invasion events through the phosphorylation of components of its membrane and cytoskeleton. Taken together, these findings provide strong support for a shift in how we conceptualise invasion, from paradigm that focuses almost exclusively on the activity of the parasite towards one in which both the merozoite and the erythrocyte act cooperatively to achieve the requisite remodelling events that lead to successful intracellular infection. By further expounding the way in which the malaria merozoite orchestrates its interaction with its target red blood cell during invasion, and in particular shedding light on the potential host-‐cell contribution to this process, this work informs future endeavours aimed at the development of novel chemotherapeutic targets to stop invasion and hence prevent or treat malaria disease.