Identifying and prioritising new malaria vaccine candidates
Supervisor: Professor Julian Rayner, Professor of Cell Biology and Director, Cambridge Institute for Medical Research (contact)
Principle Supervisor Department: Cambridge Institute for Medical Research
More than a third of the world’s population is at risk of contracting malaria. Most malaria research focuses on Plasmodium falciparum, the dominant species in Africa, which causes the majority of malaria deaths. By contrast research into Plasmodium vivax has been neglected, despite it being the globally most widely distributed malaria parasite and the cause of significant morbidity and mortality in Latin America and Asia. While the first ever vaccine has just been approved for P. falciparum, no P. vivax vaccine has ever progressed to Phase II human trials.
This project focuses on an understudied family of P. vivax proteins, the Tryptophan Rich Antigens (TRAgs). TRAgs are found in all Plasmodium species, but are significantly expanded in number in P. vivax, implying that they have important functions in this species. We have established that antibodies raised against them can significantly inhibit parasite growth and by solving the structure of one P. vivax TRAg, we have established that they may be involved in reshaping host cell membranes during the processes by which P. vivax invades and parasitises human red blood cells.
In this interdisciplinary project you will use genetic, biochemical and structural tools to systematically explore the function of P. vivax TRAgs and explore their potential as vaccine targets. You will gain experience in protein expression, structural biology, parasite culture and CRISPR-Cas9 genome engineering. As P. vivax can not be cultured in vitro, the majority of your work will involve a closely related Plasmodium species that can be grown in our lab, but there is also the potential to work with collaborators in India and Brazil and carry out some experiments in the field using ex vivo isolates. The project is linked to a large collaboration advancing P. vivax candidates to human clinical trials, so you will have the opportunity to see the full process of vaccine development first-hand.
How does maternal immunity regulate placentation and offspring health?
A woman dies of pregnancy complications every two minutes and one tenth of all diseases are due to something gone wrong around childbirth. For example, birth weight is a predictor of cardiovascular and metabolic disease in adult life . Foetuses exposed to maternal immune activation are predisposed to autism spectrum disorders . Prenatal maternal infections shape offspring immunity . Tissue lymphocytes are integral to health and disease, including the disorder of pregnancy pre-eclampsia . Tissue lymphocytes in the womb orchestrate key vascular adaptations in the uterus that facilitate placentation and foetal growth. A better understanding of how the maternal immune system contributes to pregnancy complications will help to improve women’s and offspring’s health. We have discovered that the immune pathway involving the NKG2A receptor is key for optimal foetal growth, placental gene expression and brain development . We now seek to:
1. Determine gene networks downstream of the NKG2A pathway;
2. Understand how perturbations of these gene networks affect offspring’s health.
We will determine differentially expressed genes (DEGs) in human uNK cells educated or not through NKG2A by bulk RNA-Seq. Functions and roles of selected DEGs will be determined in established cellular assays and in NK-specific Cre-loxP mutant mice. Readouts will be NK cell activity, trophoblast migration and differentiation; utero-placental flow, placental gene expression and foetal organ development.
To determine underlying mechanisms of how prenatal perturbations of maternal immunity affect offspring’s health, we will analyse gene expression and epigenetic alterations in brain and immune cells of offspring born from infected or genetically modified mice by using single cells by scRNA-Seq and ATAC-Seq. New artificial intelligence-supported tools (SmartKages®) will be used to quantitatively phenotyping offspring cognition and behaviour. Deep flow cytometry phenotyping and responses to pathogens will be measured to assess offspring immunity.
Treatments to enhance maternal immunity and achieve optimal foetal development are unavailable. We will identify components of the NKG2A pathway. Our unpublished preliminary data show that one component of the pathway is targetable by existing drugs. Drugs may ultimately be administered to pregnant women genetically predisposed to underutilise the NKG2A pathway. These may boost uterine lymphocytes, stimulate blood flow to the placenta, promoting healthy gestation, optimal foetal growth and offspring health. The NKG2A pathway is also relevant to cancer immunotherapies and immunity to HIV and SARS-Cov-2.
 Li X et al. Association of low birth weight with cardiometabolic diseases in Swedish twins: a population-based cohort study. BMJ Open 2021; 11:e048030. doi:10.1136/ bmjopen-2020-048030
 Estes ML, Mc Allister AK. Maternal immune activation: Implications for neuropsychiatric disorders. Science 2016 Aug 19;353(6301):772-7
 Lim AI, et al. Prenatal maternal infection promotes tissue-specific immunity and inflammation in offspring. Science 2021 Aug 27;373(6558)
 Colucci F. The Immunological Code of Pregnancy. Science. 2019 Aug 30;365(6456):862-86
 Shreeve N, … Colucci F. The CD94/NKG2A inhibitory receptor educates uterine NK cells to optimise pregnancy outcomes in humans and mice. Immunity, 2021: Apr 19:S1074-7613(21)00133-3
Patho-adaptation of Pseudomonas aeruginosa during chronic lung infection
“Pseudomonas aeruginosa is a major human pathogen and causes chronic lung infection in over 40% of people with Cystic Fibrosis (CF) or non-CF Bronchiectasis and over 20% of people with smoking-related lung disease (COPD). Applying similar analytical approaches to our mycobacterial work (Science 2006, Science 2016, Science 2021, Nature Micro 2021, Nature Micro 2022), we have defined critical steps involved the pathogenic evolution and patho-adaptation of P. aeruginosa with CF and non-CF lungs, and have identified a key set of potential gene mutations responsible.
Our PhD proposal aims to (i) experimentally examine the impact of these mutations (using isogenic strains) on bacterial and host cell behaviours in vitro and within our lung-on-a-chip organ system; (ii) explore the impact of these pathogenic mutations on host-bacteria interactions in vivo through dual RNAseq analysis of bronchoscopic samples from CF patients; (iii) explore molecular mechanisms of action using advanced optical microscopy, CRISPR knockout, knockdown, and knock-in methods, and proteomic methods.
Students will be trained in both wet lab techniques and bioinformatic analysis. For those interested, there will be opportunities to develop and/or deploy cutting-edge machine learning methods (developed with CCAIM; https://ccaim.cam.ac.uk) to model bacterial behaviour through geometric deep learning approaches.
Identification and characterisation of novel antiviral restriction factors
“Antiviral restriction factors (ARF) are a critical element of cellular innate immunity, representing the first barrier to viral infection that can determine outcome. We aim to identify and characterise novel ARF and their viral antagonists, since therapeutic interruption of viral antagonism can enable restoration of endogenous antiviral activity.
We employ a number of human pathogens, in particular Human Cytomegalovirus (HCMV), Monkeypox virus (MPXV) and its vaccine, Modified Vaccinia Ankara (MVA). Our systematic proteomic analyses determine which cellular factors each pathogen targets for destruction, since we have shown these to be enriched in novel ARFs. For example, we recently developed a multiplexed proteomic technique that identified proteins degraded in the proteasome or lysosome very early during HCMV infection (Nightingale et al, Cell Host & Microbe 2018). A shortlist of 35 proteins were degraded with high confidence, and we have since shown that several are novel ARF, with characterisation of these factors forming ongoing projects. Application to MVA infection indicated further candidates, and identified novel mechanisms of vaccine action (Albarnaz et al, in review, https://www.researchsquare.com/article/rs-1850393/v1). Furthermore, interactome screens can identify the viral factor(s) responsible for targeting each ARF, and indicate mechanism (Nobre et al eLife 2019).
This project will now identify and characterise critical pan-viral ARF, which can restrict diverse viruses. For the most potent, we will determine both the mechanism of restriction and the mechanism of virally mediated protein degradation. In order to prioritise the most important factors, there will also be the opportunity to use novel multiplexed proteomic screens.