Internship projects 2019

This page will be updated as more projects become available.

 

Antigen design for a single-dose adenovirus-vectored rabies vaccine

Supervisor: Alexander (Sandy) Douglas

Rabies is a uniquely lethal viral infection, with nearly 100% mortality. Although a rabies vaccine has been available since the 19th century, around 60,000 people still die of the disease each year. Current vaccines are based on old technology, require multiple doses, and are too expensive for inclusion in routine childhood immunisation programmes.

A single dose of an adenovirus-vectored rabies vaccine is highly protective in animal models, and our group is therefore preparing for a clinical trial of such a vaccine: we aim to enable low-cost single-dose routine vaccination of children in rabies-endemic areas.

Our current vaccine candidate uses the wild-type rabies glycoprotein transgene(1). The protein is expressed in the recipients’ cells, leading to induction of virus neutralising antibody. This design is simple and effective, but we also know that it induces a large amount of non-neutralising antibody, suggesting that much of the expressed protein is conformationally inaccurate.

It is likely to be possible to improve the efficacy of the vaccine by optimising the transgene to favour the expression of correctly folded trimeric antigen. The project will explore a variety of approaches to achieve this. Successful constructs would be taken forward to produce new candidate vaccines.

The project will provide training in a range of molecular biology, cell-based and immunological techniques, within the environment of a translationally-focused group. It will last for four months (longer than the typical NDM internship, but with additional funding provided). The intention would be for the work to lead to publication. The ideal applicant would have an interest in a career in vaccine development, and possibly some experience of DNA cloning and mammalian cell culture.

1. Wang C, Dulal P, Zhou X, Xiang Z, Goharriz H, Banyard A, et al. A simian-adenovirus-vectored rabies vaccine suitable for thermostabilisation and clinical development for low-cost single-dose pre-exposure prophylaxis. PLOS Neglected Tropical Diseases. 2018;12(10):e0006870.

 

A vaccine for multiple sclerosis? Structure, function and immunology of Epstein Barr virus glycoproteins

Supervisor: Alexander (Sandy) Douglas

EBV causes >100,000 deaths due to cancer each year, and there is increasingly strong evidence it contributes to – or perhaps is even necessary for – the development of multiple sclerosis. We already have vaccines against another herpesvirus, VZV, and there are good grounds to believe that a vaccine against EBV is also possible.

The lab has a track record in the development of antibody-inducing vaccines against malaria and rabies, and in the study of related protein-protein and protein-antibody interactions. We are starting an exciting new project to design and test vaccines for EBV, and to perform collaborative structural studies.

The project will involve expression and purification from mammalian cells of a candidate vaccine antigen. It will provide training in a range of molecular biology, cell-based and immunological techniques, within the environment of a translationally-focused group. It will last for four months (longer than the typical NDM internship, but with additional funding provided). The intention would be for the work to lead to publication. The ideal applicant would have an interest in a career in vaccine development, and possibly some experience of DNA cloning and mammalian cell culture.

1. Cohen JI. Epstein-barr virus vaccines. Clin Transl Immunology. 2015;4(1):e32.

2. Douglas AD, Williams AR, Knuepfer E, Illingworth JJ, Furze JM, Crosnier C, et al. Neutralization of Plasmodium falciparum merozoites by antibodies against PfRH5. J Immunol. 2014;192(1):245-58.

3. Wright KE, Hjerrild KA, Bartlett J, Douglas AD, Jin J, Brown RE, et al. Structure of malaria invasion protein RH5 with erythrocyte basigin and blocking antibodies. Nature. 2014;515(7527):427-30.

 

Bisulfite-free and base-resolution cell-free DNA epigenetic sequencing for cancer diagnostics

Supervisor: Chunxiao Song

5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the two major epigenetic modifications found in the mammalian genome and they played important roles in a broad range of biological processes from gene regulation to initiation and progression of many human diseases. Therefore, epigenetic modifications are valuable biomarkers for diagnostics. Circulating cell-free DNA (cfDNA) is the DNA found in our bloodstream, which provides a noninvasive window for disease diagnosis. Although there has been great interest in using cfDNA as liquid biopsies for cancer detection, it has been challenging to identify the tissue-of-origin of cfDNA and hence the location of the tumour. Detecting epigenetic information such as 5mC and 5hmC in cfDNA is attractive for early cancer detection because it is known to be tissue and cancer-specific. Despite both a strong need and a compelling hypothesis for using epigenetic information in cfDNA for noninvasive diagnostics, it is far less explored than genetic information because the current methods (bisulfite sequencing) for detecting DNA epigenetic modifications are not feasible for the low amounts of highly fragmented cfDNA.

We combine various chemical biology and genome technologies to develop novel tools in epigenetics. Recently we developed novel bisulfite-free and base-resolution sequencing technologies for DNA methylation and hydroxymethylation (bioRxiv doi: https://doi.org/10.1101/307538, Accepted in Nature Biotech). It could replace bisulfite sequencing as the new standard in DNA epigenetic analysis. We expect it to revolutionize DNA epigenetic analysis, and to have wide applications in academic research and clinical diagnostics, especially in sensitive low-input samples, such as circulating cell-free DNA and single-cell analysis. This project aims to apply this method to develop comprehensive, systematic, and unbiased sequencing of the circulating cell-free methylation and hydroxymethylation. It will be applied to cell-free DNA from various solid tumours, with a focus on extracting tissue and disease-specific information for early detection.

 

The Burden of Antimicrobial Resistance in Acinetobacter baumannii in Asia

Supervisors: Dr Catrin Moore and Prof Susanna Dunachie (Big Data Institute and the Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, U

Project duration: 8 weeks

Drug resistant infections are a major global health threat. Many estimates have been published recently, one study estimates that 700,000 people die of resistant infections every year, with low and middle income countries (LMICs) being disproportionally affected.

The Global Research on Antimicrobial Resistance (GRAM) study (previously GBD-AMR study) is a collaboration between the University of Oxford (Centre for Tropical Medicine and Global Health and the Big Data Institute) and the Institute for Health Metrics and Evaluation (IHME) at the University of Washington, USA. The project aims to synthesize drug resistance data worldwide, create geospatial maps as far as possible with the available data, of the distribution of resistance of selected bug-drug combinations and lead the incorporation of the impact of AMR into the disease estimates of the Global Burden of Disease Study.

This summer internship will focus on drug-resistance in Acinetobacter baumannii infections, which are associated with high morbidity, mortality and costs in many countries. The infection rate is higher in high dependence wards and in countries such as Asia and other resource-limited settings where significantly higher rates of resistant infections with Acinetobacter baumannii have been reported compared to developed countries. Antimicrobial resistance of these infections poses a unique challenge. This project will focus on the burden of infections caused by these resistant Gram-negative bacteria. The candidate will perform a systematic review to examine the geospatial distribution of this resistant pathogens.

 

The role of HIF in proliferation and cancer: carotid body physiology/pathology as a paradigm for pseudohypoxic cancers

Supervisors: Dr Tammie Bishop and Professor Sir Peter J. Ratcliffe

Hypoxia is common to many cancers, as the oxygen needs of proliferating tumour cells cannot be met via delivery from local blood vessels. Tumour cells must adapt to this reduced oxygen environment in order to survive. This is in part achieved through hypoxia-induced stabilisation of hypoxia-inducible factor (HIF) - a master transcription factor that activates a massive transcriptional cascade affecting multiple cellular and systemic processes. Many of these processes aid tumour growth, for example metabolic changes including a switch to glycolytic metabolism to support anaerobic ATP production; angiogenesis to support tumour growth and, potentially, metastasis1. In addition, HIF may alter processes such as proliferation and apoptosis that are less obviously concerned with oxygen balance but which may impact tumour growth/survival.

Whilst it is well documented that activation of HIF target genes may facilitate tumour growth, it is less clear whether HIF can initiate cancer per se. The high incidence of genetic mutations in HIF pathway components in tumours provides some evidence for this. For example, von Hippel Lindau (VHL) - one of the major negative regulators of HIF - is a tumour suppressor and patients with germline mutations develop VHL syndrome, a familial cancer syndrome characterised by tumours in a restricted set of tissues: haemangioblastomas (spinal and cerebellar), retinal angioblastomas, renal clear cell carcinomas, phaechromocytomas and carotid paragangliomas. Given the role of VHL in both HIF regulation and as a tumour suppressor, this suggests that activation of HIF could drive tumourigenesis, at least in certain tissues.

Tumours of the adrenal medulla or carotid body, collectively termed phaeochromocytomas/ paragangliomas (PCC/PGL), not only have a high incidence of VHL mutations, but also have been shown to contain a number of gain of function mutations in HIF-2alpha (see recent review2). Further, the carotid body is unique in that hypoxaemia, low arterial oxygen as experienced at altitude or in patients with chronic obstructive pulmonary disease (COPD), induces marked proliferation and overgrowth of the carotid body. This is thought to mediate ventilatory acclimatisation, an increase in ventilation in response to chronic hypoxia that helps redress oxygen balance. In line with this enhanced proliferation, the incidence of carotid body tumours, or carotid body paragangliomas, is ~10x more common at altitude/in COPD. Taken together, this suggests that HIF is capable of initiating tumourigenesis in sympathoadrenal tissues of the carotid body and adrenal medulla, perhaps via stimulation of proliferation.

Using transgenic mouse models, we have demonstrated that HIF-2 is necessary for hypoxia induced carotid body proliferation and the associated ventilatory acclimatisation3. Further, we have shown that inactivation of the principle negative regulator of HIF: HIF prolyl hydroxylase enzyme 2 (PHD2) results in carotid body overgrowth with near 100% incidence of markedly enlarged, dysplastic carotid bodies with features characteristic of human PGL tumours and that this process is dependent on HIF-24,5.

The aim of this studentship would be to characterise the mechanisms by which aberrant HIF-2 activation leads to the development of these PGLs. In the first instance, we would seek to understand which cellular processes (metabolic, secretory or other) are dysregulated; for example through a transcriptomic study of early HIF-2 dependent gene expression changes and through analysis of cellular features including dense core vesicle secretion. We would test whether these HIF-2 effects extend to other tissues, in particular those that develop tumours in VHL disease. From a clinical perspective, we would test whether pharmacological modulation using recently described HIF-2 antagonists can moderate the development of PGL, as has been described in renal clear cell carcinoma6.  

We anticipate that these mice will form a paradigm not only for the study of PGL tumours but also for other ‘pseudohypoxic’ cancers – that is, cancers associated with genetic mutations affecting hypoxia signalling such as renal clear cell carcinoma associated with inherited or sporadic VHL mutations.

1. Bishop T, Ratcliffe PJ. Signaling hypoxia by hypoxia-inducible factor protein hydroxylases: a historical overview and future perspectives. Hypoxia (Auckl). 2014;2:197-213.

2. Toledo RA. New HIF2alpha inhibitors: potential implications as therapeutics for advanced pheochromocytomas and paragangliomas. Endocr Relat Cancer. 2017;24(9):C9-C19.

3. Hodson EJ, Nicholls LG, Turner PJ, et al. Regulation of ventilatory sensitivity and carotid body proliferation in hypoxia by the PHD2/HIF-2 pathway. J Physiol. 2016;594(5):1179-1195.

4. Fielding JW, Hodson EJ, Cheng X, et al. PHD2 inactivation in Type I cells drives HIF-2alpha-dependent multilineage hyperplasia and the formation of paraganglioma-like carotid bodies. J Physiol. 2018.

5. Bishop T, Talbot NP, Turner PJ, et al. Carotid body hyperplasia and enhanced ventilatory responses to hypoxia in mice with heterozygous deficiency of PHD2. J Physiol. 2013;591(14):3565-3577.

6. Chen W, Hill H, Christie A, et al. Targeting renal cell carcinoma with a HIF-2 antagonist. Nature. 2016;539(7627):112-117.

 

Mapping travel patterns in relation to malaria risk with GPS trackers

Professor Richard J Maude (Epidemiology Dept, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand)

Exposure to malaria infected mosquitoes in the Greater Mekong Subregion (GMS) occurs mostly away from the home in forests and forest fringes. Sites of malaria transmission are difficult to identify due to challenges in accurately mapping where people have visited during the time in which they became infected. Reasons for this include poor recall, lack of identifiable landmarks in rural areas and an inability to track movements using cellphone records due to lack of mobile phone towers in many remote and forested areas.

MORU is collecting GPS tracking data from people at high risk of malaria using tracker devices and cellphones. This is a near continuous data stream of a person’s location over time and can be used to map their movements over a period of weeks or months. By combining GPS tracks from multiple people over time together with forest and settlement maps, a detailed understanding of locations at high risk for malaria transmission can be gained. These locations can then be targeted for more intensive investigation and measures instigated to prevent transmission.

This project will analyse GPS tracking data from studies in the Greater Mekong Subregion to identify likely areas with high risk for malaria transmission.

Methods will include GIS and spatial analysis.


Potential for prophylaxis to prevent forest malaria in the Greater Mekong Subregion

Professor Richard J Maude (Epidemiology Dept, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand)

Most malaria in the Greater Mekong Subregion (GMS) is transmitted in and around forests. However risk behaviours leading to infection have not been well characterized which makes it challenging to design appropriate interventions to prevent and treat infections. One proposed intervention that could reduce forest malaria is antimalarial prophylaxis for forest goers. Trials of this are planned in the near future however it is not clear in how it would be administered and monitored and by whom in different healthcare settings. The acceptability of prophylaxis as an intervention for populations in the GMS is also not known.

This project will design and conduct interviews among malaria control programme staff and healthcare workers in countries in the Greater Mekong Subregion to identify a mechanism for administering and monitoring antimalarial prophylaxis to forest goers. It may also be possible to conduct interviews amongst high risk forest goers to determine the acceptability of prophylaxis as an intervention.

The results will help National Malaria Control Programmes to decide how to roll out this intervention in their country.

Methods will include qualitative interviews and health systems research.


Retrospective analysis of a malaria outbreak in the Greater Mekong Subregion

Professor Richard J Maude (Epidemiology Dept, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand)

There have also been a number of focal outbreaks of malaria in the Greater Mekong Subregion (GMS) in the past few years. In many cases the causes of these outbreaks were not well understood and responses suboptimal due to limitations in data and capacity for analysis. This limits countries’ ability to act efficiently to contain these outbreaks and to prevent future outbreaks and has the potential to threaten the achievement of planned elimination timelines.

This project will analyse retrospective surveillance data together with intervention data to describe a recent malaria outbreak in the GMS and investigate possible causes. Questions that the project will aim to address will include: what was the contribution of climate factors to this outbreak/epidemic? What was the contribution of changes in treatment/vector control measures to this outbreak/epidemic? What are the geographical and temporal extent of the epidemic? Which demographic and risk groups were affected? Where data are available what was the contribution of changes in population movement patterns and antimalarial resistance to this epidemic?

Methods will include statistical analysis, GIS and spatial analysis.

The results will help the National Malaria Control Programme understand which factors contributed to the outbreak should report as possible causes of the epidemic/outbreak and inform planning of interventions for future outbreaks.

Developing viral vectored vaccines for MAGE-expressing tumours

Supervisors: Professor Benoit Van Den Eynde and Dr Carol Leung

Cancer vaccines have the potential to induce anti-tumour specific immune responses to reject tumours. This project aims to produce and test new MAGE-targeting cancer vaccines optimized to induce strong cytotoxic T lymphocyte (CTL) responses. We are using an effective viral vector platform and different immunogen design to induce potent CTL responses against tumours. Different mouse tumour models are employed to assess the vaccine efficacy.
This study will create a next - generation cancer vaccine against MAGE - positive tumours, and lay a foundation for clinical testing in cancer patients.

The project involves techniques in molecular biology and immunology.

Novel cell cycle regulators in human cells

Supervisor: Professor Catherine Green

This project will assist in the characterisation of newly identified cell cycle regulated proteins in human cells. As a collaborative project with Prof. Ross Chapman’s group we are undertaking a systematic analysis of a set of cell cycle regulated proteins identified in a screen. The screen identified known proteins essential for DNA replication and mitosis along with a set of novel genes of unknown function. We therefore predict that these uncharacterised proteins are likely to have important functions during the cell cycle. This project will use molecular biology (cloning, regulated expression of recombinant proteins, CRISPR/Cas9 knockout), advanced microscopy, FACS, and biochemical methods to determine the function of these novel proteins and the consequences of their disruption or perturbation. These proteins will then be investigated as possible targets for preventing cell proliferation in cancer of other diseases.