IDENTIFYING HOST-PATHOGEN INTERACTIONS WHICH CAUSE SEVERE MALARIA

Infectious diseases continuously challenge the body's defenses. Perhaps surprisingly, we know rather little about how many infections actually cause serious illness. Often we can't explain why the same infection causes mild illness in one person but kills another. Finding out why this happens is key to finding better treatments.

Malaria is one infection we need to understand better. It is a disease caused by tiny parasites within red blood cells which are spread from person to person by the bite of mosquitoes. Malaria infects more than 200 million people every year around the world and kills almost 1 million of them. Some features linked to severe infections have been identified, but we don't really know how these lead to severe illness and death.

This research aims to explain how interactions between the body's defenses and the malaria parasite result in differences in the severity of illness. We aim to use a new technique to do this. We will look at all the genes that are simultaneously active in the malaria parasite and the human cells in the blood, to find patterns associated with severe illness. Malaria is an ideal disease to assess with our new technique because all of the parasites live in the blood. This research will help to identify new approaches to the treatment of severe malaria. This could save many lives in the future. If we are successful, we think the approach could also be applied to many other infectious diseases.

This research will be carried out by collaborating scientists at Imperial College London, The London School of Hygiene and Tropical Medicine, University of Queensland (Australia), National Institutes of Health (USA) and MRC Laboratories, The Gambia. It draws together world leaders in malaria research, genetics, computing methods and statistics. The research will use stored samples collected from Gambian children with malaria. Some of these children had a mild illness, and some had life-threatening complications. The activity of all the human and parasite genes will be measured with a technique called "RNA Sequencing". A series of advanced computer techniques will be used to find the patterns of gene activity associated with severity of malaria. Once we have identified the patterns associated with severe malaria we will test them in the laboratory to see if we can target them to prevent severe malaria. We do this by deliberately altering genes, or by adding or blocking molecules that are important in generating the patterns we identify. This allows us to be sure our findings are causal, rather than just chance associations. The raw data and all our findings will be made publically available, so that other scientists can use the data to answer other important questions about malaria.

Aim: To explain how host and pathogen interact to cause different severe malaria syndromes.

Objectives:
1. a) To use RNA sequencing to identify differences in human and parasite gene expression which characterize cerebral malaria and hyperlactataemia.
b) To identify key host and parasite pathways in cerebral malaria and hyperlactataemia.
c) To determine interactions between host and parasite gene expression and features of severe malaria.
2. To assess how well experimental malaria infections in mice represent severe malaria in humans by comparative gene expression analysis.
3. To test the relevance of novel candidate pathways and host-pathogen interactions by manipulation in vitro and in vivo.

Methodology: Dual RNA-Sequencing will be performed on archived whole blood RNA from Gambian children with different malaria syndromes. Differential expression of genes, pathway analysis and interaction analysis will be performed to identify mechanisms associated with severe malaria. Based on existing literature, and selective experiments, we will assess to what extent different combinations of mouse and Plasmodium species exhibit similar profiles of gene and pathway activity to human severe malaria. To validate the findings from the global gene expression analysis we will test selected pathways in culture systems involving parasites, endothelial cells and leukocytes, and in vivo where homologous pathways exist.

Scientific Opportunities: This project should identify novel pathways which determine the phenotype of severe malaria, has the possibility to identify the importance of reciprocal interactions between host and pathogen in causing disease, and will generate a useful, publicly available, dataset of global host and parasite gene expression.

Medical Opportunities: The identification of novel mechanisms involved in different severe malaria syndromes may allow tailored treatment of each syndrome, and development of much needed adjunctive therapies.

ACADEMIC IMPACTS

Enhancing Knowledge: The most direct impact will be expansion of knowledge about malaria. This knowledge will have immediate applicability to guide other research on basic and clinical aspects of malaria, by academics and the pharmaceutical industry. Within 5-10 years, it may also change the direction of infectious disease research to explore what host factors alter pathogen behavior, and may be applied to other situations where virulence traits appear to be selected and persist. The knowledge and conceptual impacts will be delivered by peer reviewed publication, presentation of the research outputs at National and International conferences, and through press releases.

New Methodologies: Pioneering the "dual RNA sequencing" technique will demonstrate its usefulness to other researchers. The methods will be disseminated promptly and communicated in a similar way to the knowledge impact, becoming available from the second or third year of the project. Participation in on-line forums and technology congresses for discussion of methodology, and presentation on our group website, will ensure that these techniques are disseminated to the research and industrial communities.

Creation of Resources: All the sequencing data and accompanying data will be uploaded to a public repository, and any novel analysis software will be made publically available. This will allow free secondary analysis of our data. Access to these resources will be highlighted in publications, presentations, and from our website, and made available simultaneously with any publications, between 2-5 years from the start of the project.

Individuals and skills. The experience and specific training during the five year period, will increase academic competitiveness for myself and collaborating researchers, particularly for the use of high throughput sequencing technologies integrated into future research plans.


ECONOMIC AND SOCIETAL IMPACTS

Changing policy: If this research demonstrates differences in the pathogenesis of severe malaria syndromes, this could seed wide reaching consequences for policy on treatment, drug trials and vaccine evaluation. These implications will be discussed when we present our data throughout the fellowship, and disseminated through email discussion forums like CHILD2015, and by direct communication with Global organizations like WHO. Health Services in malaria endemic countries, Pharmaceutical Companies and their Regulators may all be affected, with global economic impacts over 10-15 years.

Health and wellbeing: We hope this research will identify new strategies to treat severe malaria. Translational research could be undertaken by our own research group and collaborators, or others based on our published findings. It is likely to take at least 10 years for any new strategies to reach the clinic and improve the outcome of individuals with severe malaria in endemic countries.

Ethical society: We aim to constantly reduce, refine or replace the use of animals in our research because society expects animals to be used only when other methods are not possible. Part of this research aims to refine the use of mice to study severe malaria, and we anticipate that this will led to reductions in animal use. If successful, we will disseminate this approach through professional and public media, aiming to persuade others to consider its adoption over the next 4-10 years.

Wealth creation: This research showcases the expertise of UK centres in apply cutting edge cross-disciplinary technology and techniques. It will highlight the academic prowess of the institutions, increasing investment from academic and commercial sector collaborators. The unique skills and opportunities will be highlighted on our group and institutional websites, and will be promoted by our institutions.