Genetic Admixture and Host-Pathogen Interactions in Helicobacter pylori Infection

Helicobacter pylori infection is one of the most common bacterial infections in the world: infection rates range from 25-50% in developed countries to 70-90% in the third world. It is well recognised that H. pylori infection causes upper gastrointestinal diseases; however, understanding how the bacteria causes disease has been challenging, because the disease risk likely depends on complex interactions between both human host human and bacterial genes, as well as dietary and other environmental factors. Until recently, most studies on host-H. pylori interactions were performed in developed countries and have focused on host or bacterial genetic factors in isolation. These studies have failed to explain the high variability in the likelihood to suffer from gastrointestinal disease seen in different individuals and populations following H. pylori infection.

H. pylori has been evolving in concert with humans since their early origins in Africa and migrations out-of Africa. As a consequence, the genomes of the bacteria are genetically differentiated in a similar way as the host genomes among human populations. This has limited past studies to specific host-pathogen combinations. The ideal experiment to understand interactions between human hosts and bacteria would be to expose individuals to random strains of H. pylori and observe disease outcomes.

Recently admixed populations, i.e. populations that derive their genetic ancestry from multiple continents, offer unique opportunities to perform such type of studies, since the mixing process most likely brought together assorted human and H. pylori genomes which are not present in the parental non-admixed populations. The main aim of this project is to characterise the complex host-pathogen-environment interactions that underlie susceptibility to H. pylori infection in the admixed population of Cape Verde. This previously uninhabited archipelago, located 450 km off the coast of Senegal, was discovered by the Portuguese in the mid-15th century and was initially populated with European immigrants and slaves from the neighbouring African mainland. As a consequence of this settlement pattern, extensive genetic admixture occurred between the African and European ancestral populations during the last few centuries. Due to the high admixture in Cape Verde and cross-infection between unrelated individuals, we expect to find not only some correlation in the European/African individual ancestry proportions between the human hosts and the bacteria, as well as individuals who have high African ancestry but are infected by H. pylori that is largely European in origin and vice versa. Specific host-bacteria combinations that are over-represented among the cases offer clues to identify host and pathogen genetic regions that underlie susceptibility to H. pylori infection.

To accomplish our main goal, we will: a) screen H. pylori infection in Cape Verde volunteers, collect DNA samples from 700 individuals and their associated bacteria, and obtain measurements of the degree of the individuals' gastric mucosa damage caused by infection. Our rationale for recruiting volunteers is that a large proportion of the affected individuals may be asymptomatic or un-diagnosed; recruiting volunteers from the general population allows unbiased assessment of both the infection rate and pattern of genetic diversities. b) To examine the association between the genetic diversity and individual ancestry of human host and H. pylori and disease outcomes.

This project establishes a unique and valuable resource for elucidating host-pathogen interactions in gastrointestinal diseases. The study also has significant public health impact, representing a first effort in assessing the infection rate and the correlation between combinations of human and H. pylori genomes and disease outcomes in Cape Verde.

The main goal of this research is to assess whether individual genomic ancestry and genomic variation of both humans and associated H. pylori affect susceptibility to infection in the admixed population of Cape Verde. To this end, we propose to screen volunteers, of both sexes and aged >35 years, and to collect blood and gastric mucus samples from 700 infected individuals in the two main hospitals of Cape Verde. The blood samples will be used for human DNA extraction, determination of H. pylori infection status through detection of Immunoglobulin G against H. pylori, and for indirect evaluation of the severity of gastric mucosa damage through measurement of the plasma biomarkers pepsinogen I and pepsinogen II. The gastric mucus samples will be used for H. pylori culture, and will be collected on an adhesive nylon string that the participants swallow and that is retrieved an hour later (gastric string). We will then perform high-throughput genotyping of human genomes and next-generation sequencing of complete bacterial genomes. This will allow us to characterise the genomic variation, the admixture structure and the correlation between the individual genomic ancestries (IA) of hosts and H. pylori in Cape Verde. We will also be able to examine the correlation between IA's and the degree of gastric mucosa damage. A significant correlation will indicate the presence of human and bacterial genetic factors that are responsible, at least in part, for the phenotypic variation in disease risk to H. pylori infection observed within and between the ancestral populations to Cape Verde. The relative contribution of these genetic factors can then be quantitated. In addition, we will be able to perform association scans between human and bacterial genotypes or between human and bacterial local ancestry (admixture mapping) and human phenotypes to gain a preliminary characterisation of the genetic architecture underlying susceptibility to H. pylori infection in Cape Verde.

The anticipated main scientific outcome of the project is a better understanding of the co-evolution between human hosts and H. pylori and of the large heterogeneity in disease outcomes underlying infection observed both within and among populations. We will identify human-H. pylori genomic combinations that are at greater risk for developing disease, and will potentially pinpoint genetic variation that confers susceptibility in humans and pathogenicity in bacteria. Such results have the potential to benefit a wide community, as well as scientists in the field.

In the mid-to-long term, this knowledge will help clinicians to identify those infected individuals that are at greater risk of developing gastric disease and to whom treatment should be targeted (i.e. personalized medicine). Identification of cellular pathways in the human host that might be disrupted in disease can lead to the identification of novel molecular targets for therapeutic drugs, potentially benefiting pharmaceutical industry researchers. This is in support of the MRC's strategic aim to translate research, since it has the potential to bring the health impacts of fundamental research to society more quickly.

There are also beneficiaries within the wider public, apart from those who will benefit from the development of better diagnostic strategies. Specifically, this project sits within MRC's strategic aim to support global research that addresses inequalities in health, which arise particularly in developing countries. Firstly, due to the design of this research programme, there will be a direct and immediate benefit to the Cape Verdean individuals that participate in the study. Infected participants showing signs of gastric disease will be immediately referred for medical consultation, examination and treatment. In the short-run, the population will also benefit from the first screen of H. pylori infection rate and its consequences in Cape Verde. This knowledge will have a large impact in terms of public health policy. Professionals in the epidemiology field will also benefit from knowing how the infection rate and associated morbidity in this particular developing country compares to the global epidemics, and how this is related with the genetic background of the individuals.

Through our communication programmes, A-level and university students in the UK, and high school and university students in Cape Verde, will have contact with the project and with subjects in the main scientific areas of the project. Such experience can direct career decisions and inspire creativity in the student's own areas of research. They will also benefit from a better understanding of how different disciplines such as evolutionary and computational biology can work in concert with medical and bacterial genetics to provide insights into a subject of clinical relevance.

This project also presents the perfect opportunity for masters and PhD students (both in UK and in Cape Verde), and PDRAs that work on the project to get excellent training in the latest computational and statistical approaches in genomics and in methodology related with microbiology and bacterial genetics. These are valuable skills that will help them in their future careers.