Preventing asthma by deep diving into host-microbial interactions

Asthma is a chronic condition affecting up to 1 in 9 Australians. Understanding the early origins of this disease is a major challenge given its complex multifactorial nature. This project aims to identify the microbial and molecular drivers of asthma in young children. This would serve as a platform for novel therapeutic interventions strategies that would set infants at high-risk on healthy trajectories.

Whilst the first symptoms can present at any age, data suggests that the disease has origins in early life, when an infant’s immune system starts to develop. A balanced maturation of the immune system during childhood is crucial to prevent inappropriate allergic reactions such as airway inflammation seen in asthma. Two leading hypotheses have emerged regarding the causes of dysregulated immune function in the early stages of asthma. First, the concept that the bacterial communities, which inhabit the body, affect immune education and maturation. Second, severe (viral) respiratory infections during childhood negatively influence immune development and increase susceptibility to airway inflammation. There are currently no therapeutic strategies for high risk children with wheeze that can prevent the development of asthma. Understanding what initiates the disease and what drives chronicity is central to informing clinical treatment decisions, and for the identification of targets that could be the focus of new therapies.

Our bodies are colonized by trillions of microbes, collectively referred to as our microbiome. Approximately 10 years ago, the lung microbiome was first described and noted to be different between healthy individuals and those with asthma. Since then, fuelled by advances in next generation sequencing techniques and bioinformatics pipelines, we are starting to gain unprecedented insight into how microbes in the airways influence chronic lung diseases, such as asthma. With this study, we aim to dive deep into the role of respiratory microbes on early life immune responses using cutting-edge advanced sequencing methods and analysis pipelines, which we have developed. As part of an international consortium led by Imperial College, London, called Breathing Together, we have access to samples from the lower airways of severe wheezing and asthmatic children. The Imperial Centre for Paediatrics and Child Health is one of the only centres in the world that acquires these types of samples, thus, we are in a privileged and unique position to be able to study the exact tissue site where wheeze and asthma occurs. A challenge is accessing control samples from non-asthmatic healthy children for whom invasive sampling is not ethically justifiable. However, we have been able to access such samples from age-matched healthy children, who had undergone elective surgery necessitating intubation (thus allowing sampling of the lower airways). With our unique samples, the latest sequencing approaches, network-based bioinformatic analysis and machine learning pipelines, we are positioned to make impactful strides forward towards discovering the fundamental basis of childhood asthma and wheeze.

The project will be divided into steps reflecting 3 distinct classes of biomolecules that could influence asthma. First, the genetic material (DNA) of all microorganisms will be extracted from lower airways samples and sequenced using shotgun metagenomics that will allow the identification of bacteria, DNA viruses and their genes. Second, the cellular transcripts (RNA) of both the child’s cells and the microbes will be sequenced in parallel –a cutting-edge method referred to as “dual RNA-sequencing”– which is a powerful way to address the function of both immune cells and microbes. Lastly, untargeted metabolomic analysis of lower airway samples will allow us to identify metabolites, which are the fundamental messengers through which microbes and immune cells communicate.
In the leadup to this application, the applicant has successfully established all of the techniques and analysis pipelines required to generate and interrogate these datasets. Pilot data indicates the project is well placed for success. Specifically, data indicates that wheezing and asthmatic children have a dysregulated microbiome, characterised by an increased abundance of inflammation-driving bacteria, as compared to healthy controls. In addition, the immunological status of the airways, as determined by gene expression, is directly linked to the constituents of the microbiome. Perhaps most importantly, and in direct support of the computationally-intensive multi-omics approach that will be deployed in this project, links between specific microbial families, immune pathways and clinical parameters only come to light when all are integrated with machine learning approaches.

Building upon these technological advances and combined with unique access to samples from the lower airways of children with asthma and healthy controls, this project is at the leading edge of discovering the fundamental pathways that drive the disease, and thus, could be targeted to stop it.