Integrating human functional genomics and transcriptomics in highly phenotyped severe asthmatics

Asthma is the most common chronic lung disease, affecting 350 million people worldwide and causing 400,000 deaths annually. Up to 10% of asthmatics have severe, treatment-refractory disease, constituting a significant unmet clinical need due to exacerbations, healthcare costs and mortality. Asthma is pathobiologically and clinically heterogeneous. Identifying 'treatable traits', including type-2 cytokine-mediated ('T2-high') eosinophilic airway inflammation, has enabled highly-effective biomarker-directed approaches, targeting novel biologics according to blood and sputum eosinophilia, and fractional exhaled nitric oxide (FeNO). However other phenotypes and pathways remain to be defined and is widely recognised as an urgent research priority. In previous decades research has also been limited by the very small quantity of biological material which can be obtained from respiratory samples. Recent advances in single cell sequencing, multi-parameter flow cytometry and detailed clinical-and physiological phenotyping now make possible detailed transcriptional and functional analyses of human airway tissue in highly-characterised asthmatic subgroups.

We set out to perform detailed transcriptomic analysis of samples from the airways of 60 selected participants who have also undergone WGS, performing paired single-cell RNAseq and single cell ATACseq using the 10X platform on bronchoscopically-obtained endobronchial brushes and scRNAseq on collagenase-dispersed bronchial biopsies. The main challenge will be to integrate the whole genome sequencing data with the transcriptomic gene expression data from airway samples obtained bronchoscopically from these patients and phenotypic data from the Oxford Airways Research Database and the NHS electronic patient record.

Sample collection has progressed over the past 10 months. I undertook validation and optimisation steps and developed a sample processing pipeline. Preliminary RNAseq data are now available from 6 individuals which I begun analysing. Mulitiome libraries have been prepared but are yet to be sequenced. I undertook relevant training to develop my bioinformatics skills and knowledge of statistics, including Wellcome Sanger Single Cell Technologies and Analysis course and University of Washington Summer Institute in Statistical Genetics.

We are aiming to collect at least 20 definitive bronchoscopy samples within the next 12 months. Subject recruitment is the rate limiting factor, but this depends on finding appropriate participants within the severe asthma clinic who are motivated to consent to this study. The clinicians review 528 new patients per year in the service and expect our accrual to continue at the current rate.