A transcriptome-driven analysis of epithelial brushings and bronchial biopsies to define asthma phenotypes in U-BIOPRED

Khuo, Chih-Hsi Scott; Pavlidis, Stelios; Loza, Matthew; Baribaud, Fred; Rowe, Anthony; Pandis, Ioannis; Hoda, Uruj; Rossios, Christos; Sousa, Ana; Wilson, Susan J.; Howarth, Peter; Dahlen, Barbro; Dahlen, Sven-Erik; Chanez, Pascal; Shaw, Dominick E.; Krug, Norbert; Sandstr�m, Thomas; De Meulder, Betrand; Lefaudeux, Diane; Fowler, Stephen; Fleming, Louise; Corfield, Julie; Auffray, Charles; Sterk, Peter J.; Djukanovic, Ratko; Guo, Yike; Adcock, Ian M.; Chung, Kian Fan

Abstract

Rationale and objectives: Asthma is a heterogeneous disease driven by diverse immunologic and inflammatory mechanisms. We used transcriptomic profiling of airway tissues to help define asthma phenotypes. Methods: The transcriptome from bronchial biopsies and epithelial brushings of 107 moderate-to-severe asthmatics were annotated by gene-set variation analysis (GSVA) using 42 gene-signatures relevant to asthma, inflammation and immune function. Topological data analysis (TDA) of clinical and histological data was used to derive clusters and the nearest shrunken centroid algorithm used for signature refinement. Results: 9 GSVA signatures expressed in bronchial biopsies and airway epithelial brushings distinguished two distinct asthma subtypes associated with high expression of T-helper type 2 (Th-2) cytokines and lack of corticosteroid response (Group 1 and Group 3). Group 1 had the highest submucosal eosinophils, high exhaled nitric oxide (FeNO) levels, exacerbation rates and oral corticosteroid (OCS) use whilst Group 3 patients showed the highest levels of sputum eosinophils and had a high BMI. In contrast, Group 2 and Group 4 patients had an 86% and 64% probability of having non-eosinophilic inflammation. Using machine-learning tools, we describe an inference scheme using the currently-available inflammatory biomarkers sputum eosinophilia and exhaled nitric oxide levels along with OCS use that could predict the subtypes of gene expression within bronchial biopsies and epithelial cells with good sensitivity and specificity. Conclusion: This analysis demonstrates the usefulness of a transcriptomic-driven approach to phenotyping that segments patients who may benefit the most from specific agents that target Th2-mediated inflammation and/or corticosteroid insensitivity.

Citation

Khuo, C.-H. S., Pavlidis, S., Loza, M., Baribaud, F., Rowe, A., Pandis, I., Hoda, U., Rossios, C., Sousa, A., Wilson, S. J., Howarth, P., Dahlen, B., Dahlen, S.-E., Chanez, P., Shaw, D. E., Krug, N., Sandström, T., De Meulder, B., Lefaudeux, D., Fowler, S., …Chung, K. F. (2017). A transcriptome-driven analysis of epithelial brushings and bronchial biopsies to define asthma phenotypes in U-BIOPRED. American Journal of Respiratory and Critical Care Medicine, 195(4), https://doi.org/10.1164/rccm.201512-2452OC

• Journal Article Type: Article
• Acceptance Date: Aug 20, 2016
• Online Publication Date: Aug 31, 2016
• Publication Date: Feb 15, 2017
• Deposit Date: Oct 24, 2016
• Publicly Available Date: Oct 24, 2016
• Journal: American Journal of Respiratory and Critical Care Medicine
• Print ISSN: 1073-449X
• Electronic ISSN: 1535-4970
• Publisher: American Thoracic Society
• Peer Reviewed: Peer Reviewed
• Volume: 195
• Issue: 4
• DOI: https://doi.org/10.1164/rccm.201512-2452OC
• Keywords: severe asthma, bronchial briushing, corticosteroid, insensitivity, T-helper Type 2 (Th2)
• Public URL: https://nottingham-repository.worktribe.com/output/803651
• Publisher URL: http://www.atsjournals.org/doi/abs/10.1164/rccm.201512-2452OC?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed&#.WA24_PkrJph
• Contract Date: Oct 24, 2016