1. Multidimensional endotyping using nasal proteomics predicts molecular phenotypes in the asthmatic airways
- Author
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Ioana Agache, Mohamed H. Shamji, Nazanin Zounemat Kermani, Giulia Vecchi, Alberto Favaro, Janice A. Layhadi, Anja Heider, Didem Sanver Akbas, Paulina Filipaviciute, Lily Y.D. Wu, Catalina Cojanu, Alexandru Laculiceanu, Cezmi A. Akdis, Ian M. Adcock, University of Zurich, Agache, Ioana, and Shamji, Mohamed H
- Subjects
2403 Immunology ,10183 Swiss Institute of Allergy and Asthma Research ,Immunology ,2723 Immunology and Allergy ,Immunology and Allergy ,610 Medicine & health - Abstract
BACKGROUND: Unsupervised clustering of biomarkers derived from non-invasive samples such as nasal fluid is less evaluated as a tool for describing asthma endotypes. OBJECTIVE: To evauate whether protein expression in nasal fluid would identify distinct clusters of asthmatics with specific lower airway molecular phenotypes. METHODS: Unsupervised clustering of 168 nasal inflammatory and immune proteins and Shapley values was used to stratify 43 severe asthmatic patients (ENDANA) using a two 'modelling blocks' machine learning (ML) approach. This algorithm was also applied to nasal brushings transcriptomics from U-BIOPRED. Feature reduction and functional gene analysis were used to compare proteomic and transcriptomic clusters. Gene set variation analysis (GSVA) provided enrichment scores (ESs) of the ENDANA protein signature within U-BIOPRED sputum and blood. RESULTS: The nasal protein ML model identified two severe asthma endotypes, which were replicated in U-BIOPRED nasal transcriptomics. Cluster 1 patients had significant airway obstruction, small airways disease, air trapping, decreased diffusing capacity and increased oxidative stress, although only 4/18 were current smokers. Shapley identified 20 cluster-defining proteins. Forty-one proteins were significantly higher in Cluster 1. Pathways associated with proteomic and transcriptomic clusters were linked to Th1, Th2, neutrophil, JAK-STAT, TLR and infection activation. GSVA analysis of the nasal protein and gene signatures were enriched in subjects with sputum neutrophilic/mixed granulocytic asthma and in subjects with a molecular phenotype found in sputum neutrophil-high subjects. CONCLUSIONS: Protein or gene analysis may indicate molecular phenotypes within the asthmatic lower airway and provide a simple, non-invasive test for non-T2 asthma that is currently unavailable.
- Published
- 2021