Gene Expression in Relation to Exhaled Nitric Oxide Identifies Novel Asthma Phenotypes with Unique Biomolecular Pathways

Abstract

Rationale: Although asthma is recognized as a heterogeneous disease associated with clinical phenotypes, the molecular basis of these phenotypes remains poorly understood. Although genomic studies have successfully broadened our understanding in diseases such as cancer, they have not been widely used in asthma studies.Objectives: To link gene expression patterns to clinical asthma phenotypes.Methods: We used a microarray platform to analyze bronchial airway epithelial cell gene expression in relation to the asthma biomarker fractional exhaled nitric oxide (FE NO ) in 155 subjects with asthma and healthy control subjects from the Severe Asthma Research Program (SARP). Measurements and Main Results:We first identified a diverse set of 549 genes whose expression correlated with FE NO . We used k-means to cluster the patient samples according to the expression of these genes, identifying five asthma clusters/phenotypes with distinct clinical, physiological, cellular, and gene transcription characteristics-termed "subject clusters" (SCs). To then investigate differences in gene expression between SCs, a total of 1,384 genes were identified that highly differentiated the SCs at an unadjusted P value , 1026 . Hierarchical clustering of these 1,384 genes identified nine gene clusters or "biclusters," whose coexpression suggested biological characteristics unique to each SC. Although genes related to type 2 inflammation were present, novel pathways, including those related to neuronal function, WNT pathways, and actin cytoskeleton, were noted.Conclusions: These findings show that bronchial epithelial cell gene expression, as related to the asthma biomarker FE NO , can identify distinct asthma phenotypes, while also suggesting the presence of underlying novel gene pathways relevant to these phenotypes.

Current concepts of severe asthma

“…The resulting 589 correlated genes were then used to cluster 155 patients. Five different clusters emerged from this analysis (16). Three of these clusters had high FeNO; two of these were associated with greater disease diversity (16).…”

“…Importantly, iNOS is also induced in human airway epithelial cells by other cytokines, particularly IFN-γ (35). To further address the complex role of FeNO in underlying molecular processes of asthma and severe asthma in particular, an epithelial cell gene-profiling study to identify genes strongly correlated with FeNO level was performed on asthmatics with a range of endotypes and healthy controls (16). The resulting 589 correlated genes were then used to cluster 155 patients.…”

“…Molecular characterization thus far has largely focused on the presence or degree of a type 2 inflammatory response, which involves the prototypical inflammatory cytokines IL-4, IL-5, and IL-13. Studies in both milder and severe asthma consistently show that approximately 50% of each group manifests a type 2 inflammatory signature (8,(15)(16)(17); however, in mild asthmatic adults, the presence of a type 2 inflammatory process appears to be linked to early onset, atopic/allergic disease, while in severe asthma, where the presence of atopy is consistently lower, the relationship to atopy/allergy is less clear (5,18,19). Interestingly, cluster analyses of cohorts…”

Immune biomarkers in the spectrum of childhood noncommunicable diseases

“…Nitric oxide is produced by the bronchial epithelium through the action of inducible nitric oxide synthase in response to IL-4 and IL-13 81 . It can be measured as fractional exhaled nitric oxide (FeNO) which is a biomarker for eosinophilic airway inflammation, is highly corticosteroid sensitive, and is relatively easily measured using point-of-care diagnostics [81][82][83][84][85][86] . Periostin is an extracellular matrix protein secreted by airway epithelial cells and lung fibroblasts that is also induced by IL-4 and IL-13 87 .…”

Phenotyping Asthma: Linking Clinical Features to Biomolecular Pathways

“…Using a microarray platform to analyse bronchial airway epithelial cell gene expression in relation to the asthma biomarker fractional FeNO in SARP, five asthma clusters/phenotypes with distinct clinical, physiological, cellular, and gene transcription characteristics were described 71 . Genes related to type 2 inflammation were present, but other novel pathways, including those related to neuronal function, Wnt pathways, and actin cytoskeleton, were defined.…”