TY - JOUR
T1 - Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways
AU - Modena, Brian D.
AU - Tedrow, John R.
AU - Milosevic, Jadranka
AU - Bleecker, Eugene R.
AU - Meyers, Deborah A.
AU - Wu, Wei
AU - Bar-Joseph, Ziv
AU - Erzurum, Serpil C.
AU - Gaston, Benjamin M.
AU - Busse, William W.
AU - Jarjour, Nizar N.
AU - Kaminski, Naftali
AU - Wenzel, Sally E.
N1 - Publisher Copyright:
Copyright © 2014 by the American Thoracic Society.
PY - 2014/12/15
Y1 - 2014/12/15
N2 - 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 (FENO) 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 FENO. 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 FENO, can identify distinct asthma phenotypes, while also suggesting the presence of underlying novel gene pathways relevant to these phenotypes.
AB - 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 (FENO) 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 FENO. 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 FENO, can identify distinct asthma phenotypes, while also suggesting the presence of underlying novel gene pathways relevant to these phenotypes.
KW - Clustering
KW - Exhaled nitric oxide
KW - Severe asthma
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U2 - 10.1164/rccm.201406-1099OC
DO - 10.1164/rccm.201406-1099OC
M3 - Article
C2 - 25338189
AN - SCOPUS:84919363553
SN - 1073-449X
VL - 190
SP - 1363
EP - 1372
JO - American journal of respiratory and critical care medicine
JF - American journal of respiratory and critical care medicine
IS - 12
ER -