BAL cell gene expression in severe asthma reveals mechanisms of severe disease and influences of medications

Rationale: Gene expression ofBALcells,which samples the cellularmilieu within the lower respiratory tract, has not been well studied insevere asthma. Objectives: To identify new biomolecularmechanisms underlying severe asthma by an unbiased, detailed interrogation of global gene expression. Methods: BAL cell expression was profiled in 154 asthma and control subjects.Of these participants, 100 had accompanying airway epithelial cell gene expression. BAL cell expression profiles were related to participant (age, sex, race, and medication) and sample traits (cell proportions), and then severity-related gene expression determined by correlating transcripts and coexpression networks to lung function, emergency department visits or hospitalizations in the last year, medication use, and quality-of-life scores. Measurements and Main Results: Age, sex, race, cell proportions, and medications strongly influenced BAL cell gene expression, but leading severity-related genes could be determined by carefully identifying and accounting for these influences. A BAL cell expression network enriched for cAMPsignaling componentsmost differentiated subjects with severe asthma from other subjects. Subsequently, an in vitro cellularmodel showed this phenomenonwas likely caused by a robust upregulation in cAMP-related expression in nonsevere and β-agonist-naive subjects given a β-agonist before cell collection. Interestingly, ELISAs performed on BAL lysates showed protein levels may partly disagree with expression changes. Conclusions: Gene expression in BAL cells is influenced by factors seldomly considered.Notably,β-agonist exposure likely had a strong and immediate impact oncellular gene expression, whichmaynot translate to important disease mechanisms or necessarily match protein levels. Leading severity-related genes were discovered in an unbiased, systemwide analysis, revealing newtargets thatmapto asthma susceptibility loci.