Early neutrophil and persistent eosinophil-associated gene signature in childhood asthma

Abstract Rationale Early childhood represents a critical window for asthma susceptibility, marked by developmental and molecular changes, yet their longitudinal pattern remains unclear. Objectives To identify differences in longitudinal whole-blood gene expression during early childhood in future asthmatics compared to healthy children. Methods We conducted a longitudinal whole-blood transcriptomic analysis at four timepoints (1, 4.5, 6, 10.5 years) in a sample of the birth cohort PASTURE (n = 378), comparing children who developed asthma between 6 and 10.5 years with non-asthmatic controls (83/295). Analyses included longitudinal differential gene expression, weighted gene co-expression network analysis, and cis-eQTL analysis. Measurements and main results At age 1, 42 genes, mostly upregulated in future asthmatics, were associated with neutrophilic inflammation and NLRP3 inflammasome-markers. By 4.5 years, this shifted to a novel eosinophil-related signature (40 genes), remaining increased in asthmatics until 10.5 years. Co-expression analysis confirmed a neutrophilic module at 1 year and eosinophilic modules at 4.5, 6 and 10.5 years, all associated with asthma. Fractional exhaled nitric oxide was associated with the eosinophilic module at age 6 (P = .003). 86 SNPs were identified modulating the expression of 10 eosinophil-associated genes and GSDMB from this eosinophilic signature. A variant-based genetic risk score was associated with asthma diagnosis (aOR95% CI= 1.471.13-1.93). Conclusion We identified a shift from a neutrophil-driven gene signature at age 1 to a persistent eosinophilic signature at 4.5 to 10.5 years in asthmatic children, highlighting the 1 to 4.5-year period as most vulnerable period. Genetic variants strongly influenced the persistent eosinophilic gene signature, comprising potential novel therapeutic targets.