The Lung Microenvironment Instructs Gene Transcription in Neonatal and Adult Alveolar Macrophages

Immaturity of alveolar macrophages (AMs) around birth contributes to the susceptibility of newborns to lung disease. However, the molecular features differentiating neonatal and mature, adult AMs are poorly understood. Here we identify the unique transcriptomes and enhancer landscapes of neonatal and adult AMs. While the core AM signature was similar, adult AMs expressed higher levels of genes involved in lipid metabolism, while neonatal AMs expressed a largely proinflammatory gene profile. Open enhancer regions identified by ATAC-seq contained motifs for nuclear receptors, MITF, and STAT in adult AMs and AP-1 and NF-kB in neonatal AMs. Intranasal LPS activated a similar innate immune response in both neonates and adults, with higher basal expression of inflammatory genes in neonates. The lung microenvironment drove many of the distinguishing gene expression and open chromatin characteristics of neonatal and adult AMs. Neonatal AMs retained high expression of some proinflammatory genes, suggesting the differences in neonatal AMs result from both inherent cell properties and environmental influences. RNA-seq and ATAC-seq for FACS sorted AMs from C57BL/6 mice at postnatal day 4 (P4) and 8 week of age following intranasal administration of LPS or PBS (control). RNA-seq and ATAC-seq for freshly isolated adult and neonatal AMs and after maintenance in culture for 20h.