Transcriptomic characterisation of differentiation-driven priming of the interferon-α response in THP-1 macrophages

Monocytes and macrophages are important coordinators of the innate response to infectious disease. During infection, monocytes are recruited to tissues where they differentiate into macrophages, which mount interferon (IFN)-driven antiviral responses through the expression of IFN-stimulated genes (ISGs). While ISG expression is classically attributed to IFN signalling, the contribution of monocyte-to-macrophage differentiation to priming this response remains poorly understood. Differential gene expression with DESeq2 on RNA-seq from THP-1 macrophages differentiated with PMA and stimulated with IFN-α2 identified 978 significantly differentially expressed ISGs. Cap Analysis of Gene Expression (CAGE-seq) across 96 hours of differentiation revealed progressive ISG induction, increasing from 24 differentially expressed ISGs early to 173 ISGs by 24 hours without cytokine stimulation. Hierarchical clustering revealed early-induced and sustained, late-induced, and transiently induced ISGs. Motif-enrichment analysis identified EGR1, EGR2, SP1, and IRF8 as potential key regulators. Together, these findings suggest that differentiation progressively rewires ISG expression through distinct regulatory waves that prime macrophages for a robust IFN response.