Dual RNASeq unveils NTHi-macrophage transcriptomic changes during intracellular persistence

Nontypeable Haemophilus influenzae (NTHi) is a respiratory tract pathogen associated with severe, neutrophilic asthma. Although macrophages are responsible for orchestrating the immune response and pathogen clearance in the lung, NTHi is able to persist within macrophages. The mechanism of NTHi intracellular persistence is not understood, therefore the aim of this work was to use dual RNASeq to investigate the host-pathogen interactions that allow this persistence. Monocyte-derived macrophages (MDM) were used to model NTHi-macrophage infection. RNA was isolated after 6h and 24h of infection and sequenced using the Illumina NovaSeq 6000 platform. Differential gene expression analysis found expression of 863 MDM genes (FDR p<0.05) conserved across 6h and 24h. Gene set enrichment analysis (GSEA) identified these 863 genes as a core transcriptomic immune response profile, featuring enrichment of defence response and cytokine-mediated signalling pathways. Furthermore, KEGG pathway analysis revealed enriched pathways involved in the response to an intracellular pathogen. In comparison, GSEA of 108 differentially expressed NTHi genes (FDR p<0.05) showed enrichment of ribosome and metabolic pathways, suggesting transcriptomic adaptation of NTHi to intracellular residence within MDM. Taken together, host and pathogen transcriptomic data indicate NTHi intracellular persistence in this model, despite upregulation of macrophage immune response pathways. Ongoing work using lung macrophages from asthma patients will assess whether these gene pathways are detectable and correlate with NTHi persistence in asthma