Background: Human Rhinovirus (HRV) is critically associated with asthma development. Viral infections are also known to cause altered DNA methylation levels and gene expression profile in nasal and bronchial epithelium. However, the role of trained immunity as a consequence of multiple infections of HRV and its role in asthma development remains unclear.

Objective: The purpose of this study was to identify the underlying gene-gene interaction of trainable and untrainable traits after recurrent HRV infections in vitro.

Methods: BEAS-2Bs were infected with HRV-16 for 24 h. Cells were then split into two parts (for DNA/RNA extraction) then re-seeded for up to five consecutive infections (5CI). Samples were analysed after first, third and fifth infection. The genome-wide DNA methylation and mRNA expression were analyzed with HumanMethylation450 BeadChip Kit and RNA sequencing. All results were fitted into a mixed model to identify the trainable (T) and untrainable (UT) genes.

Results: We identified 250 T and 359 UT genes (FDR<0.05) after 5CI. The immunology network (T vs. UT genes) indicates training in antiviral innate immune response, elastic fiber formation and in respiratory epithelial cell senescence (e.g. CDKN2A). Basic Fc receptor mediated signaling pathways, pattern recognition receptor signaling or cell- extracellular matrix interaction were enriched in the UT gene sets.

Conclusions: The meta-analysis to identify trained immunity genes indicate enhanced training in antiviral responses, remodeling and cellular aging, whilst pathogen detection (pattern recognition) remained unaffected. This data may help to shine light on the role of viral infection in chronification of asthma.