Integrated multi-PTM omics reveals key host pathways in human coronavirus 229E infection

Viruses manipulate host cellular functions to promote replication and evade antiviral responses, and many processes in host-virus interactions are regulated by protein post-translational modifications (PTMs). While previous studies have examined individual PTMs in host-virus interactions, a comprehensive, multi-PTM perspective of host remodeling during coronavirus infection remains lacking. To address this gap, we applied our multi-PTM omics platform to simultaneously quantify protein abundance, cysteine oxidation, phosphorylation, and lysine acetylation in human lung fibroblasts (MRC5) and epithelial cells (A549) infected with human coronavirus strain 229E (HCoV-229E) at 8, 16, and 24 h post-infection. We observed modest changes in the global host proteome, with only a small fraction of proteins affected even 24 h post-infection. In contrast, host PTM landscapes were rapidly and extensively remodeled, exhibiting pronounced and cell type-specific alterations in redox and phosphorylation states as early as 8 h post-infection. Phosphorylation profiling revealed widespread remodeling of host signaling networks with distinct temporal and directional patterns between MRC5 and A549 cells, while redox profiling uncovered divergent oxidative regulation of proteins involved in infection-related pathways. Notably, a subset of host proteins showed coordinated regulation across multiple PTM types without corresponding changes in abundance, highlighting potential PTM crosstalk during HCoV-229E infection. Among these, heat shock protein 90 beta (HSP90B) displayed dynamic regulation across cysteine oxidation, phosphorylation, and acetylation, and pharmacological inhibition of HSP90B significantly suppressed HCoV-229E replication. Together, these results provide a comprehensive, multi-dimensional view of host PTM remodeling during HCoV-229E infection and demonstrate that integrated multi-PTM omics can reveal functionally relevant host factors and therapeutic vulnerabilities not apparent from protein abundance measurements.